[{"author":[{"first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:10:29Z","volume":210,"year":"2018","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"doi":"10.1534/genetics.118.301429","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000452315900021"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/379578v1","open_access":"1"}],"isi":1,"quality_controlled":"1","month":"12","publication_identifier":{"issn":["00166731"]},"oa_version":"Preprint","_id":"39","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Replicability of introgression under linked, polygenic selection","intvolume":" 210","abstract":[{"text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2018-12-04T00:00:00Z","publication":"Genetics","citation":{"ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429."},"article_type":"original","page":"1411-1427","day":"04","article_processing_charge":"No","scopus_import":"1"},{"publist_id":"7402","volume":32,"date_updated":"2023-09-18T08:09:59Z","date_created":"2018-12-11T11:46:22Z","author":[{"full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","last_name":"Bighin"},{"last_name":"Salasnich","first_name":"Luca","full_name":"Salasnich, Luca"}],"department":[{"_id":"MiLe"}],"publisher":"World Scientific Publishing","publication_status":"published","year":"2018","month":"07","language":[{"iso":"eng"}],"doi":"10.1142/S0217979218400222","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.11171"}],"external_id":{"isi":["000438217300007"]},"oa":1,"issue":"17","abstract":[{"lang":"eng","text":"We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 32","title":"Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover","status":"public","_id":"420","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"10","scopus_import":"1","date_published":"2018-07-10T00:00:00Z","page":"1840022","citation":{"short":"G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022.","mla":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:10.1142/S0217979218400222.","chicago":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222.","ama":"Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022. doi:10.1142/S0217979218400222","ieee":"G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.","apa":"Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222","ista":"Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022."},"publication":"International Journal of Modern Physics B"},{"month":"10","publication_identifier":{"issn":["00278424"]},"doi":"10.1073/pnas.1801832115","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:46:16Z","publist_id":"8017","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"full_name":"Tavares, Hugo","last_name":"Tavares","first_name":"Hugo"},{"full_name":"Whitley, Annabel","first_name":"Annabel","last_name":"Whitley"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"full_name":"Copsey, Lucy","last_name":"Copsey","first_name":"Lucy"},{"last_name":"Elleouet","first_name":"Joane","full_name":"Elleouet, Joane"},{"last_name":"Burrus","first_name":"Monique","full_name":"Burrus, Monique"},{"first_name":"Christophe","last_name":"Andalo","full_name":"Andalo, Christophe"},{"first_name":"Miaomiao","last_name":"Li","full_name":"Li, Miaomiao"},{"last_name":"Li","first_name":"Qun","full_name":"Li, Qun"},{"full_name":"Xue, Yongbiao","first_name":"Yongbiao","last_name":"Xue"},{"full_name":"Rebocho, Alexandra B","last_name":"Rebocho","first_name":"Alexandra B"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"date_updated":"2023-09-18T08:36:49Z","date_created":"2018-12-11T11:44:18Z","volume":115,"year":"2018","acknowledgement":" ERC Grant 201252 (to N.H.B.)","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"day":"23","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-10-23T00:00:00Z","publication":"PNAS","citation":{"chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115"},"page":"11006 - 11011","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"issue":"43","type":"journal_article","file":[{"file_name":"11006.full.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1911302,"creator":"dernst","relation":"main_file","file_id":"5683","date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-17T08:44:03Z","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1"}],"oa_version":"Published Version","_id":"38","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Selection and gene flow shape genomic islands that control floral guides","status":"public","ddc":["570"],"intvolume":" 115"},{"abstract":[{"text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource.","lang":"eng"}],"alternative_title":["Proceedings of SPIE"],"type":"conference","oa_version":"Preprint","intvolume":" 10672","title":"Routing thermal noise through quantum networks","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"155","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2018-05-04T00:00:00Z","citation":{"mla":"Xuereb, André, et al. Routing Thermal Noise through Quantum Networks. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928.","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928.","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.","apa":"Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672."},"publist_id":"7766","article_number":"106721N","volume":10672,"date_updated":"2023-09-18T08:12:24Z","date_created":"2018-12-11T11:44:55Z","author":[{"full_name":"Xuereb, André","first_name":"André","last_name":"Xuereb"},{"first_name":"Matteo","last_name":"Aquilina","full_name":"Aquilina, Matteo"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir"}],"editor":[{"last_name":"Andrews","first_name":"D L","full_name":"Andrews, D L"},{"full_name":"Ostendorf, A","last_name":"Ostendorf","first_name":"A"},{"full_name":"Bain, A J","first_name":"A J","last_name":"Bain"},{"full_name":"Nunzi, J M","last_name":"Nunzi","first_name":"J M"}],"publisher":"SPIE","department":[{"_id":"JoFi"}],"publication_status":"published","year":"2018","month":"05","language":[{"iso":"eng"}],"doi":"10.1117/12.2309928","conference":{"end_date":"2018-04-26","start_date":"2018-04-22","location":"Strasbourg, France","name":"SPIE: The international society for optical engineering"},"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"external_id":{"isi":["000453298500019"],"arxiv":["1806.01000"]},"oa":1},{"date_published":"2018-12-14T00:00:00Z","citation":{"ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275. doi:10.1126/science.aao0980","ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","ieee":"K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” Science, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018.","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao0980","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980.","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.","chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aao0980."},"publication":"Science","page":"1271-1275","article_type":"original","article_processing_charge":"No","day":"14","scopus_import":"1","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5767","intvolume":" 362","title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","status":"public","issue":"6420","abstract":[{"lang":"eng","text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. "}],"type":"journal_article","doi":"10.1126/science.aao0980","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000452994400048"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aao0980"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"12","author":[{"full_name":"Gotlieb, Kenneth","first_name":"Kenneth","last_name":"Gotlieb"},{"full_name":"Lin, Chiu-Yun","first_name":"Chiu-Yun","last_name":"Lin"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"last_name":"Zhang","first_name":"Wentao","full_name":"Zhang, Wentao"},{"first_name":"Christopher L.","last_name":"Smallwood","full_name":"Smallwood, Christopher L."},{"first_name":"Christopher","last_name":"Jozwiak","full_name":"Jozwiak, Christopher"},{"last_name":"Eisaki","first_name":"Hiroshi","full_name":"Eisaki, Hiroshi"},{"last_name":"Hussain","first_name":"Zahid","full_name":"Hussain, Zahid"},{"first_name":"Ashvin","last_name":"Vishwanath","full_name":"Vishwanath, Ashvin"},{"last_name":"Lanzara","first_name":"Alessandra","full_name":"Lanzara, Alessandra"}],"volume":362,"date_created":"2018-12-19T14:53:50Z","date_updated":"2023-09-18T08:11:56Z","acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","year":"2018","department":[{"_id":"MaSe"}],"publisher":"American Association for the Advancement of Science","publication_status":"published"},{"month":"01","language":[{"iso":"eng"}],"doi":"10.1109/TITS.2017.2778077","isi":1,"quality_controlled":"1","external_id":{"isi":["000446651100020"]},"publist_id":"7389","date_created":"2018-12-11T11:46:27Z","date_updated":"2023-09-18T08:12:49Z","volume":19,"author":[{"full_name":"Jiang, Yu","first_name":"Yu","last_name":"Jiang"},{"first_name":"Han","last_name":"Liu","full_name":"Liu, Han"},{"full_name":"Song, Huobing","last_name":"Song","first_name":"Huobing"},{"full_name":"Kong, Hui","first_name":"Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941"},{"last_name":"Wang","first_name":"Rui","full_name":"Wang, Rui"},{"last_name":"Guan","first_name":"Yong","full_name":"Guan, Yong"},{"last_name":"Sha","first_name":"Lui","full_name":"Sha, Lui"}],"related_material":{"record":[{"id":"1205","status":"public","relation":"earlier_version"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IEEE","year":"2018","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-01-01T00:00:00Z","page":"3320 - 3333","publication":"IEEE Transactions on Intelligent Transportation Systems","citation":{"ista":"Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 19(10), 3320–3333.","apa":"Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., & Sha, L. (2018). Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. IEEE. https://doi.org/10.1109/TITS.2017.2778077","ieee":"Y. Jiang et al., “Safety-assured model-driven design of the multifunction vehicle bus controller,” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.","ama":"Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 2018;19(10):3320-3333. doi:10.1109/TITS.2017.2778077","chicago":"Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems. IEEE, 2018. https://doi.org/10.1109/TITS.2017.2778077.","mla":"Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:10.1109/TITS.2017.2778077.","short":"Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions on Intelligent Transportation Systems 19 (2018) 3320–3333."},"abstract":[{"text":"In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network.","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"None","status":"public","title":"Safety-assured model-driven design of the multifunction vehicle bus controller","intvolume":" 19","_id":"434","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"volume":7,"date_updated":"2023-09-18T09:29:07Z","date_created":"2018-12-11T11:44:57Z","related_material":{"record":[{"id":"9838","status":"public","relation":"research_data"}]},"author":[{"first_name":"Marketa","last_name":"Kaucka","full_name":"Kaucka, Marketa"},{"last_name":"Petersen","first_name":"Julian","full_name":"Petersen, Julian"},{"last_name":"Tesarova","first_name":"Marketa","full_name":"Tesarova, Marketa"},{"last_name":"Szarowska","first_name":"Bara","full_name":"Szarowska, Bara"},{"full_name":"Kastriti, Maria","last_name":"Kastriti","first_name":"Maria"},{"first_name":"Meng","last_name":"Xie","full_name":"Xie, Meng"},{"first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"},{"full_name":"Annusver, Karl","first_name":"Karl","last_name":"Annusver"},{"full_name":"Kasper, Maria","first_name":"Maria","last_name":"Kasper"},{"full_name":"Symmons, Orsolya","first_name":"Orsolya","last_name":"Symmons"},{"last_name":"Pan","first_name":"Leslie","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","last_name":"Spitz","first_name":"Francois"},{"first_name":"Jozef","last_name":"Kaiser","full_name":"Kaiser, Jozef"},{"full_name":"Hovorakova, Maria","last_name":"Hovorakova","first_name":"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","first_name":"Michael P","last_name":"Matise"},{"first_name":"Hui","last_name":"Wang","full_name":"Wang, Hui"},{"full_name":"Marklund, Ulrika","first_name":"Ulrika","last_name":"Marklund"},{"full_name":"Abdo, Hind","first_name":"Hind","last_name":"Abdo"},{"full_name":"Ernfors, Patrik","last_name":"Ernfors","first_name":"Patrik"},{"full_name":"Maire, Pascal","last_name":"Maire","first_name":"Pascal"},{"full_name":"Wurmser, Maud","first_name":"Maud","last_name":"Wurmser"},{"full_name":"Chagin, Andrei S","last_name":"Chagin","first_name":"Andrei S"},{"full_name":"Fried, Kaj","last_name":"Fried","first_name":"Kaj"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"}],"publisher":"eLife Sciences Publications","department":[{"_id":"AnKi"}],"publication_status":"published","year":"2018","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"publist_id":"7759","file_date_updated":"2020-07-14T12:45:07Z","article_number":"e34465","language":[{"iso":"eng"}],"doi":"10.7554/eLife.34465","project":[{"call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"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"},"external_id":{"isi":["000436227500001"]},"oa":1,"month":"06","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":9816484,"creator":"dernst","access_level":"open_access","file_name":"2018_eLife_Kaucka.pdf","checksum":"da2378cdcf6b5461dcde194e4d608343","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-17T16:41:58Z","relation":"main_file","file_id":"5727"}],"intvolume":" 7","ddc":["571"],"title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","status":"public","_id":"162","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"type":"journal_article","date_published":"2018-06-13T00:00:00Z","citation":{"short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465, eLife Sciences Publications, 2018, doi:10.7554/eLife.34465.","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 2018;7. doi:10.7554/eLife.34465","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.34465","ieee":"M. Kaucka et al., “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” eLife, vol. 7. eLife Sciences Publications, 2018.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465."},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"No","day":"13","scopus_import":"1"},{"doi":"10.1007/978-3-319-78375-8_15","conference":{"location":"Tel Aviv, Israel","start_date":"2018-04-29","end_date":"2018-05-03","name":"Eurocrypt: Advances in Cryptology"},"language":[{"iso":"eng"}],"external_id":{"isi":["000517098700015"]},"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2018/183.pdf","open_access":"1"}],"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"isi":1,"quality_controlled":"1","month":"05","author":[{"first_name":"Bram","last_name":"Cohen","full_name":"Cohen, Bram"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"volume":10821,"date_created":"2018-12-11T11:45:42Z","date_updated":"2023-09-18T09:29:33Z","year":"2018","department":[{"_id":"KrPi"}],"publisher":"Springer","publication_status":"published","ec_funded":1,"publist_id":"7579","date_published":"2018-05-29T00:00:00Z","citation":{"ama":"Cohen B, Pietrzak KZ. Simple proofs of sequential work. In: Vol 10821. Springer; 2018:451-467. doi:10.1007/978-3-319-78375-8_15","ieee":"B. Cohen and K. Z. Pietrzak, “Simple proofs of sequential work,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 451–467.","apa":"Cohen, B., & Pietrzak, K. Z. (2018). Simple proofs of sequential work (Vol. 10821, pp. 451–467). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_15","ista":"Cohen B, Pietrzak KZ. 2018. Simple proofs of sequential work. Eurocrypt: Advances in Cryptology, LNCS, vol. 10821, 451–467.","short":"B. Cohen, K.Z. Pietrzak, in:, Springer, 2018, pp. 451–467.","mla":"Cohen, Bram, and Krzysztof Z. Pietrzak. Simple Proofs of Sequential Work. Vol. 10821, Springer, 2018, pp. 451–67, doi:10.1007/978-3-319-78375-8_15.","chicago":"Cohen, Bram, and Krzysztof Z Pietrzak. “Simple Proofs of Sequential Work,” 10821:451–67. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_15."},"page":"451 - 467","article_processing_charge":"No","day":"29","scopus_import":"1","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"302","intvolume":" 10821","title":"Simple proofs of sequential work","status":"public","abstract":[{"lang":"eng","text":"At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly verifiable proofs of sequential work, which is a protocol for proving that one spent sequential computational work related to some statement. The original motivation for such proofs included non-interactive time-stamping and universally verifiable CPU benchmarks. A more recent application, and our main motivation, are blockchain designs, where proofs of sequential work can be used – in combination with proofs of space – as a more ecological and economical substitute for proofs of work which are currently used to secure Bitcoin and other cryptocurrencies. The construction proposed by [MMV13] is based on a hash function and can be proven secure in the random oracle model, or assuming inherently sequential hash-functions, which is a new standard model assumption introduced in their work. In a proof of sequential work, a prover gets a “statement” χ, a time parameter N and access to a hash-function H, which for the security proof is modelled as a random oracle. Correctness requires that an honest prover can make a verifier accept making only N queries to H, while soundness requires that any prover who makes the verifier accept must have made (almost) N sequential queries to H. Thus a solution constitutes a proof that N time passed since χ was received. Solutions must be publicly verifiable in time at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust” graphs, and as a consequence has rather poor concrete parameters. But the major drawback is that the prover needs not just N time, but also N space to compute a proof. In this work we propose a proof of sequential work which is much simpler, more efficient and achieves much better concrete bounds. Most importantly, the space required can be as small as log (N) (but we get better soundness using slightly more memory than that). An open problem stated by [MMV13] that our construction does not solve either is achieving a “unique” proof, where even a cheating prover can only generate a single accepting proof. This property would be extremely useful for applications to blockchains."}],"type":"conference","alternative_title":["LNCS"]},{"article_type":"original","publication":"Physical Review E","citation":{"ista":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410.","ieee":"U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018.","apa":"Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410","ama":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410","chicago":"Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.","mla":"Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.","short":"U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018)."},"date_published":"2018-10-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"No","title":"Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons","status":"public","intvolume":" 98","_id":"31","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus."}],"issue":"4","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","grant_number":"785907","_id":"26436750-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/243816v2.full","open_access":"1"}],"external_id":{"isi":["000447486100004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.98.042410","month":"10","publication_identifier":{"issn":["24700045"]},"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"American Physical Society","acknowledgement":"This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).","year":"2018","date_created":"2018-12-11T11:44:15Z","date_updated":"2023-09-18T09:18:44Z","volume":98,"author":[{"first_name":"Ulisse","last_name":"Ferrari","full_name":"Ferrari, Ulisse"},{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"full_name":"Chalk, Matthew J","last_name":"Chalk","first_name":"Matthew J"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"}],"article_number":"042410","ec_funded":1,"publist_id":"8024"},{"_id":"64","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","status":"public","intvolume":" 115","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"35","publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","citation":{"chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.","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.","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.","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.","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.","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"},"article_type":"original","page":"E8135 - E8142","date_published":"2018-08-28T00:00:00Z","scopus_import":"1","day":"28","article_processing_charge":"No","year":"2018","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"TaHa"}],"author":[{"full_name":"Kalinin, Nikita","first_name":"Nikita","last_name":"Kalinin"},{"first_name":"Aldo","last_name":"Guzmán Sáenz","full_name":"Guzmán Sáenz, Aldo"},{"full_name":"Prieto, Y","first_name":"Y","last_name":"Prieto"},{"id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","first_name":"Mikhail","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail"},{"full_name":"Kalinina, V","last_name":"Kalinina","first_name":"V"},{"last_name":"Lupercio","first_name":"Ernesto","full_name":"Lupercio, Ernesto"}],"date_created":"2018-12-11T11:44:26Z","date_updated":"2023-09-18T08:41:16Z","volume":115,"ec_funded":1,"publist_id":"7990","oa":1,"external_id":{"arxiv":["1806.09153"],"isi":["000442861600009"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.09153"}],"quality_controlled":"1","isi":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"doi":"10.1073/pnas.1805847115","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["00278424"]}},{"doi":"10.5061/dryad.f1s76f2","date_published":"2018-06-14T00:00:00Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.f1s76f2","open_access":"1"}],"citation":{"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.","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.","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.","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"},"article_processing_charge":"No","month":"06","day":"14","related_material":{"record":[{"id":"162","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"full_name":"Petersen, Julian","first_name":"Julian","last_name":"Petersen"},{"full_name":"Tesarova, Marketa","first_name":"Marketa","last_name":"Tesarova"},{"full_name":"Szarowska, Bara","last_name":"Szarowska","first_name":"Bara"},{"first_name":"Maria Eleni","last_name":"Kastriti","full_name":"Kastriti, Maria Eleni"},{"first_name":"Meng","last_name":"Xie","full_name":"Xie, Meng"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna"},{"full_name":"Annusver, Karl","last_name":"Annusver","first_name":"Karl"},{"full_name":"Kasper, Maria","last_name":"Kasper","first_name":"Maria"},{"first_name":"Orsolya","last_name":"Symmons","full_name":"Symmons, Orsolya"},{"full_name":"Pan, Leslie","first_name":"Leslie","last_name":"Pan"},{"full_name":"Spitz, Francois","first_name":"Francois","last_name":"Spitz"},{"last_name":"Kaiser","first_name":"Jozef","full_name":"Kaiser, Jozef"},{"full_name":"Hovorakova, Maria","first_name":"Maria","last_name":"Hovorakova"},{"last_name":"Zikmund","first_name":"Tomas","full_name":"Zikmund, Tomas"},{"full_name":"Sunadome, Kazunori","first_name":"Kazunori","last_name":"Sunadome"},{"full_name":"Matise, Michael P","first_name":"Michael P","last_name":"Matise"},{"full_name":"Wang, Hui","last_name":"Wang","first_name":"Hui"},{"first_name":"Ulrika","last_name":"Marklund","full_name":"Marklund, Ulrika"},{"full_name":"Abdo, Hind","first_name":"Hind","last_name":"Abdo"},{"last_name":"Ernfors","first_name":"Patrik","full_name":"Ernfors, Patrik"},{"first_name":"Pascal","last_name":"Maire","full_name":"Maire, Pascal"},{"last_name":"Wurmser","first_name":"Maud","full_name":"Wurmser, Maud"},{"full_name":"Chagin, Andrei S","first_name":"Andrei S","last_name":"Chagin"},{"full_name":"Fried, Kaj","last_name":"Fried","first_name":"Kaj"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"}],"oa_version":"Published Version","date_updated":"2023-09-18T09:29:07Z","date_created":"2021-08-09T12:54:35Z","_id":"9838","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"AnKi"}],"status":"public","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"type":"research_data_reference"},{"file_date_updated":"2020-07-14T12:46:23Z","publist_id":"8013","ec_funded":1,"article_number":"311","date_created":"2018-12-11T11:44:19Z","date_updated":"2023-09-18T09:31:18Z","volume":12,"author":[{"full_name":"Luján, Rafæl","first_name":"Rafæl","last_name":"Luján"},{"full_name":"Aguado, Carolina","first_name":"Carolina","last_name":"Aguado"},{"full_name":"Ciruela, Francisco","first_name":"Francisco","last_name":"Ciruela"},{"full_name":"Arus, Xavier","last_name":"Arus","first_name":"Xavier"},{"first_name":"Alejandro","last_name":"Martín Belmonte","full_name":"Martín Belmonte, Alejandro"},{"last_name":"Alfaro Ruiz","first_name":"Rocío","full_name":"Alfaro Ruiz, Rocío"},{"first_name":"Jesus","last_name":"Martinez Gomez","full_name":"Martinez Gomez, Jesus"},{"full_name":"De La Ossa, Luis","last_name":"De La Ossa","first_name":"Luis"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"full_name":"Adelman, John","first_name":"John","last_name":"Adelman"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"}],"publication_status":"published","publisher":"Frontiers Media","department":[{"_id":"RySh"}],"year":"2018","month":"09","publication_identifier":{"issn":["16625102"]},"language":[{"iso":"eng"}],"doi":"10.3389/fncel.2018.00311","quality_controlled":"1","isi":1,"project":[{"name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270"}],"external_id":{"isi":["000445090100002"]},"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,"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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":6834251,"content_type":"application/pdf","creator":"dernst","file_name":"fncel-12-00311.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:23Z","date_created":"2018-12-17T08:49:03Z","checksum":"0bcaec8d596162af0b7fe3f31325d480","relation":"main_file","file_id":"5684"}],"title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells","status":"public","ddc":["570"],"intvolume":" 12","_id":"41","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"19","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-09-19T00:00:00Z","article_type":"original","publication":"Frontiers in Cellular Neuroscience","citation":{"mla":"Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12, 311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311.","short":"R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018).","chicago":"Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311.","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","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.","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"}},{"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","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.","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.","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","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.","short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145.","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."},"publication":"Nano Letters","page":"7141 - 7145","date_published":"2018-10-25T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"25","_id":"23","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 18","status":"public","ddc":["530"],"title":"Single-shot readout of hole spins in Ge","pubrep_id":"1065","file":[{"file_size":1361441,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf","checksum":"3e6034a94c6b5335e939145d88bdb371","date_updated":"2020-07-14T12:45:37Z","date_created":"2018-12-12T10:16:08Z","relation":"main_file","file_id":"5194"}],"oa_version":"Published Version","type":"journal_article","issue":"11","abstract":[{"text":"The strong atomistic spin–orbit coupling of holes makes single-shot spin readout measurements difficult because it reduces the spin lifetimes. By integrating the charge sensor into a high bandwidth radio frequency reflectometry setup, we were able to demonstrate single-shot readout of a germanium quantum dot hole spin and measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT are reported, with a total readout visibility of about 70%. By analyzing separately the spin-to-charge conversion and charge readout fidelities, we have obtained insight into the processes limiting the visibilities of hole spins. The analyses suggest that high hole visibilities are feasible at realistic experimental conditions, underlying the potential of hole spins for the realization of viable qubit devices.","lang":"eng"}],"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":["000451102100064"],"pmid":["30359041"]},"oa":1,"project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"doi":"10.1021/acs.nanolett.8b03217","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_identifier":{"issn":["15306984"]},"month":"10","pmid":1,"year":"2018","publisher":"American Chemical Society","department":[{"_id":"GeKa"}],"publication_status":"published","related_material":{"record":[{"id":"7977","relation":"popular_science"},{"relation":"dissertation_contains","status":"public","id":"69"},{"status":"public","relation":"dissertation_contains","id":"7996"}]},"author":[{"full_name":"Vukušić, Lada","last_name":"Vukušić","first_name":"Lada","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kukucka, Josip","first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger"},{"id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87","first_name":"Joshua M","last_name":"Milem","full_name":"Milem, Joshua M"},{"full_name":"Schäffler, Friedrich","last_name":"Schäffler","first_name":"Friedrich"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"volume":18,"date_created":"2018-12-11T11:44:13Z","date_updated":"2023-09-18T09:30:37Z","ec_funded":1,"publist_id":"8032","file_date_updated":"2020-07-14T12:45:37Z"},{"alternative_title":["LNCS"],"type":"conference","abstract":[{"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.","lang":"eng"}],"intvolume":" 11014","title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","ddc":["000"],"status":"public","_id":"85","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"creator":"dernst","file_size":665372,"content_type":"application/pdf","file_name":"2018_Brown.pdf","access_level":"open_access","date_created":"2019-02-12T07:40:40Z","date_updated":"2020-07-14T12:48:14Z","checksum":"13a3f250be8878405e791b53c19722ad","file_id":"5954","relation":"main_file"}],"oa_version":"Preprint","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"465 - 479","citation":{"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","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.","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.","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","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.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","mla":"Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33."},"date_published":"2018-08-01T00:00:00Z","publist_id":"7969","file_date_updated":"2020-07-14T12:48:14Z","publisher":"Springer","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2018","acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","volume":11014,"date_created":"2018-12-11T11:44:33Z","date_updated":"2023-09-18T09:32:36Z","author":[{"full_name":"Gilad, Eran","first_name":"Eran","last_name":"Gilad"},{"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_identifier":{"issn":["03029743"]},"month":"08","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000851042300031"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96983-1_33","conference":{"end_date":"2018-08-31","location":"Turin, Italy","start_date":"2018-08-27","name":"Euro-Par: European Conference on Parallel Processing"}},{"main_file_link":[{"url":"https://arxiv.org/abs/1706.05026","open_access":"1"}],"oa":1,"external_id":{"isi":["000427798800005"]},"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevB.97.104307","language":[{"iso":"eng"}],"month":"03","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.).","year":"2018","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"author":[{"full_name":"Michailidis, Alexios","last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marko","last_name":"Žnidarič","full_name":"Žnidarič, Marko"},{"last_name":"Medvedyeva","first_name":"Mariya","full_name":"Medvedyeva, Mariya"},{"last_name":"Abanin","first_name":"Dmitry","full_name":"Abanin, Dmitry"},{"last_name":"Prosen","first_name":"Tomaž","full_name":"Prosen, Tomaž"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"date_created":"2018-12-11T11:45:50Z","date_updated":"2023-09-18T09:31:46Z","volume":97,"article_number":"104307","publist_id":"7538","publication":"Physical Review B","citation":{"chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307.","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.","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (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.","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.","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307"},"date_published":"2018-03-19T00:00:00Z","scopus_import":"1","day":"19","article_processing_charge":"No","_id":"327","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Slow dynamics in translation-invariant quantum lattice models","intvolume":" 97","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.","lang":"eng"}],"issue":"10"},{"publist_id":"8026","file_date_updated":"2020-07-14T12:45:52Z","volume":8,"date_created":"2018-12-11T11:44:15Z","date_updated":"2023-09-19T09:29:12Z","author":[{"full_name":"Viljakainen, Lumi","last_name":"Viljakainen","first_name":"Lumi"},{"last_name":"Jurvansuu","first_name":"Jaana","full_name":"Jurvansuu, Jaana"},{"full_name":"Holmberg, Ida","first_name":"Ida","last_name":"Holmberg"},{"full_name":"Pamminger, Tobias","last_name":"Pamminger","first_name":"Tobias"},{"first_name":"Silvio","last_name":"Erler","full_name":"Erler, Silvio"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"publisher":"Wiley","department":[{"_id":"SyCr"}],"publication_status":"published","year":"2018","publication_identifier":{"issn":["20457758"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1002/ece3.4573","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":["000451611000032"]},"issue":"22","abstract":[{"lang":"eng","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."}],"type":"journal_article","file":[{"date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-17T08:27:04Z","checksum":"0d1355c78627ca7210aadd9a17a01915","relation":"main_file","file_id":"5682","file_size":1272096,"content_type":"application/pdf","creator":"dernst","file_name":"Viljakainen_et_al-2018-Ecology_and_Evolution.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 8","title":"Social environment affects the transcriptomic response to bacteria in ant queens","status":"public","ddc":["576","591"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"29","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2018-11-01T00:00:00Z","page":"11031-11070","citation":{"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.","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.","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","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."},"publication":"Ecology and Evolution"},{"publist_id":"6844","volume":63,"date_created":"2018-12-11T11:48:36Z","date_updated":"2023-09-19T09:29:45Z","related_material":{"record":[{"id":"819","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"},{"last_name":"Pull","first_name":"Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","full_name":"Pull, Christopher"},{"last_name":"Fürst","first_name":"Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias"}],"publisher":"Annual Reviews","department":[{"_id":"SyCr"}],"publication_status":"published","year":"2018","publication_identifier":{"issn":["1545-4487"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1146/annurev-ento-020117-043110","quality_controlled":"1","isi":1,"external_id":{"isi":["000424633700008"]},"abstract":[{"text":"Social insect colonies have evolved many collectively performed adaptations that reduce the impact of infectious disease and that are expected to maximize their fitness. This colony-level protection is termed social immunity, and it enhances the health and survival of the colony. In this review, we address how social immunity emerges from its mechanistic components to produce colony-level disease avoidance, resistance, and tolerance. To understand the evolutionary causes and consequences of social immunity, we highlight the need for studies that evaluate the effects of social immunity on colony fitness. We discuss the role that host life history and ecology have on predicted eco-evolutionary dynamics, which differ among the social insect lineages. Throughout the review, we highlight current gaps in our knowledge and promising avenues for future research, which we hope will bring us closer to an integrated understanding of socio-eco-evo-immunology.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 63","status":"public","title":"Social immunity: Emergence and evolution of colony-level disease protection","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"806","article_processing_charge":"No","day":"07","scopus_import":"1","date_published":"2018-01-07T00:00:00Z","page":"105 - 123","citation":{"mla":"Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology, vol. 63, Annual Reviews, 2018, pp. 105–23, doi:10.1146/annurev-ento-020117-043110.","short":"S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.","chicago":"Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology. Annual Reviews, 2018. https://doi.org/10.1146/annurev-ento-020117-043110.","ama":"Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 2018;63:105-123. doi:10.1146/annurev-ento-020117-043110","ista":"Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 63, 105–123.","ieee":"S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution of colony-level disease protection,” Annual Review of Entomology, vol. 63. Annual Reviews, pp. 105–123, 2018.","apa":"Cremer, S., Pull, C., & Fürst, M. (2018). Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. Annual Reviews. https://doi.org/10.1146/annurev-ento-020117-043110"},"publication":"Annual Review of Entomology"},{"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","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."}],"intvolume":" 10981","title":"Space-time interpolants","ddc":["005"],"status":"public","_id":"140","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"creator":"system","file_size":563710,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","checksum":"6dca832f575d6b3f0ea9dff56f579142","date_created":"2018-12-12T10:17:53Z","date_updated":"2020-07-14T12:44:50Z","file_id":"5310","relation":"main_file"}],"pubrep_id":"1010","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"18","page":"468 - 486","citation":{"short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","mla":"Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer, 2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25.","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","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.","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486."},"date_published":"2018-07-18T00:00:00Z","publist_id":"7783","file_date_updated":"2020-07-14T12:44:50Z","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2018","volume":10981,"date_created":"2018-12-11T11:44:50Z","date_updated":"2023-09-19T09:30:43Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6894"}]},"author":[{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"publication_identifier":{"issn":["03029743"]},"month":"07","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-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":["000491481600025"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96145-3_25","conference":{"name":"CAV: Computer Aided Verification","location":"Oxford, United Kingdom","start_date":"2018-07-14","end_date":"2018-07-17"}},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-09-01T00:00:00Z","publication":"Mathematical Physics Analysis and Geometry","citation":{"short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","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.","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","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","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.","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19."},"article_type":"original","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","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"5729","relation":"main_file","checksum":"411c4db5700d7297c9cd8ebc5dd29091","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-17T16:49:02Z","access_level":"open_access","file_name":"2018_MathPhysics_Moser.pdf","creator":"dernst","file_size":496973,"content_type":"application/pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"154","status":"public","ddc":["530"],"title":"Stability of the 2+2 fermionic system with point interactions","intvolume":" 21","month":"09","publication_identifier":{"issn":["13850172"],"eissn":["15729656"]},"doi":"10.1007/s11040-018-9275-3","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":["000439639700001"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"file_date_updated":"2020-07-14T12:45:01Z","publist_id":"7767","ec_funded":1,"article_number":"19","author":[{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","last_name":"Moser","first_name":"Thomas","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","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:44:55Z","date_updated":"2023-09-19T09:31:15Z","volume":21,"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}]},{"issue":"9","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"a6d30b0785db902c734a84fecb2eadd9","date_updated":"2020-07-14T12:47:11Z","date_created":"2019-02-06T10:40:46Z","file_id":"5933","relation":"main_file","creator":"dernst","file_size":1313606,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_DevGrowh_Hannezo.pdf"}],"intvolume":" 60","title":"Statistical theory of branching morphogenesis","ddc":["570"],"status":"public","_id":"5787","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"09","scopus_import":"1","date_published":"2018-12-09T00:00:00Z","page":"512-521","citation":{"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.","ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","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","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.","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570"},"publication":"Development Growth and Differentiation","file_date_updated":"2020-07-14T12:47:11Z","volume":60,"date_updated":"2023-09-19T09:32:49Z","date_created":"2018-12-30T22:59:14Z","author":[{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"}],"publisher":"Wiley","department":[{"_id":"EdHa"}],"year":"2018","publication_identifier":{"issn":["00121592"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1111/dgd.12570","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"]}},{"doi":"10.1007/978-3-319-89960-2_21","conference":{"end_date":"2018-04-20","start_date":"2018-04-14","location":"Thessaloniki, Greece","name":"TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems"},"language":[{"iso":"eng"}],"external_id":{"isi":["000546326300021"]},"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,"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"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","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","isi":1,"month":"04","author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan"},{"full_name":"Toman, Viktor","last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"volume":10805,"date_created":"2018-12-11T11:45:41Z","date_updated":"2023-09-19T09:57:08Z","year":"2018","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","publist_id":"7584","ec_funded":1,"file_date_updated":"2020-07-14T12:45:57Z","date_published":"2018-04-12T00:00:00Z","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.","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","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.","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."},"page":"385 - 407","article_processing_charge":"No","has_accepted_license":"1","day":"12","scopus_import":"1","file":[{"file_name":"2018_LNCS_Brazdil.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1829940,"file_id":"5723","relation":"main_file","date_created":"2018-12-17T16:29:08Z","date_updated":"2020-07-14T12:45:57Z","checksum":"b13874ffb114932ad9cc2586b7469db4"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"297","intvolume":" 10805","status":"public","ddc":["000"],"title":"Strategy representation by decision trees in reactive synthesis","abstract":[{"lang":"eng","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."}],"type":"conference","alternative_title":["LNCS"]},{"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"]},"isi":1,"quality_controlled":"1","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","start_date":"2018-07-14","location":"Oxford, United Kingdom"},"doi":"10.1007/978-3-319-96142-2_13","language":[{"iso":"eng"}],"month":"07","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.","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"},{"full_name":"Oraee, Simin","last_name":"Oraee","first_name":"Simin"},{"last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","full_name":"Toman, Viktor"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10199"}]},"date_updated":"2023-09-19T09:59:55Z","date_created":"2018-12-11T11:44:51Z","volume":10982,"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"7782","ec_funded":1,"citation":{"short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","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.","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","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","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."},"page":"178-197","date_published":"2018-07-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"No","has_accepted_license":"1","_id":"141","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","status":"public","intvolume":" 10982","file":[{"creator":"dernst","file_size":675606,"content_type":"application/pdf","file_name":"2018_LNCS_Chatterjee.pdf","access_level":"open_access","date_created":"2018-12-18T08:52:38Z","date_updated":"2020-07-14T12:44:53Z","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","file_id":"5737","relation":"main_file"}],"oa_version":"Published Version","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","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."}]},{"day":"31","article_processing_charge":"No","scopus_import":"1","date_published":"2018-03-31T00:00:00Z","page":"99 - 130","citation":{"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.","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","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","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.","ista":"Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt 2018: Advances in Cryptology, LNCS, vol. 10821, 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⋅"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"Sustained space complexity","intvolume":" 10821","_id":"298","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"03","language":[{"iso":"eng"}],"conference":{"name":"Eurocrypt 2018: Advances in Cryptology","start_date":"2018-04-29","location":"Tel Aviv, Israel","end_date":"2018-05-03"},"doi":"10.1007/978-3-319-78375-8_4","quality_controlled":"1","isi":1,"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"external_id":{"arxiv":["1705.05313"],"isi":["000517098700004"]},"main_file_link":[{"url":"https://arxiv.org/abs/1705.05313","open_access":"1"}],"oa":1,"publist_id":"7583","ec_funded":1,"date_updated":"2023-09-19T09:59:30Z","date_created":"2018-12-11T11:45:41Z","volume":10821,"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F"},{"full_name":"Blocki, Jeremiah","first_name":"Jeremiah","last_name":"Blocki"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","year":"2018"},{"intvolume":" 69","ddc":["581"],"status":"public","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"36","oa_version":"Published Version","file":[{"file_size":3359316,"content_type":"application/pdf","creator":"dernst","file_name":"2018_JournalExperimBotany_Vu.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:13Z","date_created":"2018-12-18T09:47:51Z","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","relation":"main_file","file_id":"5741"}],"type":"journal_article","issue":"19","abstract":[{"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.","lang":"eng"}],"page":"4609 - 4624","citation":{"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.","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","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.","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."},"publication":"Journal of Experimental Botany","date_published":"2018-08-31T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"31","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"publication_status":"published","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","year":"2018","volume":69,"date_updated":"2023-09-19T10:00:46Z","date_created":"2018-12-11T11:44:17Z","author":[{"last_name":"Vu","first_name":"Lam","full_name":"Vu, Lam"},{"last_name":"Zhu","first_name":"Tingting","full_name":"Zhu, Tingting"},{"orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge","full_name":"Verstraeten, Inge"},{"full_name":"Van De Cotte, Brigitte","first_name":"Brigitte","last_name":"Van De Cotte"},{"full_name":"Gevaert, Kris","last_name":"Gevaert","first_name":"Kris"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"}],"publist_id":"8019","file_date_updated":"2020-07-14T12:46:13Z","quality_controlled":"1","isi":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":["000443568700010"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/jxb/ery204","month":"08"},{"file_date_updated":"2020-07-14T12:46:06Z","publist_id":"7539","license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"first_name":"Kazuaki","last_name":"Sawada","full_name":"Sawada, Kazuaki"},{"full_name":"Kawakami, Ryosuke","first_name":"Ryosuke","last_name":"Kawakami"},{"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"}],"date_created":"2018-12-11T11:45:50Z","date_updated":"2023-09-19T09:58:40Z","volume":47,"year":"2018","publication_status":"published","publisher":"Wiley","department":[{"_id":"RySh"}],"month":"03","doi":"10.1111/ejn.13901","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"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"]},"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","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."}],"issue":"9","type":"journal_article","file":[{"relation":"main_file","file_id":"5721","checksum":"98e901d8229e44aa8f3b51d248dedd09","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-17T16:16:50Z","access_level":"open_access","file_name":"2018_EJN_Sawada.pdf","file_size":4850261,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"326","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","status":"public","ddc":["570"],"intvolume":" 47","day":"07","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-03-07T00:00:00Z","publication":"European Journal of Neuroscience","citation":{"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.","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.","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","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."},"page":"1033 - 1042"},{"date_published":"2018-12-11T00:00:00Z","page":"E11751-E11760","citation":{"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.","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.","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","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.","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."},"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","day":"11","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 115","title":"Structure and architecture of immature and mature murine leukemia virus capsids","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5770","issue":"50","abstract":[{"lang":"eng","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."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1811580115","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000452866000022"],"pmid":["30478053"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053"}],"publication_identifier":{"issn":["00278424"]},"month":"12","volume":115,"date_created":"2018-12-20T21:09:37Z","date_updated":"2023-09-19T09:57:45Z","author":[{"last_name":"Qu","first_name":"Kun","full_name":"Qu, Kun"},{"full_name":"Glass, Bärbel","first_name":"Bärbel","last_name":"Glass"},{"last_name":"Doležal","first_name":"Michal","full_name":"Doležal, Michal"},{"full_name":"Schur, Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian","last_name":"Schur"},{"full_name":"Murciano, Brice","first_name":"Brice","last_name":"Murciano"},{"full_name":"Rein, Alan","last_name":"Rein","first_name":"Alan"},{"full_name":"Rumlová, Michaela","first_name":"Michaela","last_name":"Rumlová"},{"full_name":"Ruml, Tomáš","last_name":"Ruml","first_name":"Tomáš"},{"full_name":"Kräusslich, Hans-Georg","first_name":"Hans-Georg","last_name":"Kräusslich"},{"first_name":"John A. G.","last_name":"Briggs","full_name":"Briggs, John A. G."}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"FlSc"}],"publication_status":"published","pmid":1,"year":"2018"},{"publist_id":"7197","ec_funded":1,"author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"date_created":"2018-12-11T11:47:28Z","date_updated":"2023-09-19T10:00:21Z","volume":712,"year":"2018","publication_status":"published","publisher":"Elsevier","department":[{"_id":"ToHe"}],"month":"02","doi":"10.1016/j.tcs.2017.11.001","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529","open_access":"1"}],"oa":1,"external_id":{"isi":["000424959200003"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"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"}],"type":"journal_article","oa_version":"Published Version","_id":"608","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Synthesis from component libraries with costs","intvolume":" 712","day":"15","article_processing_charge":"No","scopus_import":"1","date_published":"2018-02-15T00:00:00Z","publication":"Theoretical Computer Science","citation":{"short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","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.","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.","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","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","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","ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72."},"article_type":"original","page":"50 - 72"},{"intvolume":" 55","status":"public","title":"Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"705","oa_version":"None","type":"journal_article","issue":"6","abstract":[{"text":"Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins.","lang":"eng"}],"page":"4857 – 4869","citation":{"short":"A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.","mla":"Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology, vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:10.1007/s12035-017-0688-y.","chicago":"Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology. Springer, 2018. https://doi.org/10.1007/s12035-017-0688-y.","ama":"Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 2018;55(6):4857 – 4869. doi:10.1007/s12035-017-0688-y","apa":"Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D., & Lubec, G. (2018). Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. Springer. https://doi.org/10.1007/s12035-017-0688-y","ieee":"A. Miklosi et al., “Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” Molecular Neurobiology, vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.","ista":"Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G. 2018. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869."},"publication":"Molecular Neurobiology","date_published":"2018-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","department":[{"_id":"RySh"}],"publisher":"Springer","publication_status":"published","year":"2018","volume":55,"date_created":"2018-12-11T11:48:02Z","date_updated":"2023-09-19T09:58:11Z","author":[{"full_name":"Miklosi, Andras","last_name":"Miklosi","first_name":"Andras"},{"full_name":"Del Favero, Giorgia","last_name":"Del Favero","first_name":"Giorgia"},{"full_name":"Bulat, Tanja","first_name":"Tanja","last_name":"Bulat"},{"first_name":"Harald","last_name":"Höger","full_name":"Höger, Harald"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"first_name":"Doris","last_name":"Marko","full_name":"Marko, Doris"},{"full_name":"Lubec, Gert","last_name":"Lubec","first_name":"Gert"}],"publist_id":"6991","quality_controlled":"1","isi":1,"external_id":{"isi":["000431991500025"]},"language":[{"iso":"eng"}],"doi":"10.1007/s12035-017-0688-y","month":"06"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"2","_id":"148","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","intvolume":" 174","oa_version":"Published Version","scopus_import":"1","day":"12","article_processing_charge":"No","publication":"Cell","citation":{"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","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.","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","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.","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.","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."},"page":"448 - 464.e24","date_published":"2018-07-12T00:00:00Z","ec_funded":1,"publist_id":"7774","year":"2018","acknowledgement":"In-Data-Review","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Cell Press","author":[{"full_name":"Nishiyama, Tomoaki","first_name":"Tomoaki","last_name":"Nishiyama"},{"first_name":"Hidetoshi","last_name":"Sakayama","full_name":"Sakayama, Hidetoshi"},{"full_name":"De Vries, Jan","first_name":"Jan","last_name":"De Vries"},{"full_name":"Buschmann, Henrik","last_name":"Buschmann","first_name":"Henrik"},{"first_name":"Denis","last_name":"Saint Marcoux","full_name":"Saint Marcoux, Denis"},{"first_name":"Kristian","last_name":"Ullrich","full_name":"Ullrich, Kristian"},{"full_name":"Haas, Fabian","first_name":"Fabian","last_name":"Haas"},{"full_name":"Vanderstraeten, Lisa","first_name":"Lisa","last_name":"Vanderstraeten"},{"full_name":"Becker, Dirk","first_name":"Dirk","last_name":"Becker"},{"full_name":"Lang, Daniel","first_name":"Daniel","last_name":"Lang"},{"full_name":"Vosolsobě, Stanislav","first_name":"Stanislav","last_name":"Vosolsobě"},{"full_name":"Rombauts, Stephane","first_name":"Stephane","last_name":"Rombauts"},{"first_name":"Per","last_name":"Wilhelmsson","full_name":"Wilhelmsson, Per"},{"last_name":"Janitza","first_name":"Philipp","full_name":"Janitza, Philipp"},{"full_name":"Kern, Ramona","last_name":"Kern","first_name":"Ramona"},{"last_name":"Heyl","first_name":"Alexander","full_name":"Heyl, Alexander"},{"full_name":"Rümpler, Florian","last_name":"Rümpler","first_name":"Florian"},{"full_name":"Calderón Villalobos, Luz","last_name":"Calderón Villalobos","first_name":"Luz"},{"last_name":"Clay","first_name":"John","full_name":"Clay, John"},{"full_name":"Skokan, Roman","last_name":"Skokan","first_name":"Roman"},{"full_name":"Toyoda, Atsushi","first_name":"Atsushi","last_name":"Toyoda"},{"full_name":"Suzuki, Yutaka","last_name":"Suzuki","first_name":"Yutaka"},{"full_name":"Kagoshima, Hiroshi","last_name":"Kagoshima","first_name":"Hiroshi"},{"last_name":"Schijlen","first_name":"Elio","full_name":"Schijlen, Elio"},{"full_name":"Tajeshwar, Navindra","first_name":"Navindra","last_name":"Tajeshwar"},{"first_name":"Bruno","last_name":"Catarino","full_name":"Catarino, Bruno"},{"full_name":"Hetherington, Alexander","last_name":"Hetherington","first_name":"Alexander"},{"full_name":"Saltykova, Assia","first_name":"Assia","last_name":"Saltykova"},{"full_name":"Bonnot, Clemence","last_name":"Bonnot","first_name":"Clemence"},{"full_name":"Breuninger, Holger","last_name":"Breuninger","first_name":"Holger"},{"full_name":"Symeonidi, Aikaterini","last_name":"Symeonidi","first_name":"Aikaterini"},{"first_name":"Guru","last_name":"Radhakrishnan","full_name":"Radhakrishnan, Guru"},{"full_name":"Van Nieuwerburgh, Filip","last_name":"Van Nieuwerburgh","first_name":"Filip"},{"full_name":"Deforce, Dieter","first_name":"Dieter","last_name":"Deforce"},{"full_name":"Chang, Caren","first_name":"Caren","last_name":"Chang"},{"full_name":"Karol, Kenneth","last_name":"Karol","first_name":"Kenneth"},{"first_name":"Rainer","last_name":"Hedrich","full_name":"Hedrich, Rainer"},{"first_name":"Peter","last_name":"Ulvskov","full_name":"Ulvskov, Peter"},{"first_name":"Gernot","last_name":"Glöckner","full_name":"Glöckner, Gernot"},{"last_name":"Delwiche","first_name":"Charles","full_name":"Delwiche, Charles"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"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"},{"full_name":"Beilby, Mary","first_name":"Mary","last_name":"Beilby"},{"full_name":"Dolan, Liam","first_name":"Liam","last_name":"Dolan"},{"last_name":"Kohara","first_name":"Yuji","full_name":"Kohara, Yuji"},{"first_name":"Sumio","last_name":"Sugano","full_name":"Sugano, Sumio"},{"last_name":"Fujiyama","first_name":"Asao","full_name":"Fujiyama, Asao"},{"first_name":"Pierre Marc","last_name":"Delaux","full_name":"Delaux, Pierre Marc"},{"first_name":"Marcel","last_name":"Quint","full_name":"Quint, Marcel"},{"first_name":"Gunter","last_name":"Theissen","full_name":"Theissen, Gunter"},{"last_name":"Hagemann","first_name":"Martin","full_name":"Hagemann, Martin"},{"full_name":"Harholt, Jesper","first_name":"Jesper","last_name":"Harholt"},{"full_name":"Dunand, Christophe","first_name":"Christophe","last_name":"Dunand"},{"first_name":"Sabine","last_name":"Zachgo","full_name":"Zachgo, Sabine"},{"full_name":"Langdale, Jane","first_name":"Jane","last_name":"Langdale"},{"first_name":"Florian","last_name":"Maumus","full_name":"Maumus, Florian"},{"last_name":"Van Der Straeten","first_name":"Dominique","full_name":"Van Der Straeten, Dominique"},{"last_name":"Gould","first_name":"Sven B","full_name":"Gould, Sven B"},{"full_name":"Rensing, Stefan","last_name":"Rensing","first_name":"Stefan"}],"date_updated":"2023-09-19T10:02:47Z","date_created":"2018-12-11T11:44:53Z","volume":174,"month":"07","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"oa":1,"external_id":{"pmid":["30007417"],"isi":["000438482800019"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"doi":"10.1016/j.cell.2018.06.033","language":[{"iso":"eng"}]},{"doi":"10.1111/tpj.13914","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":["000434365500008"]},"oa":1,"quality_controlled":"1","isi":1,"month":"06","author":[{"full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari"},{"full_name":"Nibau, Candida","first_name":"Candida","last_name":"Nibau"},{"last_name":"Fuchs","first_name":"Armin","full_name":"Fuchs, Armin"},{"last_name":"Dadarou","first_name":"Despoina","full_name":"Dadarou, Despoina"},{"last_name":"Barta","first_name":"Andrea","full_name":"Barta, Andrea"},{"full_name":"Doonan, John","first_name":"John","last_name":"Doonan"}],"date_created":"2018-12-11T11:46:17Z","date_updated":"2023-09-19T10:07:08Z","volume":94,"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]","publication_status":"published","publisher":"Wiley","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7426","date_published":"2018-06-01T00:00:00Z","publication":"The Plant Journal","citation":{"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.","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.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","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.","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.","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"},"page":"1010 - 1022","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2018_PlantJourn_Cavallari.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1543354,"file_id":"5934","relation":"main_file","date_created":"2019-02-06T11:40:54Z","date_updated":"2020-07-14T12:46:22Z","checksum":"d9d3ad3215ac0e581731443fca312266"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"403","status":"public","ddc":["580"],"title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","intvolume":" 94","abstract":[{"lang":"eng","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."}],"issue":"6","type":"journal_article"},{"date_published":"2018-07-12T00:00:00Z","citation":{"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","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.","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","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","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.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","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."},"page":"147 - 164","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"creator":"dernst","content_type":"application/pdf","file_size":485576,"access_level":"open_access","file_name":"2018_LNCS_Ferrere.pdf","success":1,"checksum":"a045c213c42c445f1889326f8db82a0a","date_created":"2020-10-09T06:22:41Z","date_updated":"2020-10-09T06:22:41Z","file_id":"8637","relation":"main_file"}],"oa_version":"Submitted Version","_id":"156","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"status":"public","title":"The compound interest in relaxing punctuality","intvolume":" 10951","abstract":[{"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.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"conference":{"location":"Oxford, UK","start_date":"2018-07-15","end_date":"2018-07-17","name":"FM: International Symposium on Formal Methods"},"doi":"10.1007/978-3-319-95582-7_9","language":[{"iso":"eng"}],"external_id":{"isi":["000489765800009"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"month":"07","author":[{"full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere"}],"date_created":"2018-12-11T11:44:55Z","date_updated":"2023-09-19T10:05:37Z","volume":10951,"year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-09T06:22:41Z","publist_id":"7765"},{"publication_status":"published","publisher":"Wiley","department":[{"_id":"GradSch"}],"year":"2018","acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","date_created":"2018-12-11T11:44:39Z","date_updated":"2023-09-19T10:06:42Z","volume":19,"author":[{"last_name":"Seitner","first_name":"Denise","full_name":"Seitner, Denise"},{"full_name":"Uhse, Simon","last_name":"Uhse","first_name":"Simon"},{"first_name":"Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"full_name":"Djamei, Armin","last_name":"Djamei","first_name":"Armin"}],"file_date_updated":"2018-12-18T09:46:00Z","publist_id":"7950","quality_controlled":"1","isi":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":["000445624100006"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/mpp.12698","month":"10","ddc":["580"],"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","status":"public","intvolume":" 19","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"104","oa_version":"Published Version","file":[{"file_name":"2018_MolecPlantPath_Seitner.pdf","access_level":"open_access","file_size":682335,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5740","date_created":"2018-12-18T09:46:00Z","date_updated":"2018-12-18T09:46:00Z","success":1}],"type":"journal_article","abstract":[{"text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host.","lang":"eng"}],"issue":"10","page":"2277 - 2287","publication":"Molecular Plant Pathology","citation":{"ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” Molecular Plant Pathology, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.","apa":"Seitner, D., Uhse, S., Gallei, M. C., & Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. Wiley. https://doi.org/10.1111/mpp.12698","ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287.","ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 2018;19(10):2277-2287. doi:10.1111/mpp.12698","chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology. Wiley, 2018. https://doi.org/10.1111/mpp.12698.","short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:10.1111/mpp.12698."},"date_published":"2018-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"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":["000454600500001"],"pmid":["30599087"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.14950","publication_identifier":{"issn":["1365294X"]},"month":"12","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2018","volume":27,"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-19T10:06:08Z","related_material":{"record":[{"id":"9805","relation":"research_data","status":"public"}]},"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"publist_id":"8014","file_date_updated":"2020-07-14T12:46:22Z","page":"4973-4975","article_type":"letter_note","citation":{"mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018."},"publication":"Molecular Ecology","date_published":"2018-12-31T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"31","intvolume":" 27","status":"public","ddc":["576"],"title":"The consequences of an introgression event","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"40","oa_version":"Published Version","file":[{"date_created":"2019-07-19T06:54:46Z","date_updated":"2020-07-14T12:46:22Z","relation":"main_file","file_id":"6652","file_size":295452,"content_type":"application/pdf","creator":"apreinsp","file_name":"2018_MolecularEcology_BartonNick.pdf","access_level":"open_access"}],"type":"journal_article","issue":"24","abstract":[{"lang":"eng","text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance."}]},{"month":"06","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.37888","quality_controlled":"1","isi":1,"external_id":{"isi":["000434375000001"]},"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,"file_date_updated":"2020-07-14T12:47:13Z","article_number":"e37888","date_updated":"2023-09-19T10:01:39Z","date_created":"2019-01-20T22:59:19Z","volume":7,"author":[{"full_name":"Alanko, Jonna H","last_name":"Alanko","first_name":"Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"eLife Sciences Publications","year":"2018","day":"06","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-06-06T00:00:00Z","article_type":"original","publication":"eLife","citation":{"mla":"Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” ELife, vol. 7, e37888, eLife Sciences Publications, 2018, doi:10.7554/eLife.37888.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.37888.","ama":"Alanko JH, Sixt MK. The cell sets the tone. eLife. 2018;7. doi:10.7554/eLife.37888","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","apa":"Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.37888","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018."},"abstract":[{"lang":"eng","text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":358141,"creator":"dernst","access_level":"open_access","file_name":"2018_eLife_Alanko.pdf","checksum":"f1c7ec2a809408d763c4b529a98f9a3b","date_created":"2019-02-13T10:52:11Z","date_updated":"2020-07-14T12:47:13Z","relation":"main_file","file_id":"5973"}],"ddc":["570"],"status":"public","title":"The cell sets the tone","intvolume":" 7","_id":"5861","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"abstract":[{"lang":"eng","text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development."}],"issue":"10","type":"journal_article","oa_version":"Published Version","status":"public","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","intvolume":" 30","_id":"147","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"12","article_processing_charge":"No","scopus_import":"1","date_published":"2018-11-12T00:00:00Z","article_type":"original","page":"2553 - 2572","publication":"The Plant Cell","citation":{"chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:10.1105/tpc.18.00127.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","ieee":"U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127"},"publist_id":"7776","ec_funded":1,"date_created":"2018-12-11T11:44:52Z","date_updated":"2023-09-19T10:09:12Z","volume":30,"author":[{"first_name":"Urszula","last_name":"Kania","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"full_name":"Lu, Qing","first_name":"Qing","last_name":"Lu"},{"last_name":"Hicks","first_name":"Glenn R","full_name":"Hicks, Glenn R"},{"last_name":"Nerinckx","first_name":"Wim","full_name":"Nerinckx, Wim"},{"first_name":"Kiril","last_name":"Mishev","full_name":"Mishev, Kiril"},{"last_name":"Peurois","first_name":"Francois","full_name":"Peurois, Francois"},{"full_name":"Cherfils, Jacqueline","first_name":"Jacqueline","last_name":"Cherfils"},{"full_name":"De, Rycke Riet Maria","last_name":"De","first_name":"Rycke Riet Maria"},{"full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Grones"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","year":"2018","acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","pmid":1,"month":"11","publication_identifier":{"issn":["1040-4651"]},"language":[{"iso":"eng"}],"doi":"10.1105/tpc.18.00127","isi":1,"quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1105/tpc.18.00127","open_access":"1"}],"external_id":{"pmid":["30018156"],"isi":["000450000500023"]}},{"oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2018_NaturePlants_Shi.pdf","creator":"dernst","file_size":226829,"content_type":"application/pdf","file_id":"7043","relation":"main_file","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","date_updated":"2020-07-14T12:44:56Z","date_created":"2019-11-18T16:24:07Z"}],"status":"public","title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","ddc":["580"],"intvolume":" 4","_id":"146","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity.","lang":"eng"}],"issue":"8","type":"journal_article","date_published":"2018-07-30T00:00:00Z","article_type":"original","page":"596 - 604","publication":"Nature Plants","citation":{"short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z.","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z.","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604. doi:10.1038/s41477-018-0212-z","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0212-z","ieee":"C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604."},"day":"30","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-09-19T10:08:45Z","date_created":"2018-12-11T11:44:52Z","volume":4,"author":[{"last_name":"Shi","first_name":"Chun Lin","full_name":"Shi, Chun Lin"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel"},{"first_name":"Ullrich","last_name":"Herrmann","full_name":"Herrmann, Ullrich"},{"last_name":"Wildhagen","first_name":"Mari","full_name":"Wildhagen, Mari"},{"full_name":"Kulik, Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","last_name":"Kulik","first_name":"Ivan"},{"full_name":"Kopf, Andreas","last_name":"Kopf","first_name":"Andreas"},{"full_name":"Ishida, Takashi","first_name":"Takashi","last_name":"Ishida"},{"full_name":"Olsson, Vilde","last_name":"Olsson","first_name":"Vilde"},{"last_name":"Anker","first_name":"Mari Kristine","full_name":"Anker, Mari Kristine"},{"full_name":"Albert, Markus","last_name":"Albert","first_name":"Markus"},{"full_name":"Butenko, Melinka A","first_name":"Melinka A","last_name":"Butenko"},{"last_name":"Felix","first_name":"Georg","full_name":"Felix, Georg"},{"first_name":"Shinichiro","last_name":"Sawa","full_name":"Sawa, Shinichiro"},{"full_name":"Claassen, Manfred","first_name":"Manfred","last_name":"Claassen"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Aalen, Reidunn B","last_name":"Aalen","first_name":"Reidunn B"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/"}]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","year":"2018","pmid":1,"file_date_updated":"2020-07-14T12:44:56Z","publist_id":"7777","language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0212-z","quality_controlled":"1","isi":1,"external_id":{"pmid":["30061750"],"isi":["000443861300016"]},"oa":1,"month":"07"},{"author":[{"full_name":"Hoffman, Moshe","first_name":"Moshe","last_name":"Hoffman"},{"orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/the-logic-of-modesty-why-it-pays-to-be-humble/"}]},"date_updated":"2023-09-19T10:12:03Z","date_created":"2018-12-11T11:45:39Z","volume":2,"acknowledgement":"This work was supported by a grant from the John Templeton Foundation and by the Office of Naval Research Grant N00014-16-1-2914 (M.A.N.). C.H. acknowledges generous support from the ISTFELLOW programme and by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","year":"2018","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:54Z","publist_id":"7588","ec_funded":1,"doi":"10.1038/s41562-018-0354-z","language":[{"iso":"eng"}],"external_id":{"isi":["000435551300009"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"month":"05","oa_version":"Submitted Version","file":[{"file_id":"7051","relation":"main_file","checksum":"32efaf06a597495c184df91b3fbb19c0","date_created":"2019-11-19T08:17:23Z","date_updated":"2020-07-14T12:45:54Z","access_level":"open_access","file_name":"2018_NatureHumanBeh_Hoffman.pdf","creator":"dernst","file_size":194734,"content_type":"application/pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"293","title":"The signal-burying game can explain why we obscure positive traits and good deeds","status":"public","ddc":["000"],"intvolume":" 2","abstract":[{"text":"People sometimes make their admirable deeds and accomplishments hard to spot, such as by giving anonymously or avoiding bragging. Such ‘buried’ signals are hard to reconcile with standard models of signalling or indirect reciprocity, which motivate costly pro-social behaviour by reputational gains. To explain these phenomena, we design a simple game theory model, which we call the signal-burying game. This game has the feature that senders can bury their signal by deliberately reducing the probability of the signal being observed. If the signal is observed, however, it is identified as having been buried. We show under which conditions buried signals can be maintained, using static equilibrium concepts and calculations of the evolutionary dynamics. We apply our analysis to shed light on a number of otherwise puzzling social phenomena, including modesty, anonymous donations, subtlety in art and fashion, and overeagerness.","lang":"eng"}],"type":"journal_article","date_published":"2018-05-28T00:00:00Z","publication":"Nature Human Behaviour","citation":{"chicago":"Hoffman, Moshe, Christian Hilbe, and Martin Nowak. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0354-z.","mla":"Hoffman, Moshe, et al. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 397–404, doi:10.1038/s41562-018-0354-z.","short":"M. Hoffman, C. Hilbe, M. Nowak, Nature Human Behaviour 2 (2018) 397–404.","ista":"Hoffman M, Hilbe C, Nowak M. 2018. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2, 397–404.","ieee":"M. Hoffman, C. Hilbe, and M. Nowak, “The signal-burying game can explain why we obscure positive traits and good deeds,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 397–404, 2018.","apa":"Hoffman, M., Hilbe, C., & Nowak, M. (2018). The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0354-z","ama":"Hoffman M, Hilbe C, Nowak M. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2018;2:397-404. doi:10.1038/s41562-018-0354-z"},"article_type":"original","page":"397 - 404","day":"28","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"publisher":"Birkhäuser","department":[{"_id":"RoSe"}],"publication_status":"published","year":"2018","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","volume":19,"date_created":"2018-12-11T11:46:34Z","date_updated":"2023-09-19T10:07:41Z","author":[{"first_name":"Niels P","last_name":"Benedikter","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P"},{"last_name":"Sok","first_name":"Jérémy","full_name":"Sok, Jérémy"},{"last_name":"Solovej","first_name":"Jan","full_name":"Solovej, Jan"}],"publist_id":"7367","file_date_updated":"2020-07-14T12:46:31Z","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"},"external_id":{"isi":["000427578900006"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00023-018-0644-z","month":"04","intvolume":" 19","status":"public","ddc":["510","539"],"title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"455","oa_version":"Published Version","file":[{"creator":"system","file_size":923252,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf","checksum":"883eeccba8384ad7fcaa28761d99a0fa","date_updated":"2020-07-14T12:46:31Z","date_created":"2018-12-12T10:11:57Z","file_id":"4914","relation":"main_file"}],"pubrep_id":"993","alternative_title":["Annales Henri Poincare"],"type":"journal_article","issue":"4","abstract":[{"text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities","lang":"eng"}],"page":"1167 - 1214","citation":{"chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare. Birkhäuser, 2018. https://doi.org/10.1007/s00023-018-0644-z.","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214.","mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:10.1007/s00023-018-0644-z.","apa":"Benedikter, N. P., Sok, J., & Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-018-0644-z","ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” Annales Henri Poincare, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214.","ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 2018;19(4):1167-1214. doi:10.1007/s00023-018-0644-z"},"publication":"Annales Henri Poincare","date_published":"2018-04-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.cels.2018.04.003","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cels.2018.04.003"}],"external_id":{"pmid":["29698645"],"isi":["000432192100003"]},"oa":1,"month":"04","publication_identifier":{"eissn":["2405-4712"]},"date_updated":"2023-09-19T10:11:25Z","date_created":"2018-12-11T11:45:46Z","volume":6,"author":[{"full_name":"Bauer, Guntram","last_name":"Bauer","first_name":"Guntram"},{"full_name":"Fakhri, Nikta","first_name":"Nikta","last_name":"Fakhri"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna"},{"first_name":"Jané","last_name":"Kondev","full_name":"Kondev, Jané"},{"full_name":"Kruse, Karsten","first_name":"Karsten","last_name":"Kruse"},{"full_name":"Noji, Hiroyuki","first_name":"Hiroyuki","last_name":"Noji"},{"last_name":"Riveline","first_name":"Daniel","full_name":"Riveline, Daniel"},{"first_name":"Timothy","last_name":"Saunders","full_name":"Saunders, Timothy"},{"first_name":"Mukund","last_name":"Thatta","full_name":"Thatta, Mukund"},{"full_name":"Wieschaus, Eric","first_name":"Eric","last_name":"Wieschaus"}],"publication_status":"published","publisher":"Cell Press","department":[{"_id":"AnKi"}],"year":"2018","pmid":1,"publist_id":"7551","date_published":"2018-04-25T00:00:00Z","article_type":"letter_note","page":"400 - 402","publication":"Cell Systems","citation":{"ama":"Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. Cell Systems. 2018;6(4):400-402. doi:10.1016/j.cels.2018.04.003","ista":"Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402.","ieee":"G. Bauer et al., “The science of living matter for tomorrow,” Cell Systems, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","apa":"Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2018.04.003","mla":"Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” Cell Systems, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:10.1016/j.cels.2018.04.003.","short":"G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402.","chicago":"Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” Cell Systems. Cell Press, 2018. https://doi.org/10.1016/j.cels.2018.04.003."},"day":"25","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","title":"The science of living matter for tomorrow","status":"public","intvolume":" 6","_id":"314","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations.","lang":"eng"}],"issue":"4","type":"journal_article"},{"type":"journal_article","abstract":[{"text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. ","lang":"eng"}],"issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"565","title":"The spread of an inversion with migration and selection","status":"public","intvolume":" 208","oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Genetics","citation":{"ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382."},"article_type":"original","page":"377 - 382","date_published":"2018-01-01T00:00:00Z","publist_id":"7249","year":"2018","pmid":1,"publication_status":"published","publisher":"Genetics ","department":[{"_id":"NiBa"}],"author":[{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"date_updated":"2023-09-19T10:12:31Z","date_created":"2018-12-11T11:47:12Z","volume":208,"month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/"}],"external_id":{"isi":["000419356300025"],"pmid":["29158424"]},"isi":1,"quality_controlled":"1","doi":"10.1534/genetics.117.300426","language":[{"iso":"eng"}]},{"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"RoSe"}],"year":"2018","acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","date_created":"2018-12-11T11:46:31Z","date_updated":"2023-09-19T10:09:40Z","volume":71,"author":[{"last_name":"Frank","first_name":"Rupert","full_name":"Frank, Rupert"},{"last_name":"Phan Thanh","first_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan Thanh, Nam"},{"full_name":"Van Den Bosch, Hanne","first_name":"Hanne","last_name":"Van Den Bosch"}],"publist_id":"7377","isi":1,"quality_controlled":"1","external_id":{"isi":["000422675800004"],"arxiv":["1606.07355"]},"main_file_link":[{"url":"https://arxiv.org/abs/1606.07355","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/cpa.21717","month":"03","title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","status":"public","intvolume":" 71","_id":"446","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential."}],"issue":"3","article_type":"original","page":"577 - 614","publication":"Communications on Pure and Applied Mathematics","citation":{"ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717","ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","apa":"Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717","ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614.","chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717."},"date_published":"2018-03-01T00:00:00Z","day":"01","article_processing_charge":"No"},{"page":"1351 - 1355","publication":"Genetics","citation":{"ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786."},"date_published":"2018-04-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","title":"Tread lightly interpreting polygenic tests of selection","status":"public","ddc":["576"],"intvolume":" 208","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"430","file":[{"creator":"system","content_type":"application/pdf","file_size":500129,"file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","access_level":"open_access","date_created":"2018-12-12T10:12:40Z","date_updated":"2020-07-14T12:46:26Z","checksum":"3d838dc285df394376555b794b6a5ad1","file_id":"4958","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"1012","type":"journal_article","abstract":[{"text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly.","lang":"eng"}],"issue":"4","quality_controlled":"1","isi":1,"external_id":{"isi":["000429094400005"]},"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,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.300786","month":"04","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","year":"2018","date_created":"2018-12-11T11:46:26Z","date_updated":"2023-09-19T10:17:30Z","volume":208,"author":[{"full_name":"Novembre, John","first_name":"John","last_name":"Novembre"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"file_date_updated":"2020-07-14T12:46:26Z","publist_id":"7393"},{"type":"journal_article","issue":"6","abstract":[{"text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"199","intvolume":" 9","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3985796,"creator":"dernst","file_name":"2018_Genes_Ma.pdf","access_level":"open_access","date_created":"2019-02-01T07:52:28Z","date_updated":"2020-07-14T12:45:22Z","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","relation":"main_file","file_id":"5905"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"12","citation":{"ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294."},"publication":"Genes","date_published":"2018-06-12T00:00:00Z","article_number":"294","publist_id":"7714","file_date_updated":"2020-07-14T12:45:22Z","year":"2018","department":[{"_id":"BeVi"}],"publisher":"MDPI AG","publication_status":"published","author":[{"full_name":"Ma, Wen","last_name":"Ma","first_name":"Wen"},{"full_name":"Veltsos, Paris","first_name":"Paris","last_name":"Veltsos"},{"last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"full_name":"Rodrigues, Nicolas","last_name":"Rodrigues","first_name":"Nicolas"},{"full_name":"Sermier, Roberto","last_name":"Sermier","first_name":"Roberto"},{"full_name":"Jeffries, Daniel","last_name":"Jeffries","first_name":"Daniel"},{"full_name":"Perrin, Nicolas","last_name":"Perrin","first_name":"Nicolas"}],"volume":9,"date_created":"2018-12-11T11:45:09Z","date_updated":"2023-09-19T10:15:31Z","month":"06","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":["000436494200026"]},"quality_controlled":"1","isi":1,"doi":"10.3390/genes9060294","language":[{"iso":"eng"}]},{"external_id":{"isi":["000419128700049"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"oa":1,"project":[{"name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1711114115","language":[{"iso":"eng"}],"month":"01","year":"2018","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","publication_status":"published","author":[{"full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","first_name":"Matthew J","last_name":"Chalk"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"volume":115,"date_updated":"2023-09-19T10:16:35Z","date_created":"2018-12-11T11:47:04Z","publist_id":"7273","citation":{"ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1711114115","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.","short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1711114115."},"publication":"PNAS","page":"186 - 191","date_published":"2018-01-02T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"02","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"543","intvolume":" 115","status":"public","title":"Toward a unified theory of efficient, predictive, and sparse coding","oa_version":"Submitted Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits."}]},{"publist_id":"7403","year":"2018","department":[{"_id":"EdHa"}],"publisher":"Biophysical Society","publication_status":"published","author":[{"first_name":"Kinjal","last_name":"Dasbiswas","full_name":"Dasbiswas, Kinjal"},{"last_name":"Hannezo","first_name":"Claude-Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Claude-Edouard B"},{"full_name":"Gov, Nir","first_name":"Nir","last_name":"Gov"}],"volume":114,"date_updated":"2023-09-19T10:13:55Z","date_created":"2018-12-11T11:46:23Z","month":"02","oa":1,"external_id":{"arxiv":["1709.01486"],"isi":["000428016700021"]},"main_file_link":[{"url":"https://arxiv.org/abs/1709.01486","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.bpj.2017.12.022","language":[{"iso":"eng"}],"type":"journal_article","issue":"4","abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"421","intvolume":" 114","status":"public","title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"27","citation":{"chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022.","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","apa":"Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022"},"publication":"Biophysical Journal","page":"968 - 977","date_published":"2018-02-27T00:00:00Z"},{"publist_id":"7991","ec_funded":1,"file_date_updated":"2020-07-14T12:47:27Z","article_number":"480","author":[{"full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger","first_name":"William J"},{"full_name":"Kocher, Thomas","first_name":"Thomas","last_name":"Kocher"}],"volume":9,"date_updated":"2023-09-19T10:37:03Z","date_created":"2018-12-11T11:44:26Z","year":"2018","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","publisher":"MDPI AG","department":[{"_id":"BeVi"}],"publication_status":"published","month":"10","doi":"10.3390/genes9100480","language":[{"iso":"eng"}],"external_id":{"isi":["000448656700018"]},"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,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"quality_controlled":"1","issue":"10","abstract":[{"lang":"eng","text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5743","date_updated":"2020-07-14T12:47:27Z","date_created":"2018-12-18T09:54:46Z","checksum":"bec527692e2c9b56919c0429634ff337","file_name":"2018_Genes_Gammerdinger.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1415791,"creator":"dernst"}],"_id":"63","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 9","title":"Unusual diversity of sex chromosomes in African cichlid fishes","ddc":["570"],"status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2018-10-04T00:00:00Z","citation":{"chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9100480.","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI AG, 2018, doi:10.3390/genes9100480.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480.","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018.","apa":"Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI AG. https://doi.org/10.3390/genes9100480","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480"},"publication":"Genes"},{"publist_id":"7585","author":[{"last_name":"Turner","first_name":"Christopher","full_name":"Turner, Christopher"},{"full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","first_name":"Alexios","last_name":"Michailidis"},{"full_name":"Abanin, Dmitry","first_name":"Dmitry","last_name":"Abanin"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"}],"volume":14,"date_updated":"2023-09-19T10:37:55Z","date_created":"2018-12-11T11:45:40Z","acknowledgement":"C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1 and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support from the Swiss National Science Foundation.","year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"MaSe"}],"publication_status":"published","month":"05","doi":"10.1038/s41567-018-0137-5","language":[{"iso":"eng"}],"external_id":{"isi":["000438253600028"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://eprints.whiterose.ac.uk/130860/"}],"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"The thermodynamic description of many-particle systems rests on the assumption of ergodicity, the ability of a system to explore all allowed configurations in the phase space. Recent studies on many-body localization have revealed the existence of systems that strongly violate ergodicity in the presence of quenched disorder. Here, we demonstrate that ergodicity can be weakly broken by a different mechanism, arising from the presence of special eigenstates in the many-body spectrum that are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle case, quantum scars correspond to wavefunctions that concentrate in the vicinity of unstable periodic classical trajectories. We show that many-body scars appear in the Fibonacci chain, a model with a constrained local Hilbert space that has recently been experimentally realized in a Rydberg-atom quantum simulator. The quantum scarred eigenstates are embedded throughout the otherwise thermalizing many-body spectrum but lead to direct experimental signatures, as we show for periodic recurrences that reproduce those observed in the experiment. Our results suggest that scarred many-body bands give rise to a new universality class of quantum dynamics, opening up opportunities for the creation of novel states with long-lived coherence in systems that are now experimentally realizable."}],"type":"journal_article","oa_version":"Submitted Version","_id":"296","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 14","status":"public","title":"Weak ergodicity breaking from quantum many-body scars","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2018-05-14T00:00:00Z","citation":{"ama":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 2018;14:745-749. doi:10.1038/s41567-018-0137-5","apa":"Turner, C., Michailidis, A., Abanin, D., Serbyn, M., & Papić, Z. (2018). Weak ergodicity breaking from quantum many-body scars. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0137-5","ieee":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity breaking from quantum many-body scars,” Nature Physics, vol. 14. Nature Publishing Group, pp. 745–749, 2018.","ista":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 14, 745–749.","short":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics 14 (2018) 745–749.","mla":"Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 745–49, doi:10.1038/s41567-018-0137-5.","chicago":"Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn, and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0137-5."},"publication":"Nature Physics","page":"745 - 749","article_type":"original"},{"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1704.08757","open_access":"1"}],"oa":1,"external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.physd.2017.10.015","month":"08","publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"year":"2018","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","date_created":"2018-12-11T11:47:28Z","date_updated":"2023-09-19T10:38:34Z","volume":"376-377","author":[{"full_name":"Bodova, Katarina","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bodova","first_name":"Katarina"},{"first_name":"Jan","last_name":"Haskovec","full_name":"Haskovec, Jan"},{"full_name":"Markowich, Peter","last_name":"Markowich","first_name":"Peter"}],"publist_id":"7198","page":"108-120","publication":"Physica D: Nonlinear Phenomena","citation":{"ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015."},"date_published":"2018-08-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"607","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}]},{"quality_controlled":"1","isi":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"external_id":{"isi":["000430296800008"],"arxiv":["1801.06892"]},"main_file_link":[{"url":"https://arxiv.org/abs/1801.06892","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.97.043842","month":"04","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"year":"2018","date_updated":"2023-09-19T10:17:56Z","date_created":"2018-12-11T11:45:40Z","volume":97,"author":[{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"},{"first_name":"Laleh","last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh"},{"full_name":"Amaro, Pedro","first_name":"Pedro","last_name":"Amaro"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"}],"ec_funded":1,"publist_id":"7587","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","citation":{"chicago":"Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043842.","mla":"Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043842.","short":"F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","ista":"Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4).","apa":"Fratini, F., Safari, L., Amaro, P., & Santos, J. (2018). Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043842","ieee":"F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based on quantum commutators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","ama":"Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043842"},"date_published":"2018-04-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"No","title":"Two-photon processes based on quantum commutators","status":"public","intvolume":" 97","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"294","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed."}],"issue":"4"},{"scopus_import":"1","day":"01","article_processing_charge":"No","page":"1267-1319","publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","citation":{"chicago":"Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004.","short":"M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 35 (2018) 1267–1319.","mla":"Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004.","ieee":"M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.","apa":"Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004","ista":"Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 35(5), 1267–1319.","ama":"Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004"},"date_published":"2018-08-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We establish the existence of a global solution for a new family of fluid-like equations, which are obtained in certain regimes in as the mean-field evolution of the supercurrent density in a (2D section of a) type-II superconductor with pinning and with imposed electric current. We also consider general vortex-sheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the so-called lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data."}],"issue":"5","status":"public","title":"Well-posedness for mean-field evolutions arising in superconductivity","intvolume":" 35","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"606","oa_version":"Submitted Version","month":"08","isi":1,"quality_controlled":"1","external_id":{"isi":["000437975500005"],"arxiv":["1607.00268"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00268"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.anihpc.2017.11.004","publist_id":"7199","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JuFi"}],"year":"2018","acknowledgement":"The work of the author is supported by F.R.S.-FNRS ( Fonds de la Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n","date_updated":"2023-09-19T10:39:09Z","date_created":"2018-12-11T11:47:27Z","volume":35,"author":[{"last_name":"Duerinckx","first_name":"Mitia","full_name":"Duerinckx, Mitia"},{"full_name":"Fischer, Julian L","first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"}]}]