[{"ec_funded":1,"volume":115,"issue":"35","publication_status":"published","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1806.09153","open_access":"1"}],"scopus_import":"1","intvolume":" 115","month":"08","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"oa_version":"Preprint","department":[{"_id":"TaHa"}],"date_updated":"2023-09-18T08:41:16Z","article_type":"original","type":"journal_article","status":"public","_id":"64","page":"E8135 - E8142","date_created":"2018-12-11T11:44:26Z","date_published":"2018-08-28T00:00:00Z","doi":"10.1073/pnas.1805847115","year":"2018","isi":1,"publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","day":"28","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","external_id":{"arxiv":["1806.09153"],"isi":["000442861600009"]},"article_processing_charge":"No","author":[{"last_name":"Kalinin","full_name":"Kalinin, Nikita","first_name":"Nikita"},{"first_name":"Aldo","full_name":"Guzmán Sáenz, Aldo","last_name":"Guzmán Sáenz"},{"first_name":"Y","full_name":"Prieto, Y","last_name":"Prieto"},{"first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail"},{"first_name":"V","last_name":"Kalinina","full_name":"Kalinina, V"},{"first_name":"Ernesto","last_name":"Lupercio","full_name":"Lupercio, Ernesto"}],"publist_id":"7990","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","citation":{"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.","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","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","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.","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.","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"date_updated":"2023-09-18T09:29:07Z","citation":{"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.","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.","ieee":"M. Kaucka et al., “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2","ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:10.5061/dryad.f1s76f2","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Kaucka","full_name":"Kaucka, Marketa","first_name":"Marketa"},{"full_name":"Petersen, Julian","last_name":"Petersen","first_name":"Julian"},{"first_name":"Marketa","last_name":"Tesarova","full_name":"Tesarova, Marketa"},{"last_name":"Szarowska","full_name":"Szarowska, Bara","first_name":"Bara"},{"last_name":"Kastriti","full_name":"Kastriti, Maria Eleni","first_name":"Maria Eleni"},{"last_name":"Xie","full_name":"Xie, Meng","first_name":"Meng"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"last_name":"Annusver","full_name":"Annusver, Karl","first_name":"Karl"},{"full_name":"Kasper, Maria","last_name":"Kasper","first_name":"Maria"},{"last_name":"Symmons","full_name":"Symmons, Orsolya","first_name":"Orsolya"},{"first_name":"Leslie","last_name":"Pan","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","last_name":"Spitz","first_name":"Francois"},{"full_name":"Kaiser, Jozef","last_name":"Kaiser","first_name":"Jozef"},{"first_name":"Maria","full_name":"Hovorakova, Maria","last_name":"Hovorakova"},{"last_name":"Zikmund","full_name":"Zikmund, Tomas","first_name":"Tomas"},{"first_name":"Kazunori","full_name":"Sunadome, Kazunori","last_name":"Sunadome"},{"first_name":"Michael P","full_name":"Matise, Michael P","last_name":"Matise"},{"last_name":"Wang","full_name":"Wang, Hui","first_name":"Hui"},{"last_name":"Marklund","full_name":"Marklund, Ulrika","first_name":"Ulrika"},{"first_name":"Hind","full_name":"Abdo, Hind","last_name":"Abdo"},{"first_name":"Patrik","full_name":"Ernfors, Patrik","last_name":"Ernfors"},{"first_name":"Pascal","last_name":"Maire","full_name":"Maire, Pascal"},{"first_name":"Maud","last_name":"Wurmser","full_name":"Wurmser, Maud"},{"first_name":"Andrei S","full_name":"Chagin, Andrei S","last_name":"Chagin"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"}],"article_processing_charge":"No","department":[{"_id":"AnKi"}],"title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","_id":"9838","type":"research_data_reference","status":"public","year":"2018","day":"14","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"162"}]},"doi":"10.5061/dryad.f1s76f2","date_published":"2018-06-14T00:00:00Z","date_created":"2021-08-09T12:54:35Z","abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"oa_version":"Published Version","publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.f1s76f2","open_access":"1"}],"month":"06"},{"abstract":[{"text":"The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"09","publication_status":"published","publication_identifier":{"issn":["16625102"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"0bcaec8d596162af0b7fe3f31325d480","file_id":"5684","creator":"dernst","file_size":6834251,"date_updated":"2020-07-14T12:46:23Z","file_name":"fncel-12-00311.pdf","date_created":"2018-12-17T08:49:03Z"}],"ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","volume":12,"_id":"41","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-18T09:31:18Z","ddc":["570"],"file_date_updated":"2020-07-14T12:46:23Z","department":[{"_id":"RySh"}],"oa":1,"publisher":"Frontiers Media","quality_controlled":"1","year":"2018","isi":1,"has_accepted_license":"1","publication":"Frontiers in Cellular Neuroscience","day":"19","date_created":"2018-12-11T11:44:19Z","doi":"10.3389/fncel.2018.00311","date_published":"2018-09-19T00:00:00Z","article_number":"311","project":[{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270"}],"citation":{"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.","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.","ieee":"R. Luján et al., “Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience, vol. 12. Frontiers Media, 2018.","short":"R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018).","ama":"Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 2018;12. doi:10.3389/fncel.2018.00311","apa":"Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz, R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2018.00311","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000445090100002"]},"publist_id":"8013","author":[{"first_name":"Rafæl","last_name":"Luján","full_name":"Luján, Rafæl"},{"last_name":"Aguado","full_name":"Aguado, Carolina","first_name":"Carolina"},{"first_name":"Francisco","full_name":"Ciruela, Francisco","last_name":"Ciruela"},{"first_name":"Xavier","last_name":"Arus","full_name":"Arus, Xavier"},{"full_name":"Martín Belmonte, Alejandro","last_name":"Martín Belmonte","first_name":"Alejandro"},{"first_name":"Rocío","full_name":"Alfaro Ruiz, Rocío","last_name":"Alfaro Ruiz"},{"first_name":"Jesus","last_name":"Martinez Gomez","full_name":"Martinez Gomez, Jesus"},{"first_name":"Luis","full_name":"De La Ossa, Luis","last_name":"De La Ossa"},{"full_name":"Watanabe, Masahiko","last_name":"Watanabe","first_name":"Masahiko"},{"full_name":"Adelman, John","last_name":"Adelman","first_name":"John"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"}],"title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells"},{"oa":1,"quality_controlled":"1","publisher":"American Chemical Society","year":"2018","has_accepted_license":"1","isi":1,"publication":"Nano Letters","day":"25","page":"7141 - 7145","date_created":"2018-12-11T11:44:13Z","date_published":"2018-10-25T00:00:00Z","doi":"10.1021/acs.nanolett.8b03217","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497"}],"citation":{"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.","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.","ama":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. Nano Letters. 2018;18(11):7141-7145. doi:10.1021/acs.nanolett.8b03217","apa":"Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., & Katsaros, G. (2018). Single-shot readout of hole spins in Ge. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b03217","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b03217.","ista":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018. Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["30359041"],"isi":["000451102100064"]},"article_processing_charge":"No","publist_id":"8032","author":[{"last_name":"Vukušić","orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","full_name":"Watzinger, Hannes"},{"full_name":"Milem, Joshua M","last_name":"Milem","id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87","first_name":"Joshua M"},{"full_name":"Schäffler, Friedrich","last_name":"Schäffler","first_name":"Friedrich"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"title":"Single-shot readout of hole spins in Ge","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"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"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 18","month":"10","publication_status":"published","publication_identifier":{"issn":["15306984"]},"language":[{"iso":"eng"}],"file":[{"checksum":"3e6034a94c6b5335e939145d88bdb371","file_id":"5194","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf","date_created":"2018-12-12T10:16:08Z","creator":"system","file_size":1361441,"date_updated":"2020-07-14T12:45:37Z"}],"ec_funded":1,"issue":"11","volume":18,"related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","id":"69","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"7996"}]},"_id":"23","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"1065","status":"public","date_updated":"2023-09-18T09:30:37Z","ddc":["530"],"department":[{"_id":"GeKa"}],"file_date_updated":"2020-07-14T12:45:37Z"},{"_id":"85","status":"public","conference":{"location":"Turin, Italy","end_date":"2018-08-31","start_date":"2018-08-27","name":"Euro-Par: European Conference on Parallel Processing"},"type":"conference","ddc":["000"],"date_updated":"2023-09-18T09:32:36Z","file_date_updated":"2020-07-14T12:48:14Z","department":[{"_id":"DaAl"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use."}],"intvolume":" 11014","month":"08","alternative_title":["LNCS"],"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"13a3f250be8878405e791b53c19722ad","file_id":"5954","creator":"dernst","date_updated":"2020-07-14T12:48:14Z","file_size":665372,"date_created":"2019-02-12T07:40:40Z","file_name":"2018_Brown.pdf"}],"publication_status":"published","publication_identifier":{"issn":["03029743"]},"volume":11014,"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","ieee":"E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.","chicago":"Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33.","ista":"Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479."},"title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","external_id":{"isi":["000851042300031"]},"article_processing_charge":"No","publist_id":"7969","author":[{"first_name":"Eran","full_name":"Gilad, Eran","last_name":"Gilad"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Trevor A"},{"full_name":"Oskin, Mark","last_name":"Oskin","first_name":"Mark"},{"last_name":"Etsion","full_name":"Etsion, Yoav","first_name":"Yoav"}],"acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","oa":1,"quality_controlled":"1","publisher":"Springer","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:33Z","doi":"10.1007/978-3-319-96983-1_33","date_published":"2018-08-01T00:00:00Z","page":"465 - 479"},{"type":"journal_article","status":"public","_id":"327","department":[{"_id":"MaSe"}],"date_updated":"2023-09-18T09:31:46Z","main_file_link":[{"url":"https://arxiv.org/abs/1706.05026","open_access":"1"}],"scopus_import":"1","intvolume":" 97","month":"03","abstract":[{"lang":"eng","text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations."}],"oa_version":"Preprint","volume":97,"issue":"10","publication_status":"published","language":[{"iso":"eng"}],"article_number":"104307","external_id":{"isi":["000427798800005"]},"article_processing_charge":"No","author":[{"last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Žnidarič","full_name":"Žnidarič, Marko","first_name":"Marko"},{"last_name":"Medvedyeva","full_name":"Medvedyeva, Mariya","first_name":"Mariya"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry"},{"first_name":"Tomaž","last_name":"Prosen","full_name":"Prosen, Tomaž"},{"first_name":"Zlatko","full_name":"Papić, Zlatko","last_name":"Papić"}],"publist_id":"7538","title":"Slow dynamics in translation-invariant quantum lattice models","citation":{"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.","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"American Physical Society","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.).","date_created":"2018-12-11T11:45:50Z","doi":"10.1103/PhysRevB.97.104307","date_published":"2018-03-19T00:00:00Z","year":"2018","isi":1,"publication":"Physical Review B","day":"19"},{"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"0d1355c78627ca7210aadd9a17a01915","file_id":"5682","creator":"dernst","file_size":1272096,"date_updated":"2020-07-14T12:45:52Z","file_name":"Viljakainen_et_al-2018-Ecology_and_Evolution.pdf","date_created":"2018-12-17T08:27:04Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20457758"]},"publication_status":"published","issue":"22","volume":8,"oa_version":"Published Version","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."}],"month":"11","intvolume":" 8","scopus_import":"1","ddc":["576","591"],"date_updated":"2023-09-19T09:29:12Z","file_date_updated":"2020-07-14T12:45:52Z","department":[{"_id":"SyCr"}],"_id":"29","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","publication":"Ecology and Evolution","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1002/ece3.4573","date_published":"2018-11-01T00:00:00Z","date_created":"2018-12-11T11:44:15Z","page":"11031-11070","quality_controlled":"1","publisher":"Wiley","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","short":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer, Ecology and Evolution 8 (2018) 11031–11070.","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.","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.","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."},"title":"Social environment affects the transcriptomic response to bacteria in ant queens","author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana","first_name":"Jaana"},{"first_name":"Ida","last_name":"Holmberg","full_name":"Holmberg, Ida"},{"last_name":"Pamminger","full_name":"Pamminger, Tobias","first_name":"Tobias"},{"first_name":"Silvio","full_name":"Erler, Silvio","last_name":"Erler"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8026","external_id":{"isi":["000451611000032"]},"article_processing_charge":"No"},{"volume":63,"related_material":{"record":[{"relation":"dissertation_contains","id":"819","status":"public"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1545-4487"]},"publication_status":"published","month":"01","intvolume":" 63","scopus_import":"1","oa_version":"None","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"}],"department":[{"_id":"SyCr"}],"date_updated":"2023-09-19T09:29:45Z","status":"public","type":"journal_article","_id":"806","date_published":"2018-01-07T00:00:00Z","doi":"10.1146/annurev-ento-020117-043110","date_created":"2018-12-11T11:48:36Z","page":"105 - 123","day":"07","publication":"Annual Review of Entomology","isi":1,"year":"2018","publisher":"Annual Reviews","quality_controlled":"1","title":"Social immunity: Emergence and evolution of colony-level disease protection","publist_id":"6844","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher"},{"first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X"}],"external_id":{"isi":["000424633700008"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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.","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","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"}},{"title":"Space-time interpolants","author":[{"last_name":"Frehse","full_name":"Frehse, Goran","first_name":"Goran"},{"first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","last_name":"Giacobbe","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7783","external_id":{"isi":["000491481600025"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","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.","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","mla":"Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer, 2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25.","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486.","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."},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"}],"doi":"10.1007/978-3-319-96145-3_25","date_published":"2018-07-18T00:00:00Z","date_created":"2018-12-11T11:44:50Z","page":"468 - 486","day":"18","isi":1,"has_accepted_license":"1","year":"2018","publisher":"Springer","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:44:50Z","department":[{"_id":"ToHe"}],"ddc":["005"],"date_updated":"2023-09-19T09:30:43Z","status":"public","pubrep_id":"1010","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","location":"Oxford, United Kingdom","start_date":"2018-07-14"},"_id":"140","related_material":{"record":[{"relation":"dissertation_contains","id":"6894","status":"public"}]},"volume":10981,"file":[{"file_size":563710,"date_updated":"2020-07-14T12:44:50Z","creator":"system","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","date_created":"2018-12-12T10:17:53Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5310","checksum":"6dca832f575d6b3f0ea9dff56f579142"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03029743"]},"publication_status":"published","month":"07","intvolume":" 10981","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools.","lang":"eng"}]},{"scopus_import":"1","intvolume":" 21","month":"09","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"3","volume":21,"related_material":{"record":[{"id":"52","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"issn":["13850172"],"eissn":["15729656"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2018_MathPhysics_Moser.pdf","date_created":"2018-12-17T16:49:02Z","creator":"dernst","file_size":496973,"date_updated":"2020-07-14T12:45:01Z","checksum":"411c4db5700d7297c9cd8ebc5dd29091","file_id":"5729","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"154","file_date_updated":"2020-07-14T12:45:01Z","department":[{"_id":"RoSe"}],"date_updated":"2023-09-19T09:31:15Z","ddc":["530"],"oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","date_created":"2018-12-11T11:44:55Z","doi":"10.1007/s11040-018-9275-3","date_published":"2018-09-01T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Mathematical Physics Analysis and Geometry","day":"01","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"article_number":"19","article_processing_charge":"No","external_id":{"isi":["000439639700001"]},"author":[{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Moser, Thomas","last_name":"Moser"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7767","title":"Stability of the 2+2 fermionic system with point interactions","citation":{"mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry, vol. 21, no. 3, 19, Springer, 2018, doi:10.1007/s11040-018-9275-3.","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","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","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.","short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry. Springer, 2018. https://doi.org/10.1007/s11040-018-9275-3.","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-09-19T09:32:49Z","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"5787","issue":"9","volume":60,"file":[{"creator":"dernst","file_size":1313606,"date_updated":"2020-07-14T12:47:11Z","file_name":"2018_DevGrowh_Hannezo.pdf","date_created":"2019-02-06T10:40:46Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"a6d30b0785db902c734a84fecb2eadd9","file_id":"5933"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00121592"]},"month":"12","intvolume":" 60","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Branching morphogenesis remains a subject of abiding interest. Although much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions and cell lineage tracing, it has been argued that morphogenesis follows \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, set of local rules, \r\nwithout recourse to a rigid and deterministic sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications.","lang":"eng"}],"title":"Statistical theory of branching morphogenesis","author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"first_name":"Benjamin D.","last_name":"Simons","full_name":"Simons, Benjamin D."}],"external_id":{"isi":["000453555100002"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","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.","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570","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.","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521."},"date_published":"2018-12-09T00:00:00Z","doi":"10.1111/dgd.12570","date_created":"2018-12-30T22:59:14Z","page":"512-521","day":"09","publication":"Development Growth and Differentiation","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"Wiley","oa":1},{"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"publist_id":"7584","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","first_name":"Viktor"}],"external_id":{"isi":["000546326300021"]},"article_processing_charge":"No","title":"Strategy representation by decision trees in reactive synthesis","citation":{"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","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","short":"T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp. 385–407.","ieee":"T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10805, pp. 385–407.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Springer","oa":1,"page":"385 - 407","doi":"10.1007/978-3-319-89960-2_21","date_published":"2018-04-12T00:00:00Z","date_created":"2018-12-11T11:45:41Z","has_accepted_license":"1","isi":1,"year":"2018","day":"12","type":"conference","conference":{"start_date":"2018-04-14","end_date":"2018-04-20","location":"Thessaloniki, Greece","name":"TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"297","file_date_updated":"2020-07-14T12:45:57Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-19T09:57:08Z","ddc":["000"],"scopus_import":"1","alternative_title":["LNCS"],"month":"04","intvolume":" 10805","abstract":[{"text":"Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs.","lang":"eng"}],"oa_version":"Published Version","volume":10805,"ec_funded":1,"publication_status":"published","file":[{"file_id":"5723","checksum":"b13874ffb114932ad9cc2586b7469db4","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T16:29:08Z","file_name":"2018_LNCS_Brazdil.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:57Z","file_size":1829940}],"language":[{"iso":"eng"}]},{"status":"public","type":"conference","conference":{"name":"CAV: Computer Aided Verification","location":"Oxford, United Kingdom","end_date":"2018-07-17","start_date":"2018-07-14"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"141","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:44:53Z","ddc":["000"],"date_updated":"2023-09-19T09:59:55Z","month":"07","intvolume":" 10982","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Published Version","abstract":[{"text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.","lang":"eng"}],"related_material":{"record":[{"id":"10199","status":"public","relation":"dissertation_contains"}]},"volume":10982,"ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","file_id":"5737","file_size":675606,"date_updated":"2020-07-14T12:44:53Z","creator":"dernst","file_name":"2018_LNCS_Chatterjee.pdf","date_created":"2018-12-18T08:52:38Z"}],"language":[{"iso":"eng"}],"publication_status":"published","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","publist_id":"7782","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika","first_name":"Veronika"},{"last_name":"Oraee","full_name":"Oraee, Simin","first_name":"Simin"},{"first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X"}],"article_processing_charge":"No","external_id":{"isi":["000491469700013"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp. 178–97, doi:10.1007/978-3-319-96142-2_13.","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","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","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.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13.","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."},"quality_controlled":"1","publisher":"Springer","oa":1,"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.","date_published":"2018-07-18T00:00:00Z","doi":"10.1007/978-3-319-96142-2_13","date_created":"2018-12-11T11:44:51Z","page":"178-197","day":"18","has_accepted_license":"1","isi":1,"year":"2018"},{"oa_version":"Preprint","abstract":[{"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⋅","lang":"eng"}],"month":"03","intvolume":" 10821","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05313"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":10821,"ec_funded":1,"_id":"298","status":"public","type":"conference","conference":{"name":"Eurocrypt 2018: Advances in Cryptology","end_date":"2018-05-03","location":"Tel Aviv, Israel","start_date":"2018-04-29"},"date_updated":"2023-09-19T09:59:30Z","department":[{"_id":"KrPi"}],"quality_controlled":"1","publisher":"Springer","oa":1,"day":"31","isi":1,"year":"2018","doi":"10.1007/978-3-319-78375-8_4","date_published":"2018-03-31T00:00:00Z","date_created":"2018-12-11T11:45:41Z","page":"99 - 130","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt 2018: Advances in Cryptology, LNCS, vol. 10821, 99–130.","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.","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.","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, Springer, 2018, pp. 99–130.","apa":"Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2018). Sustained space complexity (Vol. 10821, pp. 99–130). Presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_4","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","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."},"title":"Sustained space complexity","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"first_name":"Jeremiah","last_name":"Blocki","full_name":"Blocki, Jeremiah"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"publist_id":"7583","external_id":{"arxiv":["1705.05313"],"isi":["000517098700004"]},"article_processing_charge":"No"},{"oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","date_created":"2018-12-11T11:44:17Z","doi":"10.1093/jxb/ery204","date_published":"2018-08-31T00:00:00Z","page":"4609 - 4624","publication":"Journal of Experimental Botany","day":"31","year":"2018","has_accepted_license":"1","isi":1,"title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","article_processing_charge":"No","external_id":{"isi":["000443568700010"]},"author":[{"first_name":"Lam","full_name":"Vu, Lam","last_name":"Vu"},{"first_name":"Tingting","last_name":"Zhu","full_name":"Zhu, Tingting"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"first_name":"Brigitte","last_name":"Van De Cotte","full_name":"Van De Cotte, Brigitte"},{"full_name":"Gevaert, Kris","last_name":"Gevaert","first_name":"Kris"},{"full_name":"De Smet, Ive","last_name":"De Smet","first_name":"Ive"}],"publist_id":"8019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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","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","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","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."},"intvolume":" 69","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity."}],"volume":69,"issue":"19","language":[{"iso":"eng"}],"file":[{"file_id":"5741","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-18T09:47:51Z","file_name":"2018_JournalExperimBotany_Vu.pdf","date_updated":"2020-07-14T12:46:13Z","file_size":3359316,"creator":"dernst"}],"publication_status":"published","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"36","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:46:13Z","ddc":["581"],"date_updated":"2023-09-19T10:00:46Z"},{"publisher":"Wiley","quality_controlled":"1","oa":1,"date_published":"2018-03-07T00:00:00Z","doi":"10.1111/ejn.13901","date_created":"2018-12-11T11:45:50Z","page":"1033 - 1042","day":"07","publication":"European Journal of Neuroscience","isi":1,"has_accepted_license":"1","year":"2018","title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","author":[{"last_name":"Sawada","full_name":"Sawada, Kazuaki","first_name":"Kazuaki"},{"first_name":"Ryosuke","full_name":"Kawakami, Ryosuke","last_name":"Kawakami"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"full_name":"Nemoto, Tomomi","last_name":"Nemoto","first_name":"Tomomi"}],"publist_id":"7539","article_processing_charge":"No","external_id":{"isi":["000431496400001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 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.","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","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."},"month":"03","intvolume":" 47","scopus_import":"1","oa_version":"Published Version","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."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"volume":47,"issue":"9","license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5721","checksum":"98e901d8229e44aa8f3b51d248dedd09","creator":"dernst","date_updated":"2020-07-14T12:46:06Z","file_size":4850261,"date_created":"2018-12-17T16:16:50Z","file_name":"2018_EJN_Sawada.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"326","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:46:06Z","ddc":["570"],"date_updated":"2023-09-19T09:58:40Z"},{"pmid":1,"oa_version":"Submitted Version","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."}],"month":"12","intvolume":" 115","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"publication_status":"published","issue":"50","volume":115,"_id":"5770","status":"public","type":"journal_article","date_updated":"2023-09-19T09:57:45Z","department":[{"_id":"FlSc"}],"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"day":"11","publication":"Proceedings of the National Academy of Sciences","isi":1,"year":"2018","date_published":"2018-12-11T00:00:00Z","doi":"10.1073/pnas.1811580115","date_created":"2018-12-20T21:09:37Z","page":"E11751-E11760","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115.","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.","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.","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","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","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.","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."},"title":"Structure and architecture of immature and mature murine leukemia virus capsids","author":[{"full_name":"Qu, Kun","last_name":"Qu","first_name":"Kun"},{"full_name":"Glass, Bärbel","last_name":"Glass","first_name":"Bärbel"},{"last_name":"Doležal","full_name":"Doležal, Michal","first_name":"Michal"},{"first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","last_name":"Schur"},{"first_name":"Brice","full_name":"Murciano, Brice","last_name":"Murciano"},{"last_name":"Rein","full_name":"Rein, Alan","first_name":"Alan"},{"first_name":"Michaela","last_name":"Rumlová","full_name":"Rumlová, Michaela"},{"first_name":"Tomáš","full_name":"Ruml, Tomáš","last_name":"Ruml"},{"full_name":"Kräusslich, Hans-Georg","last_name":"Kräusslich","first_name":"Hans-Georg"},{"first_name":"John A. G.","full_name":"Briggs, John A. G.","last_name":"Briggs"}],"article_processing_charge":"No","external_id":{"isi":["000452866000022"],"pmid":["30478053"]}},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Theoretical Computer Science","day":"15","year":"2018","isi":1,"date_created":"2018-12-11T11:47:28Z","date_published":"2018-02-15T00:00:00Z","doi":"10.1016/j.tcs.2017.11.001","page":"50 - 72","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","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.","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","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","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","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."},"title":"Synthesis from component libraries with costs","article_processing_charge":"No","external_id":{"isi":["000424959200003"]},"author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"publist_id":"7197","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 712","month":"02","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":712,"_id":"608","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-19T10:00:21Z","department":[{"_id":"ToHe"}]},{"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"}],"oa_version":"None","scopus_import":"1","month":"06","intvolume":" 55","publication_status":"published","language":[{"iso":"eng"}],"issue":"6","volume":55,"_id":"705","type":"journal_article","status":"public","date_updated":"2023-09-19T09:58:11Z","department":[{"_id":"RySh"}],"publisher":"Springer","quality_controlled":"1","isi":1,"year":"2018","day":"01","publication":"Molecular Neurobiology","page":"4857 – 4869","date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s12035-017-0688-y","date_created":"2018-12-11T11:48:02Z","citation":{"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.","short":"A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6991","author":[{"first_name":"Andras","last_name":"Miklosi","full_name":"Miklosi, Andras"},{"last_name":"Del Favero","full_name":"Del Favero, Giorgia","first_name":"Giorgia"},{"first_name":"Tanja","last_name":"Bulat","full_name":"Bulat, Tanja"},{"first_name":"Harald","last_name":"Höger","full_name":"Höger, Harald"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Doris","last_name":"Marko","full_name":"Marko, Doris"},{"first_name":"Gert","full_name":"Lubec, Gert","last_name":"Lubec"}],"article_processing_charge":"No","external_id":{"isi":["000431991500025"]},"title":"Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":174,"issue":"2","ec_funded":1,"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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"month":"07","intvolume":" 174","date_updated":"2023-09-19T10:02:47Z","department":[{"_id":"JiFr"}],"_id":"148","type":"journal_article","status":"public","isi":1,"year":"2018","day":"12","publication":"Cell","page":"448 - 464.e24","date_published":"2018-07-12T00:00:00Z","doi":"10.1016/j.cell.2018.06.033","date_created":"2018-12-11T11:44:53Z","acknowledgement":"In-Data-Review","quality_controlled":"1","publisher":"Cell Press","oa":1,"citation":{"mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.","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","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","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7774","author":[{"last_name":"Nishiyama","full_name":"Nishiyama, Tomoaki","first_name":"Tomoaki"},{"full_name":"Sakayama, Hidetoshi","last_name":"Sakayama","first_name":"Hidetoshi"},{"last_name":"De Vries","full_name":"De Vries, Jan","first_name":"Jan"},{"last_name":"Buschmann","full_name":"Buschmann, Henrik","first_name":"Henrik"},{"first_name":"Denis","full_name":"Saint Marcoux, Denis","last_name":"Saint Marcoux"},{"last_name":"Ullrich","full_name":"Ullrich, Kristian","first_name":"Kristian"},{"first_name":"Fabian","full_name":"Haas, Fabian","last_name":"Haas"},{"last_name":"Vanderstraeten","full_name":"Vanderstraeten, Lisa","first_name":"Lisa"},{"first_name":"Dirk","last_name":"Becker","full_name":"Becker, Dirk"},{"first_name":"Daniel","full_name":"Lang, Daniel","last_name":"Lang"},{"first_name":"Stanislav","full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě"},{"full_name":"Rombauts, Stephane","last_name":"Rombauts","first_name":"Stephane"},{"full_name":"Wilhelmsson, Per","last_name":"Wilhelmsson","first_name":"Per"},{"last_name":"Janitza","full_name":"Janitza, Philipp","first_name":"Philipp"},{"first_name":"Ramona","full_name":"Kern, Ramona","last_name":"Kern"},{"first_name":"Alexander","full_name":"Heyl, Alexander","last_name":"Heyl"},{"first_name":"Florian","full_name":"Rümpler, Florian","last_name":"Rümpler"},{"full_name":"Calderón Villalobos, Luz","last_name":"Calderón Villalobos","first_name":"Luz"},{"full_name":"Clay, John","last_name":"Clay","first_name":"John"},{"last_name":"Skokan","full_name":"Skokan, Roman","first_name":"Roman"},{"first_name":"Atsushi","last_name":"Toyoda","full_name":"Toyoda, Atsushi"},{"first_name":"Yutaka","full_name":"Suzuki, Yutaka","last_name":"Suzuki"},{"full_name":"Kagoshima, Hiroshi","last_name":"Kagoshima","first_name":"Hiroshi"},{"first_name":"Elio","last_name":"Schijlen","full_name":"Schijlen, Elio"},{"first_name":"Navindra","full_name":"Tajeshwar, Navindra","last_name":"Tajeshwar"},{"first_name":"Bruno","last_name":"Catarino","full_name":"Catarino, Bruno"},{"last_name":"Hetherington","full_name":"Hetherington, Alexander","first_name":"Alexander"},{"full_name":"Saltykova, Assia","last_name":"Saltykova","first_name":"Assia"},{"last_name":"Bonnot","full_name":"Bonnot, Clemence","first_name":"Clemence"},{"full_name":"Breuninger, Holger","last_name":"Breuninger","first_name":"Holger"},{"first_name":"Aikaterini","full_name":"Symeonidi, Aikaterini","last_name":"Symeonidi"},{"full_name":"Radhakrishnan, Guru","last_name":"Radhakrishnan","first_name":"Guru"},{"first_name":"Filip","last_name":"Van Nieuwerburgh","full_name":"Van Nieuwerburgh, Filip"},{"first_name":"Dieter","last_name":"Deforce","full_name":"Deforce, Dieter"},{"last_name":"Chang","full_name":"Chang, Caren","first_name":"Caren"},{"last_name":"Karol","full_name":"Karol, Kenneth","first_name":"Kenneth"},{"full_name":"Hedrich, Rainer","last_name":"Hedrich","first_name":"Rainer"},{"full_name":"Ulvskov, Peter","last_name":"Ulvskov","first_name":"Peter"},{"last_name":"Glöckner","full_name":"Glöckner, Gernot","first_name":"Gernot"},{"last_name":"Delwiche","full_name":"Delwiche, Charles","first_name":"Charles"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"last_name":"Van De Peer","full_name":"Van De Peer, Yves","first_name":"Yves"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Mary","full_name":"Beilby, Mary","last_name":"Beilby"},{"last_name":"Dolan","full_name":"Dolan, Liam","first_name":"Liam"},{"first_name":"Yuji","last_name":"Kohara","full_name":"Kohara, Yuji"},{"full_name":"Sugano, Sumio","last_name":"Sugano","first_name":"Sumio"},{"first_name":"Asao","full_name":"Fujiyama, Asao","last_name":"Fujiyama"},{"first_name":"Pierre Marc","last_name":"Delaux","full_name":"Delaux, Pierre Marc"},{"last_name":"Quint","full_name":"Quint, Marcel","first_name":"Marcel"},{"last_name":"Theissen","full_name":"Theissen, Gunter","first_name":"Gunter"},{"full_name":"Hagemann, Martin","last_name":"Hagemann","first_name":"Martin"},{"first_name":"Jesper","full_name":"Harholt, Jesper","last_name":"Harholt"},{"full_name":"Dunand, Christophe","last_name":"Dunand","first_name":"Christophe"},{"last_name":"Zachgo","full_name":"Zachgo, Sabine","first_name":"Sabine"},{"first_name":"Jane","last_name":"Langdale","full_name":"Langdale, Jane"},{"first_name":"Florian","last_name":"Maumus","full_name":"Maumus, Florian"},{"last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique","first_name":"Dominique"},{"full_name":"Gould, Sven B","last_name":"Gould","first_name":"Sven B"},{"first_name":"Stefan","last_name":"Rensing","full_name":"Rensing, Stefan"}],"article_processing_charge":"No","external_id":{"isi":["000438482800019"],"pmid":["30007417"]},"title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"date_updated":"2023-09-19T10:07:08Z","ddc":["580"],"department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:46:22Z","_id":"403","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:46:22Z","file_size":1543354,"date_created":"2019-02-06T11:40:54Z","file_name":"2018_PlantJourn_Cavallari.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5934","checksum":"d9d3ad3215ac0e581731443fca312266"}],"language":[{"iso":"eng"}],"volume":94,"issue":"6","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."}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 94","citation":{"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.","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.","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","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","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"last_name":"Fuchs","full_name":"Fuchs, Armin","first_name":"Armin"},{"first_name":"Despoina","last_name":"Dadarou","full_name":"Dadarou, Despoina"},{"first_name":"Andrea","last_name":"Barta","full_name":"Barta, Andrea"},{"first_name":"John","full_name":"Doonan, John","last_name":"Doonan"}],"publist_id":"7426","external_id":{"isi":["000434365500008"]},"article_processing_charge":"No","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"The Plant Journal","page":"1010 - 1022","date_published":"2018-06-01T00:00:00Z","doi":"10.1111/tpj.13914","date_created":"2018-12-11T11:46:17Z","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]","publisher":"Wiley","quality_controlled":"1","oa":1},{"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. https://doi.org/10.1007/978-3-319-95582-7_9.","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164."},"title":"The compound interest in relaxing punctuality","author":[{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"}],"publist_id":"7765","external_id":{"isi":["000489765800009"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Springer","oa":1,"day":"12","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-07-12T00:00:00Z","doi":"10.1007/978-3-319-95582-7_9","date_created":"2018-12-11T11:44:55Z","page":"147 - 164","_id":"156","status":"public","type":"conference","conference":{"name":"FM: International Symposium on Formal Methods","end_date":"2018-07-17","location":"Oxford, UK","start_date":"2018-07-15"},"ddc":["000"],"date_updated":"2023-09-19T10:05:37Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-09T06:22:41Z","oa_version":"Submitted Version","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"}],"month":"07","intvolume":" 10951","scopus_import":"1","alternative_title":["LNCS"],"file":[{"success":1,"checksum":"a045c213c42c445f1889326f8db82a0a","file_id":"8637","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_LNCS_Ferrere.pdf","date_created":"2020-10-09T06:22:41Z","creator":"dernst","file_size":485576,"date_updated":"2020-10-09T06:22:41Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":10951},{"oa":1,"publisher":"Wiley","quality_controlled":"1","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","doi":"10.1111/mpp.12698","date_published":"2018-10-01T00:00:00Z","page":"2277 - 2287","publication":"Molecular Plant Pathology","day":"01","year":"2018","isi":1,"has_accepted_license":"1","title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","article_processing_charge":"No","external_id":{"isi":["000445624100006"]},"author":[{"last_name":"Seitner","full_name":"Seitner, Denise","first_name":"Denise"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"full_name":"Djamei, Armin","last_name":"Djamei","first_name":"Armin"}],"publist_id":"7950","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","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.","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","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","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.","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."},"intvolume":" 19","month":"10","scopus_import":"1","oa_version":"Published Version","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","volume":19,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-18T09:46:00Z","file_name":"2018_MolecPlantPath_Seitner.pdf","date_updated":"2018-12-18T09:46:00Z","file_size":682335,"creator":"dernst","file_id":"5740","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"104","file_date_updated":"2018-12-18T09:46:00Z","department":[{"_id":"GradSch"}],"ddc":["580"],"date_updated":"2023-09-19T10:06:42Z"},{"file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2023-09-19T10:06:08Z","status":"public","type":"journal_article","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"40","volume":27,"issue":"24","related_material":{"record":[{"relation":"research_data","status":"public","id":"9805"}]},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6652","date_updated":"2020-07-14T12:46:22Z","file_size":295452,"creator":"apreinsp","date_created":"2019-07-19T06:54:46Z","file_name":"2018_MolecularEcology_BartonNick.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1365294X"]},"publication_status":"published","month":"12","intvolume":" 27","scopus_import":"1","oa_version":"Published Version","pmid":1,"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."}],"title":"The consequences of an introgression event","publist_id":"8014","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"external_id":{"isi":["000454600500001"],"pmid":["30599087"]},"article_processing_charge":"Yes (via OA deal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","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."},"doi":"10.1111/mec.14950","date_published":"2018-12-31T00:00:00Z","date_created":"2018-12-11T11:44:18Z","page":"4973-4975","day":"31","publication":"Molecular Ecology","isi":1,"has_accepted_license":"1","year":"2018","quality_controlled":"1","publisher":"Wiley","oa":1},{"date_updated":"2023-09-19T10:01:39Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"MiSi"}],"_id":"5861","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["2050084X"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"f1c7ec2a809408d763c4b529a98f9a3b","file_id":"5973","file_size":358141,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_name":"2018_eLife_Alanko.pdf","date_created":"2019-02-13T10:52:11Z"}],"language":[{"iso":"eng"}],"volume":7,"abstract":[{"text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 7","citation":{"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.","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","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.","apa":"Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. 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","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","last_name":"Alanko"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"article_processing_charge":"No","external_id":{"isi":["000434375000001"]},"title":"The cell sets the tone","article_number":"e37888","has_accepted_license":"1","isi":1,"year":"2018","day":"06","publication":"eLife","doi":"10.7554/eLife.37888","date_published":"2018-06-06T00:00:00Z","date_created":"2019-01-20T22:59:19Z","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1},{"publisher":"Oxford University Press","quality_controlled":"1","oa":1,"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.).","page":"2553 - 2572","doi":"10.1105/tpc.18.00127","date_published":"2018-11-12T00:00:00Z","date_created":"2018-12-11T11:44:52Z","isi":1,"year":"2018","day":"12","publication":"The Plant Cell","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"publist_id":"7776","author":[{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","full_name":"Kania, Urszula","last_name":"Kania"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Qing","full_name":"Lu, Qing","last_name":"Lu"},{"first_name":"Glenn R","full_name":"Hicks, Glenn R","last_name":"Hicks"},{"full_name":"Nerinckx, Wim","last_name":"Nerinckx","first_name":"Wim"},{"first_name":"Kiril","full_name":"Mishev, Kiril","last_name":"Mishev"},{"first_name":"Francois","last_name":"Peurois","full_name":"Peurois, Francois"},{"first_name":"Jacqueline","full_name":"Cherfils, Jacqueline","last_name":"Cherfils"},{"first_name":"Rycke Riet Maria","last_name":"De","full_name":"De, Rycke Riet Maria"},{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"external_id":{"isi":["000450000500023"],"pmid":["30018156"]},"article_processing_charge":"No","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","citation":{"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","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.","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1105/tpc.18.00127","open_access":"1"}],"month":"11","intvolume":" 30","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"issue":"10","volume":30,"ec_funded":1,"publication_identifier":{"issn":["1040-4651"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"147","department":[{"_id":"JiFr"}],"date_updated":"2023-09-19T10:09:12Z"},{"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"30","publication":"Nature Plants","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1038/s41477-018-0212-z","date_published":"2018-07-30T00:00:00Z","date_created":"2018-12-11T11:44:52Z","page":"596 - 604","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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","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.","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.","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.","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."},"title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","author":[{"first_name":"Chun Lin","full_name":"Shi, Chun Lin","last_name":"Shi"},{"first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel","last_name":"Von Wangenheim"},{"full_name":"Herrmann, Ullrich","last_name":"Herrmann","first_name":"Ullrich"},{"first_name":"Mari","full_name":"Wildhagen, Mari","last_name":"Wildhagen"},{"first_name":"Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","full_name":"Kulik, Ivan","last_name":"Kulik"},{"last_name":"Kopf","full_name":"Kopf, Andreas","first_name":"Andreas"},{"first_name":"Takashi","full_name":"Ishida, Takashi","last_name":"Ishida"},{"last_name":"Olsson","full_name":"Olsson, Vilde","first_name":"Vilde"},{"full_name":"Anker, Mari Kristine","last_name":"Anker","first_name":"Mari Kristine"},{"first_name":"Markus","last_name":"Albert","full_name":"Albert, Markus"},{"first_name":"Melinka A","full_name":"Butenko, Melinka A","last_name":"Butenko"},{"first_name":"Georg","full_name":"Felix, Georg","last_name":"Felix"},{"first_name":"Shinichiro","full_name":"Sawa, Shinichiro","last_name":"Sawa"},{"first_name":"Manfred","full_name":"Claassen, Manfred","last_name":"Claassen"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Aalen","full_name":"Aalen, Reidunn B","first_name":"Reidunn B"}],"publist_id":"7777","article_processing_charge":"No","external_id":{"pmid":["30061750"],"isi":["000443861300016"]},"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","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."}],"month":"07","intvolume":" 4","scopus_import":"1","file":[{"creator":"dernst","date_updated":"2020-07-14T12:44:56Z","file_size":226829,"date_created":"2019-11-18T16:24:07Z","file_name":"2018_NaturePlants_Shi.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","file_id":"7043"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":4,"issue":"8","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/"}]},"_id":"146","status":"public","article_type":"original","type":"journal_article","ddc":["580"],"date_updated":"2023-09-19T10:08:45Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:56Z"},{"page":"397 - 404","date_published":"2018-05-28T00:00:00Z","doi":"10.1038/s41562-018-0354-z","date_created":"2018-12-11T11:45:39Z","isi":1,"has_accepted_license":"1","year":"2018","day":"28","publication":"Nature Human Behaviour","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"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.","author":[{"first_name":"Moshe","full_name":"Hoffman, Moshe","last_name":"Hoffman"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"publist_id":"7588","article_processing_charge":"No","external_id":{"isi":["000435551300009"]},"title":"The signal-burying game can explain why we obscure positive traits and good deeds","citation":{"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","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","short":"M. Hoffman, C. Hilbe, M. Nowak, Nature Human Behaviour 2 (2018) 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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-logic-of-modesty-why-it-pays-to-be-humble/","relation":"press_release","description":"News on IST Homepage"}]},"volume":2,"ec_funded":1,"publication_status":"published","file":[{"file_name":"2018_NatureHumanBeh_Hoffman.pdf","date_created":"2019-11-19T08:17:23Z","file_size":194734,"date_updated":"2020-07-14T12:45:54Z","creator":"dernst","checksum":"32efaf06a597495c184df91b3fbb19c0","file_id":"7051","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 2","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:54Z","date_updated":"2023-09-19T10:12:03Z","ddc":["000"],"article_type":"original","type":"journal_article","status":"public","_id":"293"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"993","status":"public","_id":"455","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:46:31Z","date_updated":"2023-09-19T10:07:41Z","ddc":["510","539"],"scopus_import":"1","alternative_title":["Annales Henri Poincare"],"intvolume":" 19","month":"04","abstract":[{"lang":"eng","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"}],"oa_version":"Published Version","issue":"4","volume":19,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:31Z","file_size":923252,"creator":"system","date_created":"2018-12-12T10:11:57Z","file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"883eeccba8384ad7fcaa28761d99a0fa","file_id":"4914"}],"article_processing_charge":"No","external_id":{"isi":["000427578900006"]},"author":[{"id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P","orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P","last_name":"Benedikter"},{"last_name":"Sok","full_name":"Sok, Jérémy","first_name":"Jérémy"},{"last_name":"Solovej","full_name":"Solovej, Jan","first_name":"Jan"}],"publist_id":"7367","title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","citation":{"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.","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.","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","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","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Birkhäuser","quality_controlled":"1","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.","page":"1167 - 1214","date_created":"2018-12-11T11:46:34Z","date_published":"2018-04-01T00:00:00Z","doi":"10.1007/s00023-018-0644-z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Annales Henri Poincare","day":"01"},{"article_processing_charge":"No","external_id":{"pmid":["29698645"],"isi":["000432192100003"]},"publist_id":"7551","author":[{"full_name":"Bauer, Guntram","last_name":"Bauer","first_name":"Guntram"},{"last_name":"Fakhri","full_name":"Fakhri, Nikta","first_name":"Nikta"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jané","last_name":"Kondev","full_name":"Kondev, Jané"},{"last_name":"Kruse","full_name":"Kruse, Karsten","first_name":"Karsten"},{"first_name":"Hiroyuki","last_name":"Noji","full_name":"Noji, Hiroyuki"},{"first_name":"Daniel","full_name":"Riveline, Daniel","last_name":"Riveline"},{"last_name":"Saunders","full_name":"Saunders, Timothy","first_name":"Timothy"},{"full_name":"Thatta, Mukund","last_name":"Thatta","first_name":"Mukund"},{"first_name":"Eric","last_name":"Wieschaus","full_name":"Wieschaus, Eric"}],"title":"The science of living matter for tomorrow","citation":{"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.","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","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","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.","ieee":"G. Bauer et al., “The science of living matter for tomorrow,” Cell Systems, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Cell Press","quality_controlled":"1","page":"400 - 402","date_created":"2018-12-11T11:45:46Z","doi":"10.1016/j.cels.2018.04.003","date_published":"2018-04-25T00:00:00Z","year":"2018","isi":1,"publication":"Cell Systems","day":"25","type":"journal_article","article_type":"letter_note","status":"public","_id":"314","department":[{"_id":"AnKi"}],"date_updated":"2023-09-19T10:11:25Z","main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2018.04.003","open_access":"1"}],"scopus_import":"1","intvolume":" 6","month":"04","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"}],"oa_version":"Published Version","pmid":1,"issue":"4","volume":6,"publication_status":"published","publication_identifier":{"eissn":["2405-4712"]},"language":[{"iso":"eng"}]},{"department":[{"_id":"NiBa"}],"date_updated":"2023-09-19T10:12:31Z","status":"public","type":"journal_article","article_type":"original","_id":"565","issue":"1","volume":208,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 208","month":"01","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"title":"The spread of an inversion with migration and selection","article_processing_charge":"No","external_id":{"pmid":["29158424"],"isi":["000419356300025"]},"author":[{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"7249","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382."},"date_created":"2018-12-11T11:47:12Z","doi":"10.1534/genetics.117.300426","date_published":"2018-01-01T00:00:00Z","page":"377 - 382","publication":"Genetics","day":"01","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"Genetics "},{"publication":"Communications on Pure and Applied Mathematics","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:46:31Z","doi":"10.1002/cpa.21717","date_published":"2018-03-01T00:00:00Z","page":"577 - 614","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","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614.","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."},"title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","external_id":{"arxiv":["1606.07355"],"isi":["000422675800004"]},"article_processing_charge":"No","author":[{"last_name":"Frank","full_name":"Frank, Rupert","first_name":"Rupert"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Nam","last_name":"Phan Thanh","full_name":"Phan Thanh, Nam"},{"full_name":"Van Den Bosch, Hanne","last_name":"Van Den Bosch","first_name":"Hanne"}],"publist_id":"7377","language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":71,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"intvolume":" 71","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07355"}],"date_updated":"2023-09-19T10:09:40Z","department":[{"_id":"RoSe"}],"_id":"446","status":"public","article_type":"original","type":"journal_article"},{"doi":"10.1534/genetics.118.300786","date_published":"2018-04-01T00:00:00Z","date_created":"2018-12-11T11:46:26Z","page":"1351 - 1355","day":"01","publication":"Genetics","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"title":"Tread lightly interpreting polygenic tests of selection","author":[{"full_name":"Novembre, John","last_name":"Novembre","first_name":"John"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"7393","external_id":{"isi":["000429094400005"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","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.","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","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786","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.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355."},"volume":208,"issue":"4","file":[{"file_id":"4958","checksum":"3d838dc285df394376555b794b6a5ad1","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","date_created":"2018-12-12T10:12:40Z","creator":"system","file_size":500129,"date_updated":"2020-07-14T12:46:26Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 208","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2023-09-19T10:17:30Z","status":"public","pubrep_id":"1012","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"430"},{"issue":"6","volume":9,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":3985796,"date_updated":"2020-07-14T12:45:22Z","creator":"dernst","file_name":"2018_Genes_Ma.pdf","date_created":"2019-02-01T07:52:28Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","file_id":"5905"}],"scopus_import":"1","intvolume":" 9","month":"06","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:45:22Z","date_updated":"2023-09-19T10:15:31Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"199","date_created":"2018-12-11T11:45:09Z","doi":"10.3390/genes9060294","date_published":"2018-06-12T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Genes","day":"12","oa":1,"quality_controlled":"1","publisher":"MDPI AG","article_processing_charge":"No","external_id":{"isi":["000436494200026"]},"author":[{"first_name":"Wen","last_name":"Ma","full_name":"Ma, Wen"},{"first_name":"Paris","full_name":"Veltsos, Paris","last_name":"Veltsos"},{"orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rodrigues","full_name":"Rodrigues, Nicolas","first_name":"Nicolas"},{"full_name":"Sermier, Roberto","last_name":"Sermier","first_name":"Roberto"},{"first_name":"Daniel","full_name":"Jeffries, Daniel","last_name":"Jeffries"},{"last_name":"Perrin","full_name":"Perrin, Nicolas","first_name":"Nicolas"}],"publist_id":"7714","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","citation":{"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.","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.","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.","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","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","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"294"},{"department":[{"_id":"GaTk"}],"date_updated":"2023-09-19T10:16:35Z","status":"public","type":"journal_article","_id":"543","volume":115,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 115","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"title":"Toward a unified theory of efficient, predictive, and sparse coding","article_processing_charge":"No","external_id":{"isi":["000419128700049"]},"author":[{"last_name":"Chalk","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"publist_id":"7273","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.","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.","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.","short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 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","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"},"project":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2018-12-11T11:47:04Z","doi":"10.1073/pnas.1711114115","date_published":"2018-01-02T00:00:00Z","page":"186 - 191","publication":"PNAS","day":"02","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences"},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1709.01486","open_access":"1"}],"month":"02","intvolume":" 114","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","volume":114,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"421","department":[{"_id":"EdHa"}],"date_updated":"2023-09-19T10:13:55Z","publisher":"Biophysical Society","quality_controlled":"1","oa":1,"page":"968 - 977","doi":"10.1016/j.bpj.2017.12.022","date_published":"2018-02-27T00:00:00Z","date_created":"2018-12-11T11:46:23Z","isi":1,"year":"2018","day":"27","publication":"Biophysical Journal","publist_id":"7403","author":[{"last_name":"Dasbiswas","full_name":"Dasbiswas, Kinjal","first_name":"Kinjal"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Claude-Edouard B","last_name":"Hannezo","full_name":"Hannezo, Claude-Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Nir","last_name":"Gov","full_name":"Gov, Nir"}],"article_processing_charge":"No","external_id":{"arxiv":["1709.01486"],"isi":["000428016700021"]},"title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","citation":{"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.","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.","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.","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_created":"2018-12-11T11:44:26Z","date_published":"2018-10-04T00:00:00Z","doi":"10.3390/genes9100480","year":"2018","isi":1,"has_accepted_license":"1","publication":"Genes","day":"04","oa":1,"publisher":"MDPI AG","quality_controlled":"1","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","external_id":{"isi":["000448656700018"]},"article_processing_charge":"No","publist_id":"7991","author":[{"id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Gammerdinger","orcid":"0000-0001-9638-1220","full_name":"Gammerdinger, William J"},{"last_name":"Kocher","full_name":"Kocher, Thomas","first_name":"Thomas"}],"title":"Unusual diversity of sex chromosomes in African cichlid fishes","citation":{"ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480.","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.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018.","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_number":"480","ec_funded":1,"volume":9,"issue":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-18T09:54:46Z","file_name":"2018_Genes_Gammerdinger.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:27Z","file_size":1415791,"file_id":"5743","checksum":"bec527692e2c9b56919c0429634ff337","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 9","month":"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."}],"oa_version":"Published Version","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:27Z","date_updated":"2023-09-19T10:37:03Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"63"},{"main_file_link":[{"url":"http://eprints.whiterose.ac.uk/130860/","open_access":"1"}],"scopus_import":"1","intvolume":" 14","month":"05","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","volume":14,"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"296","department":[{"_id":"MaSe"}],"date_updated":"2023-09-19T10:37:55Z","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","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.","page":"745 - 749","date_created":"2018-12-11T11:45:40Z","doi":"10.1038/s41567-018-0137-5","date_published":"2018-05-14T00:00:00Z","year":"2018","isi":1,"publication":"Nature Physics","day":"14","external_id":{"isi":["000438253600028"]},"article_processing_charge":"No","author":[{"full_name":"Turner, Christopher","last_name":"Turner","first_name":"Christopher"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"full_name":"Abanin, Dmitry","last_name":"Abanin","first_name":"Dmitry"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"first_name":"Zlatko","full_name":"Papić, Zlatko","last_name":"Papić"}],"publist_id":"7585","title":"Weak ergodicity breaking from quantum many-body scars","citation":{"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.","short":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics 14 (2018) 745–749.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":"376-377","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.08757"}],"scopus_import":"1","month":"08","date_updated":"2023-09-19T10:38:34Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"_id":"607","type":"journal_article","status":"public","year":"2018","isi":1,"publication":"Physica D: Nonlinear Phenomena","day":"01","page":"108-120","date_created":"2018-12-11T11:47:28Z","date_published":"2018-08-01T00:00:00Z","doi":"10.1016/j.physd.2017.10.015","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","oa":1,"quality_controlled":"1","publisher":"Elsevier","citation":{"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.","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.","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.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"publist_id":"7198","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Bodova","full_name":"Bodova, Katarina","orcid":"0000-0002-7214-0171"},{"first_name":"Jan","last_name":"Haskovec","full_name":"Haskovec, Jan"},{"first_name":"Peter","last_name":"Markowich","full_name":"Markowich, Peter"}],"title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","day":"18","year":"2018","isi":1,"date_created":"2018-12-11T11:45:40Z","doi":"10.1103/PhysRevA.97.043842","date_published":"2018-04-18T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","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","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","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.","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).","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."},"title":"Two-photon processes based on quantum commutators","article_processing_charge":"No","external_id":{"arxiv":["1801.06892"],"isi":["000430296800008"]},"author":[{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"},{"full_name":"Safari, Laleh","last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh"},{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"}],"publist_id":"7587","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 97","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.06892"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":97,"issue":"4","_id":"294","status":"public","type":"journal_article","date_updated":"2023-09-19T10:17:56Z","department":[{"_id":"MiLe"}]},{"_id":"606","type":"journal_article","status":"public","date_updated":"2023-09-19T10:39:09Z","department":[{"_id":"JuFi"}],"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."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1607.00268","open_access":"1"}],"scopus_import":"1","intvolume":" 35","month":"08","publication_status":"published","language":[{"iso":"eng"}],"issue":"5","volume":35,"citation":{"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","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","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1607.00268"],"isi":["000437975500005"]},"publist_id":"7199","author":[{"first_name":"Mitia","full_name":"Duerinckx, Mitia","last_name":"Duerinckx"},{"last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"}],"title":"Well-posedness for mean-field evolutions arising in superconductivity","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","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2018","isi":1,"publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","day":"01","page":"1267-1319","date_created":"2018-12-11T11:47:27Z","date_published":"2018-08-01T00:00:00Z","doi":"10.1016/j.anihpc.2017.11.004"},{"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-09-19T10:41:29Z","status":"public","conference":{"name":"EMSOFT: International Conference on Embedded Software","start_date":"2018-09-30","end_date":"2018-10-05","location":"Turin, Italy"},"type":"conference","_id":"5959","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"234a33ad9055b3458fcdda6af251b33a","file_id":"7839","file_size":338006,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_name":"2018_EMSOFT_Bakhirkin.pdf","date_created":"2020-05-14T16:01:29Z"}],"publication_status":"published","publication_identifier":{"isbn":["9781538655603"]},"month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of real-valued signals. We introduce signal first-order logic (SFO) as a specification language that combines first-order logic with linear-real arithmetic and unary function symbols interpreted as piecewise-linear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of bounded-response specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with first-order quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the micro-electronics domain."}],"title":"Keynote: The first-order logic of signals","external_id":{"isi":["000492828500005"]},"article_processing_charge":"No","author":[{"full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin","first_name":"Alexey"},{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Deian","full_name":"Nickovicl, Deian","last_name":"Nickovicl"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The first-order logic of signals,” in 2018 International Conference on Embedded Software, Turin, Italy, 2018, pp. 1–10.","short":"A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10.","ama":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order logic of signals. In: 2018 International Conference on Embedded Software. IEEE; 2018:1-10. doi:10.1109/emsoft.2018.8537203","apa":"Bakhirkin, A., Ferrere, T., Henzinger, T. A., & Nickovicl, D. (2018). Keynote: The first-order logic of signals. In 2018 International Conference on Embedded Software (pp. 1–10). Turin, Italy: IEEE. https://doi.org/10.1109/emsoft.2018.8537203","mla":"Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10, doi:10.1109/emsoft.2018.8537203.","ista":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order logic of signals. 2018 International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software, 1–10.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl. “Keynote: The First-Order Logic of Signals.” In 2018 International Conference on Embedded Software, 1–10. IEEE, 2018. https://doi.org/10.1109/emsoft.2018.8537203."},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"date_created":"2019-02-13T09:19:28Z","doi":"10.1109/emsoft.2018.8537203","date_published":"2018-09-30T00:00:00Z","page":"1-10","publication":"2018 International Conference on Embedded Software","day":"30","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"IEEE"},{"author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"full_name":"De Sa, Christopher","last_name":"De Sa","first_name":"Christopher"},{"last_name":"Konstantinov","full_name":"Konstantinov, Nikola H","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000458186900022"],"arxiv":["1803.08841"]},"article_processing_charge":"No","title":"The convergence of stochastic gradient descent in asynchronous shared memory","citation":{"chicago":"Alistarh, Dan-Adrian, Christopher De Sa, and Nikola H Konstantinov. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 169–78. ACM Press, 2018. https://doi.org/10.1145/3212734.3212763.","ista":"Alistarh D-A, De Sa C, Konstantinov NH. 2018. The convergence of stochastic gradient descent in asynchronous shared memory. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 169–178.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–78, doi:10.1145/3212734.3212763.","short":"D.-A. Alistarh, C. De Sa, N.H. Konstantinov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–178.","ieee":"D.-A. Alistarh, C. De Sa, and N. H. Konstantinov, “The convergence of stochastic gradient descent in asynchronous shared memory,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 169–178.","apa":"Alistarh, D.-A., De Sa, C., & Konstantinov, N. H. (2018). The convergence of stochastic gradient descent in asynchronous shared memory. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 169–178). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212763","ama":"Alistarh D-A, De Sa C, Konstantinov NH. The convergence of stochastic gradient descent in asynchronous shared memory. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:169-178. doi:10.1145/3212734.3212763"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"ACM Press","quality_controlled":"1","oa":1,"page":"169-178","doi":"10.1145/3212734.3212763","date_published":"2018-07-23T00:00:00Z","date_created":"2019-02-13T09:58:58Z","isi":1,"year":"2018","day":"23","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","type":"conference","conference":{"start_date":"2018-07-23","end_date":"2018-07-27","location":"Egham, United Kingdom","name":"PODC: Principles of Distributed Computing"},"status":"public","_id":"5962","department":[{"_id":"DaAl"}],"date_updated":"2023-09-19T10:42:53Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08841"}],"month":"07","abstract":[{"lang":"eng","text":"Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning, representing the optimization backbone for training several classic models, from regression to neural networks. Given the recent practical focus on distributed machine learning, significant work has been dedicated to the convergence properties of this algorithm under the inconsistent and noisy updates arising from execution in a distributed environment. However, surprisingly, the convergence properties of this classic algorithm in the standard shared-memory model are still not well-understood. In this work, we address this gap, and provide new convergence bounds for lock-free concurrent stochastic gradient descent, executing in the classic asynchronous shared memory model, against a strong adaptive adversary. Our results give improved upper and lower bounds on the \"price of asynchrony'' when executing the fundamental SGD algorithm in a concurrent setting. They show that this classic optimization tool can converge faster and with a wider range of parameters than previously known under asynchronous iterations. At the same time, we exhibit a fundamental trade-off between the maximum delay in the system and the rate at which SGD can converge, which governs the set of parameters under which this algorithm can still work efficiently."}],"oa_version":"Preprint","publication_identifier":{"isbn":["9781450357951"]},"publication_status":"published","language":[{"iso":"eng"}]},{"volume":15,"issue":"149","publication_status":"published","publication_identifier":{"issn":["17425689"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1612.01605","open_access":"1"}],"scopus_import":"1","intvolume":" 15","month":"12","abstract":[{"text":"A major problem for evolutionary theory is understanding the so-called open-ended nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf's Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"EdHa"}],"date_updated":"2023-09-19T10:40:38Z","type":"journal_article","status":"public","_id":"5860","date_created":"2019-01-20T22:59:19Z","doi":"10.1098/rsif.2018.0395","date_published":"2018-12-12T00:00:00Z","year":"2018","isi":1,"publication":"Journal of the Royal Society Interface","day":"12","oa":1,"quality_controlled":"1","publisher":"Royal Society Publishing","article_processing_charge":"No","external_id":{"arxiv":["1612.01605"],"isi":["000456783800002"]},"author":[{"full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luís F.","full_name":"Seoane, Luís F.","last_name":"Seoane"},{"first_name":"Ricard","full_name":"Solé, Ricard","last_name":"Solé"}],"title":"Zipf's Law, unbounded complexity and open-ended evolution","citation":{"chicago":"Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395.","ista":"Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.","mla":"Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395.","ieee":"B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity and open-ended evolution,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","short":"B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018).","apa":"Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395","ama":"Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0395"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"20180395"},{"oa_version":"None","abstract":[{"lang":"eng","text":"The area of machine learning has made considerable progress over the past decade, enabled by the widespread availability of large datasets, as well as by improved algorithms and models. Given the large computational demands of machine learning workloads, parallelism, implemented either through single-node concurrency or through multi-node distribution, has been a third key ingredient to advances in machine learning.\r\nThe goal of this tutorial is to provide the audience with an overview of standard distribution techniques in machine learning, with an eye towards the intriguing trade-offs between synchronization and communication costs of distributed machine learning algorithms, on the one hand, and their convergence, on the other.The tutorial will focus on parallelization strategies for the fundamental stochastic gradient descent (SGD) algorithm, which is a key tool when training machine learning models, from classical instances such as linear regression, to state-of-the-art neural network architectures.\r\nThe tutorial will describe the guarantees provided by this algorithm in the sequential case, and then move on to cover both shared-memory and message-passing parallelization strategies, together with the guarantees they provide, and corresponding trade-offs. The presentation will conclude with a broad overview of ongoing research in distributed and concurrent machine learning. The tutorial will assume no prior knowledge beyond familiarity with basic concepts in algebra and analysis.\r\n"}],"month":"07","scopus_import":"1","quality_controlled":"1","publisher":"ACM Press","day":"27","language":[{"iso":"eng"}],"publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","publication_identifier":{"isbn":["9781450357951"]},"isi":1,"year":"2018","publication_status":"published","doi":"10.1145/3212734.3212798","date_published":"2018-07-27T00:00:00Z","date_created":"2019-02-13T09:48:55Z","page":"487-488","_id":"5961","status":"public","type":"conference","conference":{"name":"PODC: Principles of Distributed Computing","start_date":"2018-07-23","location":"Egham, United Kingdom","end_date":"2018-07-27"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-19T10:42:28Z","citation":{"ieee":"D.-A. Alistarh, “A brief tutorial on distributed and concurrent machine learning,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 487–488.","short":"D.-A. Alistarh, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 487–488.","apa":"Alistarh, D.-A. (2018). A brief tutorial on distributed and concurrent machine learning. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 487–488). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212798","ama":"Alistarh D-A. A brief tutorial on distributed and concurrent machine learning. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:487-488. doi:10.1145/3212734.3212798","mla":"Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 487–88, doi:10.1145/3212734.3212798.","ista":"Alistarh D-A. 2018. A brief tutorial on distributed and concurrent machine learning. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 487–488.","chicago":"Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 487–88. ACM Press, 2018. https://doi.org/10.1145/3212734.3212798."},"title":"A brief tutorial on distributed and concurrent machine learning","department":[{"_id":"DaAl"}],"author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"external_id":{"isi":["000458186900063"]},"article_processing_charge":"No"},{"_id":"5960","type":"journal_article","status":"public","date_updated":"2023-09-19T10:41:59Z","department":[{"_id":"UlWa"}],"abstract":[{"lang":"eng","text":"In this paper we present a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a bounded-error context. The loop closure detection is one of the key points in simultaneous localization and mapping (SLAM) methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles and by a mathematical discussion."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1712.01341","open_access":"1"}],"scopus_import":"1","intvolume":" 37","month":"10","publication_status":"published","publication_identifier":{"issn":["0278-3649"],"eissn":["1741-3176"]},"language":[{"iso":"eng"}],"issue":"12","volume":37,"citation":{"mla":"Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research, vol. 37, no. 12, SAGE Publications, 2018, pp. 1500–16, doi:10.1177/0278364918808367.","short":"S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics Research 37 (2018) 1500–1516.","ieee":"S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops in robot trajectories,” The International Journal of Robotics Research, vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018.","apa":"Rohou, S., Franek, P., Aubry, C., & Jaulin, L. (2018). Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. SAGE Publications. https://doi.org/10.1177/0278364918808367","ama":"Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 2018;37(12):1500-1516. doi:10.1177/0278364918808367","chicago":"Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research. SAGE Publications, 2018. https://doi.org/10.1177/0278364918808367.","ista":"Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 37(12), 1500–1516."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1712.01341"],"isi":["000456881100004"]},"article_processing_charge":"No","author":[{"first_name":"Simon","last_name":"Rohou","full_name":"Rohou, Simon"},{"id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Franek","full_name":"Franek, Peter","orcid":"0000-0001-8878-8397"},{"first_name":"Clément","full_name":"Aubry, Clément","last_name":"Aubry"},{"first_name":"Luc","last_name":"Jaulin","full_name":"Jaulin, Luc"}],"title":"Proving the existence of loops in robot trajectories","oa":1,"publisher":"SAGE Publications","quality_controlled":"1","year":"2018","isi":1,"publication":"The International Journal of Robotics Research","day":"24","page":"1500-1516","date_created":"2019-02-13T09:36:20Z","date_published":"2018-10-24T00:00:00Z","doi":"10.1177/0278364918808367"},{"title":"Relaxed schedulers can efficiently parallelize iterative algorithms","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A"},{"last_name":"Kopinsky","full_name":"Kopinsky, Justin","first_name":"Justin"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi"}],"external_id":{"arxiv":["1808.04155"],"isi":["000458186900048"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–86, doi:10.1145/3212734.3212756.","apa":"Alistarh, D.-A., Brown, T. A., Kopinsky, J., & Nadiradze, G. (2018). Relaxed schedulers can efficiently parallelize iterative algorithms. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 377–386). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212756","ama":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. Relaxed schedulers can efficiently parallelize iterative algorithms. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:377-386. doi:10.1145/3212734.3212756","short":"D.-A. Alistarh, T.A. Brown, J. Kopinsky, G. Nadiradze, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–386.","ieee":"D.-A. Alistarh, T. A. Brown, J. Kopinsky, and G. Nadiradze, “Relaxed schedulers can efficiently parallelize iterative algorithms,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 377–386.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, and Giorgi Nadiradze. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 377–86. ACM Press, 2018. https://doi.org/10.1145/3212734.3212756.","ista":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. 2018. Relaxed schedulers can efficiently parallelize iterative algorithms. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 377–386."},"quality_controlled":"1","publisher":"ACM Press","oa":1,"doi":"10.1145/3212734.3212756","date_published":"2018-07-23T00:00:00Z","date_created":"2019-02-13T10:03:25Z","page":"377-386","day":"23","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","isi":1,"year":"2018","status":"public","type":"conference","conference":{"name":"PODC: Principles of Distributed Computing","start_date":"2018-07-23","location":"Egham, United Kingdom","end_date":"2018-07-27"},"_id":"5963","department":[{"_id":"DaAl"}],"date_updated":"2023-09-19T10:43:21Z","month":"07","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04155"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"There has been significant progress in understanding the parallelism inherent to iterative sequential algorithms: for many classic algorithms, the depth of the dependence structure is now well understood, and scheduling techniques have been developed to exploit this shallow dependence structure for efficient parallel implementations. A related, applied research strand has studied methods by which certain iterative task-based algorithms can be efficiently parallelized via relaxed concurrent priority schedulers. These allow for high concurrency when inserting and removing tasks, at the cost of executing superfluous work due to the relaxed semantics of the scheduler. In this work, we take a step towards unifying these two research directions, by showing that there exists a family of relaxed priority schedulers that can efficiently and deterministically execute classic iterative algorithms such as greedy maximal independent set (MIS) and matching. Our primary result shows that, given a randomized scheduler with an expected relaxation factor of k in terms of the maximum allowed priority inversions on a task, and any graph on n vertices, the scheduler is able to execute greedy MIS with only an additive factor of \\poly(k) expected additional iterations compared to an exact (but not scalable) scheduler. This counter-intuitive result demonstrates that the overhead of relaxation when computing MIS is not dependent on the input size or structure of the input graph. Experimental results show that this overhead can be clearly offset by the gain in performance due to the highly scalable scheduler. In sum, we present an efficient method to deterministically parallelize iterative sequential algorithms, with provable runtime guarantees in terms of the number of executed tasks to completion."}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450357951"]},"publication_status":"published"},{"publication_identifier":{"isbn":["9781450357999"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"10429","status":"public"}]},"abstract":[{"lang":"eng","text":"Relaxed concurrent data structures have become increasingly popular, due to their scalability in graph processing and machine learning applications (\\citeNguyen13, gonzalez2012powergraph ). Despite considerable interest, there exist families of natural, high performing randomized relaxed concurrent data structures, such as the popular MultiQueue~\\citeMQ pattern for implementing relaxed priority queue data structures, for which no guarantees are known in the concurrent setting~\\citeAKLN17. Our main contribution is in showing for the first time that, under a set of analytic assumptions, a family of relaxed concurrent data structures, including variants of MultiQueues, but also a new approximate counting algorithm we call the MultiCounter, provides strong probabilistic guarantees on the degree of relaxation with respect to the sequential specification, in arbitrary concurrent executions. We formalize these guarantees via a new correctness condition called distributional linearizability, tailored to concurrent implementations with randomized relaxations. Our result is based on a new analysis of an asynchronous variant of the classic power-of-two-choices load balancing algorithm, in which placement choices can be based on inconsistent, outdated information (this result may be of independent interest). We validate our results empirically, showing that the MultiCounter algorithm can implement scalable relaxed timestamps."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.01018"}],"month":"07","date_updated":"2023-09-19T10:44:13Z","department":[{"_id":"DaAl"}],"_id":"5965","type":"conference","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2018-07-16","location":"Vienna, Austria","end_date":"2018-07-18"},"status":"public","isi":1,"year":"2018","day":"16","publication":"Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18","page":"133-142","doi":"10.1145/3210377.3210411","date_published":"2018-07-16T00:00:00Z","date_created":"2019-02-13T10:17:19Z","quality_controlled":"1","publisher":"ACM Press","oa":1,"citation":{"ista":"Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. 2018. Distributionally linearizable data structures. Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. SPAA: Symposium on Parallelism in Algorithms and Architectures, 133–142.","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, Jerry Z. Li, and Giorgi Nadiradze. “Distributionally Linearizable Data Structures.” In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, 133–42. ACM Press, 2018. https://doi.org/10.1145/3210377.3210411.","ama":"Alistarh D-A, Brown TA, Kopinsky J, Li JZ, Nadiradze G. Distributionally linearizable data structures. In: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. ACM Press; 2018:133-142. doi:10.1145/3210377.3210411","apa":"Alistarh, D.-A., Brown, T. A., Kopinsky, J., Li, J. Z., & Nadiradze, G. (2018). Distributionally linearizable data structures. In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18 (pp. 133–142). Vienna, Austria: ACM Press. https://doi.org/10.1145/3210377.3210411","short":"D.-A. Alistarh, T.A. Brown, J. Kopinsky, J.Z. Li, G. Nadiradze, in:, Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 133–142.","ieee":"D.-A. Alistarh, T. A. Brown, J. Kopinsky, J. Z. Li, and G. Nadiradze, “Distributionally linearizable data structures,” in Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, Vienna, Austria, 2018, pp. 133–142.","mla":"Alistarh, Dan-Adrian, et al. “Distributionally Linearizable Data Structures.” Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 133–42, doi:10.1145/3210377.3210411."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Brown","full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A"},{"first_name":"Justin","full_name":"Kopinsky, Justin","last_name":"Kopinsky"},{"last_name":"Li","full_name":"Li, Jerry Z.","first_name":"Jerry Z."},{"first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"}],"external_id":{"arxiv":["1804.01018"],"isi":["000545269600016"]},"article_processing_charge":"No","title":"Distributionally linearizable data structures"},{"citation":{"ama":"Hansen KA, Ibsen-Jensen R, Neyman A. The Big Match with a clock and a bit of memory. In: Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18. ACM Press; 2018:149-150. doi:10.1145/3219166.3219198","apa":"Hansen, K. A., Ibsen-Jensen, R., & Neyman, A. (2018). The Big Match with a clock and a bit of memory. In Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18 (pp. 149–150). Ithaca, NY, United States: ACM Press. https://doi.org/10.1145/3219166.3219198","ieee":"K. A. Hansen, R. Ibsen-Jensen, and A. Neyman, “The Big Match with a clock and a bit of memory,” in Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, Ithaca, NY, United States, 2018, pp. 149–150.","short":"K.A. Hansen, R. Ibsen-Jensen, A. Neyman, in:, Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, ACM Press, 2018, pp. 149–150.","mla":"Hansen, Kristoffer Arnsfelt, et al. “The Big Match with a Clock and a Bit of Memory.” Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, ACM Press, 2018, pp. 149–50, doi:10.1145/3219166.3219198.","ista":"Hansen KA, Ibsen-Jensen R, Neyman A. 2018. The Big Match with a clock and a bit of memory. Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18. EC: Conference on Economics and Computation, 149–150.","chicago":"Hansen, Kristoffer Arnsfelt, Rasmus Ibsen-Jensen, and Abraham Neyman. “The Big Match with a Clock and a Bit of Memory.” In Proceedings of the 2018 ACM Conference on Economics and Computation - EC ’18, 149–50. ACM Press, 2018. https://doi.org/10.1145/3219166.3219198."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000492755100020"]},"article_processing_charge":"No","author":[{"first_name":"Kristoffer Arnsfelt","full_name":"Hansen, Kristoffer Arnsfelt","last_name":"Hansen"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen"},{"first_name":"Abraham","last_name":"Neyman","full_name":"Neyman, Abraham"}],"title":"The Big Match with a clock and a bit of memory","oa":1,"quality_controlled":"1","publisher":"ACM Press","year":"2018","has_accepted_license":"1","isi":1,"publication":"Proceedings of the 2018 ACM Conference on Economics and Computation - EC '18","day":"18","page":"149-150","date_created":"2019-02-13T10:31:41Z","doi":"10.1145/3219166.3219198","date_published":"2018-06-18T00:00:00Z","_id":"5967","conference":{"name":"EC: Conference on Economics and Computation","end_date":"2018-06-22","location":"Ithaca, NY, United States","start_date":"2018-06-18"},"type":"conference","status":"public","date_updated":"2023-09-19T10:45:15Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:14Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"The Big Match is a multi-stage two-player game. In each stage Player 1 hides one or two pebbles in his hand, and his opponent has to guess that number; Player 1 loses a point if Player 2 is correct, and otherwise he wins a point. As soon as Player 1 hides one pebble, the players cannot change their choices in any future stage.\r\nBlackwell and Ferguson (1968) give an ε-optimal strategy for Player 1 that hides, in each stage, one pebble with a probability that depends on the entire past history. Any strategy that depends just on the clock or on a finite memory is worthless. The long-standing natural open problem has been whether every strategy that depends just on the clock and a finite memory is worthless. We prove that there is such a strategy that is ε-optimal. In fact, we show that just two states of memory are sufficient.\r\n"}],"oa_version":"Submitted Version","scopus_import":"1","month":"06","publication_status":"published","publication_identifier":{"isbn":["9781450358293"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2018_EC18_Hansen.pdf","date_created":"2019-11-19T08:24:24Z","creator":"dernst","file_size":302539,"date_updated":"2020-07-14T12:47:14Z","checksum":"bb52683e349cfd864f4769a8f38f2798","file_id":"7054","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}]},{"type":"conference","conference":{"location":"Vienna, Austria","end_date":"2018-07-18","start_date":"2018-07-16","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"status":"public","_id":"5966","department":[{"_id":"DaAl"}],"date_updated":"2023-09-19T10:44:49Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.00947"}],"month":"07","abstract":[{"text":"The transactional conflict problem arises in transactional systems whenever two or more concurrent transactions clash on a data item. While the standard solution to such conflicts is to immediately abort one of the transactions, some practical systems consider the alternative of delaying conflict resolution for a short interval, which may allow one of the transactions to commit. The challenge in the transactional conflict problem is to choose the optimal length of this delay interval so as to minimize the overall running time penalty for the conflicting transactions. In this paper, we propose a family of optimal online algorithms for the transactional conflict problem. Specifically, we consider variants of this problem which arise in different implementations of transactional systems, namely \"requestor wins'' and \"requestor aborts'' implementations: in the former, the recipient of a coherence request is aborted, whereas in the latter, it is the requestor which has to abort. Both strategies are implemented by real systems. We show that the requestor aborts case can be reduced to a classic instance of the ski rental problem, while the requestor wins case leads to a new version of this classical problem, for which we derive optimal deterministic and randomized algorithms. Moreover, we prove that, under a simplified adversarial model, our algorithms are constant-competitive with the offline optimum in terms of throughput. We validate our algorithmic results empirically through a hardware simulation of hardware transactional memory (HTM), showing that our algorithms can lead to non-trivial performance improvements for classic concurrent data structures.","lang":"eng"}],"oa_version":"Preprint","publication_identifier":{"isbn":["9781450357999"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"first_name":"Syed Kamran","full_name":"Haider, Syed Kamran","last_name":"Haider"},{"first_name":"Raphael","last_name":"Kübler","full_name":"Kübler, Raphael"},{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","first_name":"Giorgi"}],"external_id":{"isi":["000545269600046"],"arxiv":["1804.00947"]},"article_processing_charge":"No","title":"The transactional conflict problem","citation":{"ieee":"D.-A. Alistarh, S. K. Haider, R. Kübler, and G. Nadiradze, “The transactional conflict problem,” in Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, Vienna, Austria, 2018, pp. 383–392.","short":"D.-A. Alistarh, S.K. Haider, R. Kübler, G. Nadiradze, in:, Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 383–392.","apa":"Alistarh, D.-A., Haider, S. K., Kübler, R., & Nadiradze, G. (2018). The transactional conflict problem. In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18 (pp. 383–392). Vienna, Austria: ACM Press. https://doi.org/10.1145/3210377.3210406","ama":"Alistarh D-A, Haider SK, Kübler R, Nadiradze G. The transactional conflict problem. In: Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. ACM Press; 2018:383-392. doi:10.1145/3210377.3210406","mla":"Alistarh, Dan-Adrian, et al. “The Transactional Conflict Problem.” Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, ACM Press, 2018, pp. 383–92, doi:10.1145/3210377.3210406.","ista":"Alistarh D-A, Haider SK, Kübler R, Nadiradze G. 2018. The transactional conflict problem. Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18. SPAA: Symposium on Parallelism in Algorithms and Architectures, 383–392.","chicago":"Alistarh, Dan-Adrian, Syed Kamran Haider, Raphael Kübler, and Giorgi Nadiradze. “The Transactional Conflict Problem.” In Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA ’18, 383–92. ACM Press, 2018. https://doi.org/10.1145/3210377.3210406."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"ACM Press","oa":1,"page":"383-392","doi":"10.1145/3210377.3210406","date_published":"2018-07-16T00:00:00Z","date_created":"2019-02-13T10:26:07Z","isi":1,"year":"2018","day":"16","publication":"Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures - SPAA '18"},{"department":[{"_id":"VlKo"}],"date_updated":"2023-09-19T14:24:58Z","status":"public","type":"journal_article","_id":"5975","issue":"6","volume":47,"related_material":{"record":[{"status":"public","id":"1193","relation":"earlier_version"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"publication_status":"published","month":"11","intvolume":" 47","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1506.08547","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider the recent formulation of the algorithmic Lov ́asz Local Lemma [N. Har-vey and J. Vondr ́ak, inProceedings of FOCS, 2015, pp. 1327–1345; D. Achlioptas and F. Iliopoulos,inProceedings of SODA, 2016, pp. 2024–2038; D. Achlioptas, F. Iliopoulos, and V. Kolmogorov,ALocal Lemma for Focused Stochastic Algorithms, arXiv preprint, 2018] for finding objects that avoid“bad features,” or “flaws.” It extends the Moser–Tardos resampling algorithm [R. A. Moser andG. Tardos,J. ACM, 57 (2010), 11] to more general discrete spaces. At each step the method picks aflaw present in the current state and goes to a new state according to some prespecified probabilitydistribution (which depends on the current state and the selected flaw). However, the recent formu-lation is less flexible than the Moser–Tardos method since it requires a specific flaw selection rule,whereas the algorithm of Moser and Tardos allows an arbitrary rule (and thus can potentially beimplemented more efficiently). We formulate a new “commutativity” condition and prove that it issufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additionalassumption. We then show that existing resampling oracles for perfect matchings and permutationsdo satisfy this condition."}],"title":"Commutativity in the algorithmic Lovász local lemma","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"article_processing_charge":"No","external_id":{"isi":["000453785100001"],"arxiv":["1506.08547"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Kolmogorov, V. (2018). Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM). https://doi.org/10.1137/16m1093306","ama":"Kolmogorov V. Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. 2018;47(6):2029-2056. doi:10.1137/16m1093306","short":"V. Kolmogorov, SIAM Journal on Computing 47 (2018) 2029–2056.","ieee":"V. Kolmogorov, “Commutativity in the algorithmic Lovász local lemma,” SIAM Journal on Computing, vol. 47, no. 6. Society for Industrial & Applied Mathematics (SIAM), pp. 2029–2056, 2018.","mla":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.” SIAM Journal on Computing, vol. 47, no. 6, Society for Industrial & Applied Mathematics (SIAM), 2018, pp. 2029–56, doi:10.1137/16m1093306.","ista":"Kolmogorov V. 2018. Commutativity in the algorithmic Lovász local lemma. SIAM Journal on Computing. 47(6), 2029–2056.","chicago":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovász Local Lemma.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM), 2018. https://doi.org/10.1137/16m1093306."},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_published":"2018-11-08T00:00:00Z","doi":"10.1137/16m1093306","date_created":"2019-02-13T12:59:33Z","page":"2029-2056","day":"08","publication":"SIAM Journal on Computing","isi":1,"year":"2018","quality_controlled":"1","publisher":"Society for Industrial & Applied Mathematics (SIAM)","oa":1},{"citation":{"mla":"Aksenov, Vitaly, et al. “Brief Announcement: Performance Prediction for Coarse-Grained Locking.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 411–13, doi:10.1145/3212734.3212785.","ama":"Aksenov V, Alistarh D-A, Kuznetsov P. Brief Announcement: Performance prediction for coarse-grained locking. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:411-413. doi:10.1145/3212734.3212785","apa":"Aksenov, V., Alistarh, D.-A., & Kuznetsov, P. (2018). Brief Announcement: Performance prediction for coarse-grained locking. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 411–413). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212785","ieee":"V. Aksenov, D.-A. Alistarh, and P. Kuznetsov, “Brief Announcement: Performance prediction for coarse-grained locking,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 411–413.","short":"V. Aksenov, D.-A. Alistarh, P. Kuznetsov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 411–413.","chicago":"Aksenov, Vitaly, Dan-Adrian Alistarh, and Petr Kuznetsov. “Brief Announcement: Performance Prediction for Coarse-Grained Locking.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 411–13. ACM Press, 2018. https://doi.org/10.1145/3212734.3212785.","ista":"Aksenov V, Alistarh D-A, Kuznetsov P. 2018. Brief Announcement: Performance prediction for coarse-grained locking. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 411–413."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000458186900052"]},"author":[{"full_name":"Aksenov, Vitaly","last_name":"Aksenov","first_name":"Vitaly"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Kuznetsov","full_name":"Kuznetsov, Petr","first_name":"Petr"}],"title":"Brief Announcement: Performance prediction for coarse-grained locking","oa":1,"publisher":"ACM Press","quality_controlled":"1","year":"2018","isi":1,"publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","day":"23","page":"411-413","date_created":"2019-02-13T10:08:19Z","doi":"10.1145/3212734.3212785","date_published":"2018-07-23T00:00:00Z","_id":"5964","conference":{"name":"PODC: Principles of Distributed Computing","start_date":"2018-07-23","end_date":"2018-07-27","location":"Egham, United Kingdom"},"type":"conference","status":"public","date_updated":"2023-09-19T10:43:45Z","department":[{"_id":"DaAl"}],"abstract":[{"text":"A standard design pattern found in many concurrent data structures, such as hash tables or ordered containers, is an alternation of parallelizable sections that incur no data conflicts and critical sections that must run sequentially and are protected with locks. A lock can be viewed as a queue that arbitrates the order in which the critical sections are executed, and a natural question is whether we can use stochastic analysis to predict the resulting throughput. As a preliminary evidence to the affirmative, we describe a simple model that can be used to predict the throughput of coarse-grained lock-based algorithms. We show that our model works well for CLH lock, and we expect it to work for other popular lock designs such as TTAS, MCS, etc.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://hal-univ-lyon3.archives-ouvertes.fr/INRIA/hal-01887733v1","open_access":"1"}],"scopus_import":"1","month":"07","publication_status":"published","publication_identifier":{"isbn":["9781450357951"]},"language":[{"iso":"eng"}]},{"date_updated":"2023-09-19T14:24:05Z","department":[{"_id":"LaEr"}],"_id":"5971","type":"journal_article","status":"public","publication_identifier":{"eissn":["2010-3271"],"issn":["2010-3263"]},"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"We consider a Wigner-type ensemble, i.e. large hermitian N×N random matrices H=H∗ with centered independent entries and with a general matrix of variances Sxy=𝔼∣∣Hxy∣∣2. The norm of H is asymptotically given by the maximum of the support of the self-consistent density of states. We establish a bound on this maximum in terms of norms of powers of S that substantially improves the earlier bound 2∥S∥1/2∞ given in [O. Ajanki, L. Erdős and T. Krüger, Universality for general Wigner-type matrices, Prob. Theor. Rel. Fields169 (2017) 667–727]. The key element of the proof is an effective Markov chain approximation for the contributions of the weighted Dyck paths appearing in the iterative solution of the corresponding Dyson equation.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.05175"}],"month":"09","citation":{"apa":"Erdös, L., & Mühlbacher, P. (2018). Bounds on the norm of Wigner-type random matrices. Random Matrices: Theory and Applications. World Scientific Publishing. https://doi.org/10.1142/s2010326319500096","ama":"Erdös L, Mühlbacher P. Bounds on the norm of Wigner-type random matrices. Random matrices: Theory and applications. 2018. doi:10.1142/s2010326319500096","short":"L. Erdös, P. Mühlbacher, Random Matrices: Theory and Applications (2018).","ieee":"L. Erdös and P. Mühlbacher, “Bounds on the norm of Wigner-type random matrices,” Random matrices: Theory and applications. World Scientific Publishing, 2018.","mla":"Erdös, László, and Peter Mühlbacher. “Bounds on the Norm of Wigner-Type Random Matrices.” Random Matrices: Theory and Applications, 1950009, World Scientific Publishing, 2018, doi:10.1142/s2010326319500096.","ista":"Erdös L, Mühlbacher P. 2018. Bounds on the norm of Wigner-type random matrices. Random matrices: Theory and applications., 1950009.","chicago":"Erdös, László, and Peter Mühlbacher. “Bounds on the Norm of Wigner-Type Random Matrices.” Random Matrices: Theory and Applications. World Scientific Publishing, 2018. https://doi.org/10.1142/s2010326319500096."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"last_name":"Mühlbacher","full_name":"Mühlbacher, Peter","first_name":"Peter"}],"external_id":{"isi":["000477677200002"],"arxiv":["1802.05175"]},"article_processing_charge":"No","title":"Bounds on the norm of Wigner-type random matrices","article_number":"1950009","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"isi":1,"year":"2018","day":"26","publication":"Random matrices: Theory and applications","doi":"10.1142/s2010326319500096","date_published":"2018-09-26T00:00:00Z","date_created":"2019-02-13T10:40:54Z","publisher":"World Scientific Publishing","quality_controlled":"1","oa":1},{"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","file":[{"file_name":"2018_Springer_Morri.pdf","date_created":"2019-02-14T10:58:29Z","creator":"kschuh","file_size":1349914,"date_updated":"2020-07-14T12:47:14Z","file_id":"5985","checksum":"8325fcc194264af4749e662a73bf66b5","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"1","volume":9,"ec_funded":1,"abstract":[{"text":"G-protein-coupled receptors (GPCRs) form the largest receptor family, relay environmental stimuli to changes in cell behavior and represent prime drug targets. Many GPCRs are classified as orphan receptors because of the limited knowledge on their ligands and coupling to cellular signaling machineries. Here, we engineer a library of 63 chimeric receptors that contain the signaling domains of human orphan and understudied GPCRs functionally linked to the light-sensing domain of rhodopsin. Upon stimulation with visible light, we identify activation of canonical cell signaling pathways, including cAMP-, Ca2+-, MAPK/ERK-, and Rho-dependent pathways, downstream of the engineered receptors. For the human pseudogene GPR33, we resurrect a signaling function that supports its hypothesized role as a pathogen entry site. These results demonstrate that substituting unknown chemical activators with a light switch can reveal information about protein function and provide an optically controlled protein library for exploring the physiology and therapeutic potential of understudied GPCRs.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"12","intvolume":" 9","date_updated":"2023-09-19T14:29:32Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:14Z","department":[{"_id":"HaJa"},{"_id":"CaGu"},{"_id":"MiSi"}],"_id":"5984","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Nature Communications","doi":"10.1038/s41467-018-04342-1","date_published":"2018-12-01T00:00:00Z","date_created":"2019-02-14T10:50:24Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"short":"M. Morri, I. Sanchez-Romero, A.-M. Tichy, S. Kainrath, E.J. Gerrard, P. Hirschfeld, J. Schwarz, H.L. Janovjak, Nature Communications 9 (2018).","ieee":"M. Morri et al., “Optical functionalization of human class A orphan G-protein-coupled receptors,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.","ama":"Morri M, Sanchez-Romero I, Tichy A-M, et al. Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-04342-1","apa":"Morri, M., Sanchez-Romero, I., Tichy, A.-M., Kainrath, S., Gerrard, E. J., Hirschfeld, P., … Janovjak, H. L. (2018). Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04342-1","mla":"Morri, Maurizio, et al. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” Nature Communications, vol. 9, no. 1, 1950, Springer Nature, 2018, doi:10.1038/s41467-018-04342-1.","ista":"Morri M, Sanchez-Romero I, Tichy A-M, Kainrath S, Gerrard EJ, Hirschfeld P, Schwarz J, Janovjak HL. 2018. Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. 9(1), 1950.","chicago":"Morri, Maurizio, Inmaculada Sanchez-Romero, Alexandra-Madelaine Tichy, Stephanie Kainrath, Elliot J. Gerrard, Priscila Hirschfeld, Jan Schwarz, and Harald L Janovjak. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04342-1."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"4863116E-F248-11E8-B48F-1D18A9856A87","first_name":"Maurizio","last_name":"Morri","full_name":"Morri, Maurizio"},{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada","full_name":"Sanchez-Romero, Inmaculada","last_name":"Sanchez-Romero"},{"full_name":"Tichy, Alexandra-Madelaine","last_name":"Tichy","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra-Madelaine"},{"first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie","last_name":"Kainrath"},{"first_name":"Elliot J.","full_name":"Gerrard, Elliot J.","last_name":"Gerrard"},{"first_name":"Priscila","id":"435ACB3A-F248-11E8-B48F-1D18A9856A87","last_name":"Hirschfeld","full_name":"Hirschfeld, Priscila"},{"last_name":"Schwarz","full_name":"Schwarz, Jan","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"}],"external_id":{"isi":["000432280000006"]},"article_processing_charge":"No","title":"Optical functionalization of human class A orphan G-protein-coupled receptors","article_number":"1950","project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets"}]},{"citation":{"mla":"Malomo, Luigi, et al. “FlexMaps: Computational Design of Flat Flexible Shells for Shaping 3D Objects.” ACM Transactions on Graphics, vol. 37, no. 6, 241, Association for Computing Machinery (ACM), 2018, doi:10.1145/3272127.3275076.","short":"L. Malomo, J. Perez Rodriguez, E. Iarussi, N. Pietroni, E. Miguel, P. Cignoni, B. Bickel, ACM Transactions on Graphics 37 (2018).","ieee":"L. Malomo et al., “FlexMaps: Computational design of flat flexible shells for shaping 3D objects,” ACM Transactions on Graphics, vol. 37, no. 6. Association for Computing Machinery (ACM), 2018.","ama":"Malomo L, Perez Rodriguez J, Iarussi E, et al. FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. 2018;37(6). doi:10.1145/3272127.3275076","apa":"Malomo, L., Perez Rodriguez, J., Iarussi, E., Pietroni, N., Miguel, E., Cignoni, P., & Bickel, B. (2018). FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. Association for Computing Machinery (ACM). https://doi.org/10.1145/3272127.3275076","chicago":"Malomo, Luigi, Jesus Perez Rodriguez, Emmanuel Iarussi, Nico Pietroni, Eder Miguel, Paolo Cignoni, and Bernd Bickel. “FlexMaps: Computational Design of Flat Flexible Shells for Shaping 3D Objects.” ACM Transactions on Graphics. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3272127.3275076.","ista":"Malomo L, Perez Rodriguez J, Iarussi E, Pietroni N, Miguel E, Cignoni P, Bickel B. 2018. FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. 37(6), 241."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000455953100064"]},"article_processing_charge":"No","author":[{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"full_name":"Perez Rodriguez, Jesus","last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus"},{"full_name":"Iarussi, Emmanuel","last_name":"Iarussi","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","first_name":"Emmanuel"},{"first_name":"Nico","last_name":"Pietroni","full_name":"Pietroni, Nico"},{"last_name":"Miguel","full_name":"Miguel, Eder","first_name":"Eder"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"title":"FlexMaps: Computational design of flat flexible shells for shaping 3D objects","article_number":"241","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Soft-bodied intelligence for Manipulation","grant_number":"645599","call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"year":"2018","has_accepted_license":"1","isi":1,"publication":"ACM Transactions on Graphics","day":"01","date_created":"2019-02-13T13:12:53Z","date_published":"2018-11-01T00:00:00Z","doi":"10.1145/3272127.3275076","oa":1,"publisher":"Association for Computing Machinery (ACM)","quality_controlled":"1","date_updated":"2023-09-19T14:25:30Z","ddc":["000"],"department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:47:14Z","_id":"5976","type":"journal_article","article_type":"original","pubrep_id":"1068","status":"public","publication_status":"published","publication_identifier":{"issn":["0730-0301"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"d0529a41c78b37ab8840685579fb33b4","file_id":"6901","file_size":100109811,"date_updated":"2020-07-14T12:47:14Z","creator":"bbickel","file_name":"flexmaps_author_version.pdf","date_created":"2019-09-23T12:48:52Z"}],"ec_funded":1,"volume":37,"issue":"6","abstract":[{"lang":"eng","text":"We propose FlexMaps, a novel framework for fabricating smooth shapes out of flat, flexible panels with tailored mechanical properties. We start by mapping the 3D surface onto a 2D domain as in traditional UV mapping to design a set of deformable flat panels called FlexMaps. For these panels, we design and obtain specific mechanical properties such that, once they are assembled, the static equilibrium configuration matches the desired 3D shape. FlexMaps can be fabricated from an almost rigid material, such as wood or plastic, and are made flexible in a controlled way by using computationally designed spiraling microstructures."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 37","month":"11"},{"publication":"Physical Review B","day":"12","year":"2018","isi":1,"date_created":"2019-02-14T10:37:09Z","doi":"10.1103/physrevb.98.224506","date_published":"2018-12-12T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"American Physical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Yakaboylu, Enderalp, et al. “Theory of the Rotating Polaron: Spectrum and Self-Localization.” Physical Review B, vol. 98, no. 22, 224506, American Physical Society, 2018, doi:10.1103/physrevb.98.224506.","ieee":"E. Yakaboylu, B. Midya, A. Deuchert, N. K. Leopold, and M. Lemeshko, “Theory of the rotating polaron: Spectrum and self-localization,” Physical Review B, vol. 98, no. 22. American Physical Society, 2018.","short":"E. Yakaboylu, B. Midya, A. Deuchert, N.K. Leopold, M. Lemeshko, Physical Review B 98 (2018).","apa":"Yakaboylu, E., Midya, B., Deuchert, A., Leopold, N. K., & Lemeshko, M. (2018). Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.98.224506","ama":"Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. 2018;98(22). doi:10.1103/physrevb.98.224506","chicago":"Yakaboylu, Enderalp, Bikashkali Midya, Andreas Deuchert, Nikolai K Leopold, and Mikhail Lemeshko. “Theory of the Rotating Polaron: Spectrum and Self-Localization.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.98.224506.","ista":"Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. 2018. Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. 98(22), 224506."},"title":"Theory of the rotating polaron: Spectrum and self-localization","article_processing_charge":"No","external_id":{"isi":["000452992700008"],"arxiv":["1809.01204"]},"author":[{"last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","last_name":"Midya","full_name":"Midya, Bikashkali"},{"last_name":"Deuchert","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"last_name":"Leopold","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"article_number":"224506","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"ec_funded":1,"volume":98,"issue":"22","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study a quantum impurity possessing both translational and internal rotational degrees of freedom interacting with a bosonic bath. Such a system corresponds to a “rotating polaron,” which can be used to model, e.g., a rotating molecule immersed in an ultracold Bose gas or superfluid helium. We derive the Hamiltonian of the rotating polaron and study its spectrum in the weak- and strong-coupling regimes using a combination of variational, diagrammatic, and mean-field approaches. We reveal how the coupling between linear and angular momenta affects stable quasiparticle states, and demonstrate that internal rotation leads to an enhanced self-localization in the translational degrees of freedom."}],"intvolume":" 98","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.01204"}],"scopus_import":"1","date_updated":"2023-09-19T14:29:03Z","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"_id":"5983","status":"public","type":"journal_article"},{"publication_status":"published","publication_identifier":{"issn":["1433-7851"]},"language":[{"iso":"eng"}],"issue":"52","volume":57,"abstract":[{"lang":"eng","text":"In the present work, we detail a fast and simple solution-based method to synthesize hexagonal SnSe2 nanoplates (NPLs) and their use to produce crystallographically textured SnSe2 nanomaterials. We also demonstrate that the same strategy can be used to produce orthorhombic SnSe nanostructures and nanomaterials. NPLs are grown through a screw dislocation-driven mechanism. This mechanism typically results in pyramidal structures, but we demonstrate here that the growth from multiple dislocations results in flower-like structures. Crystallographically textured SnSe2 bulk nanomaterials obtained from the hot pressing of these SnSe2 structures display highly anisotropic charge and heat transport properties and thermoelectric (TE) figures of merit limited by relatively low electrical conductivities. To improve this parameter, SnSe2 NPLs are blended here with metal nanoparticles. The electrical conductivities of the blends are significantly improved with respect to bare SnSe2 NPLs, what translates into a three-fold increase of the TE Figure of merit, reaching unprecedented ZT values up to 0.65."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://upcommons.upc.edu/bitstream/2117/130444/1/Zhang%20preprint.pdf","open_access":"1"}],"scopus_import":"1","intvolume":" 57","month":"12","date_updated":"2023-09-19T14:28:31Z","department":[{"_id":"MaIb"}],"_id":"5982","article_type":"original","type":"journal_article","status":"public","year":"2018","isi":1,"publication":"Angewandte Chemie International Edition","day":"21","page":"17063-17068","date_created":"2019-02-14T10:23:27Z","date_published":"2018-12-21T00:00:00Z","doi":"10.1002/anie.201809847","oa":1,"publisher":"Wiley","quality_controlled":"1","citation":{"ama":"Zhang Y, Liu Y, Lim KH, et al. Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. 2018;57(52):17063-17068. doi:10.1002/anie.201809847","apa":"Zhang, Y., Liu, Y., Lim, K. H., Xing, C., Li, M., Zhang, T., … Cabot, A. (2018). Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201809847","ieee":"Y. Zhang et al., “Tin diselenide molecular precursor for solution-processable thermoelectric materials,” Angewandte Chemie International Edition, vol. 57, no. 52. Wiley, pp. 17063–17068, 2018.","short":"Y. Zhang, Y. Liu, K.H. Lim, C. Xing, M. Li, T. Zhang, P. Tang, J. Arbiol, J. Llorca, K.M. Ng, M. Ibáñez, P. Guardia, M. Prato, D. Cadavid, A. Cabot, Angewandte Chemie International Edition 57 (2018) 17063–17068.","mla":"Zhang, Yu, et al. “Tin Diselenide Molecular Precursor for Solution-Processable Thermoelectric Materials.” Angewandte Chemie International Edition, vol. 57, no. 52, Wiley, 2018, pp. 17063–68, doi:10.1002/anie.201809847.","ista":"Zhang Y, Liu Y, Lim KH, Xing C, Li M, Zhang T, Tang P, Arbiol J, Llorca J, Ng KM, Ibáñez M, Guardia P, Prato M, Cadavid D, Cabot A. 2018. Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. 57(52), 17063–17068.","chicago":"Zhang, Yu, Yu Liu, Khak Ho Lim, Congcong Xing, Mengyao Li, Ting Zhang, Pengyi Tang, et al. “Tin Diselenide Molecular Precursor for Solution-Processable Thermoelectric Materials.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201809847."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000454575500020"]},"author":[{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"first_name":"Yu","full_name":"Liu, Yu","last_name":"Liu"},{"first_name":"Khak Ho","last_name":"Lim","full_name":"Lim, Khak Ho"},{"first_name":"Congcong","last_name":"Xing","full_name":"Xing, Congcong"},{"first_name":"Mengyao","full_name":"Li, Mengyao","last_name":"Li"},{"last_name":"Zhang","full_name":"Zhang, Ting","first_name":"Ting"},{"full_name":"Tang, Pengyi","last_name":"Tang","first_name":"Pengyi"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"full_name":"Ng, Ka Ming","last_name":"Ng","first_name":"Ka Ming"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pablo","full_name":"Guardia, Pablo","last_name":"Guardia"},{"first_name":"Mirko","last_name":"Prato","full_name":"Prato, Mirko"},{"first_name":"Doris","full_name":"Cadavid, Doris","last_name":"Cadavid"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"title":"Tin diselenide molecular precursor for solution-processable thermoelectric materials"},{"scopus_import":"1","publisher":"AAAI Press","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.06370"}],"month":"02","abstract":[{"text":"We consider the MAP-inference problem for graphical models,which is a valued constraint satisfaction problem defined onreal numbers with a natural summation operation. We proposea family of relaxations (different from the famous Sherali-Adams hierarchy), which naturally define lower bounds for itsoptimum. This family always contains a tight relaxation andwe give an algorithm able to find it and therefore, solve theinitial non-relaxed NP-hard problem.The relaxations we consider decompose the original probleminto two non-overlapping parts: an easy LP-tight part and adifficult one. For the latter part a combinatorial solver must beused. As we show in our experiments, in a number of applica-tions the second, difficult part constitutes only a small fractionof the whole problem. This property allows to significantlyreduce the computational time of the combinatorial solver andtherefore solve problems which were out of reach before.","lang":"eng"}],"oa_version":"Preprint","page":"6581-6588","date_published":"2018-02-01T00:00:00Z","date_created":"2019-02-13T13:32:48Z","isi":1,"publication_status":"published","year":"2018","day":"01","language":[{"iso":"eng"}],"publication":"Proceedings of the 32st AAAI Conference on Artificial Intelligence","type":"conference","conference":{"name":"AAAI: Conference on Artificial Intelligence","location":"New Orleans, LU, United States","end_date":"2018-02-07","start_date":"2018-02-02"},"status":"public","_id":"5978","author":[{"last_name":"Haller","full_name":"Haller, Stefan","first_name":"Stefan"},{"last_name":"Swoboda","full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}],"external_id":{"arxiv":["2004.06370"],"isi":["000485488906082"]},"article_processing_charge":"No","department":[{"_id":"VlKo"}],"title":"Exact MAP-inference by confining combinatorial search with LP relaxation","date_updated":"2023-09-19T14:26:52Z","citation":{"ista":"Haller S, Swoboda P, Savchynskyy B. 2018. Exact MAP-inference by confining combinatorial search with LP relaxation. Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence, 6581–6588.","chicago":"Haller, Stefan, Paul Swoboda, and Bogdan Savchynskyy. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” In Proceedings of the 32st AAAI Conference on Artificial Intelligence, 6581–88. AAAI Press, 2018.","short":"S. Haller, P. Swoboda, B. Savchynskyy, in:, Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–6588.","ieee":"S. Haller, P. Swoboda, and B. Savchynskyy, “Exact MAP-inference by confining combinatorial search with LP relaxation,” in Proceedings of the 32st AAAI Conference on Artificial Intelligence, New Orleans, LU, United States, 2018, pp. 6581–6588.","apa":"Haller, S., Swoboda, P., & Savchynskyy, B. (2018). Exact MAP-inference by confining combinatorial search with LP relaxation. In Proceedings of the 32st AAAI Conference on Artificial Intelligence (pp. 6581–6588). New Orleans, LU, United States: AAAI Press.","ama":"Haller S, Swoboda P, Savchynskyy B. Exact MAP-inference by confining combinatorial search with LP relaxation. In: Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI Press; 2018:6581-6588.","mla":"Haller, Stefan, et al. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–88."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"_id":"5990","status":"public","type":"journal_article","date_updated":"2023-09-19T14:29:58Z","department":[{"_id":"GeKa"}],"oa_version":"Preprint","abstract":[{"text":"A Ge–Si core–shell nanowire is used to realize a Josephson field‐effect transistor with highly transparent contacts to superconducting leads. By changing the electric field, access to two distinct regimes, not combined before in a single device, is gained: in the accumulation mode the device is highly transparent and the supercurrent is carried by multiple subbands, while near depletion, the supercurrent is carried by single‐particle levels of a strongly coupled quantum dot operating in the few‐hole regime. These results establish Ge–Si nanowires as an important platform for hybrid superconductor–semiconductor physics and Majorana fermions.","lang":"eng"}],"intvolume":" 30","month":"11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.08487"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0935-9648"]},"volume":30,"issue":"44","article_number":"1802257","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ridderbos, Joost, et al. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials, vol. 30, no. 44, 1802257, Wiley, 2018, doi:10.1002/adma.201802257.","ama":"Ridderbos J, Brauns M, Shen J, et al. Josephson effect in a few-hole quantum dot. Advanced Materials. 2018;30(44). doi:10.1002/adma.201802257","apa":"Ridderbos, J., Brauns, M., Shen, J., de Vries, F. K., Li, A., Bakkers, E. P. A. M., … Zwanenburg, F. A. (2018). Josephson effect in a few-hole quantum dot. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201802257","ieee":"J. Ridderbos et al., “Josephson effect in a few-hole quantum dot,” Advanced Materials, vol. 30, no. 44. Wiley, 2018.","short":"J. Ridderbos, M. Brauns, J. Shen, F.K. de Vries, A. Li, E.P.A.M. Bakkers, A. Brinkman, F.A. Zwanenburg, Advanced Materials 30 (2018).","chicago":"Ridderbos, Joost, Matthias Brauns, Jie Shen, Folkert K. de Vries, Ang Li, Erik P. A. M. Bakkers, Alexander Brinkman, and Floris A. Zwanenburg. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201802257.","ista":"Ridderbos J, Brauns M, Shen J, de Vries FK, Li A, Bakkers EPAM, Brinkman A, Zwanenburg FA. 2018. Josephson effect in a few-hole quantum dot. Advanced Materials. 30(44), 1802257."},"title":"Josephson effect in a few-hole quantum dot","article_processing_charge":"No","external_id":{"isi":["000450232800015"],"arxiv":["1809.08487"]},"author":[{"last_name":"Ridderbos","full_name":"Ridderbos, Joost","first_name":"Joost"},{"id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Brauns, Matthias","last_name":"Brauns"},{"full_name":"Shen, Jie","last_name":"Shen","first_name":"Jie"},{"full_name":"de Vries, Folkert K.","last_name":"de Vries","first_name":"Folkert K."},{"last_name":"Li","full_name":"Li, Ang","first_name":"Ang"},{"full_name":"Bakkers, Erik P. A. M.","last_name":"Bakkers","first_name":"Erik P. A. M."},{"first_name":"Alexander","full_name":"Brinkman, Alexander","last_name":"Brinkman"},{"first_name":"Floris A.","full_name":"Zwanenburg, Floris A.","last_name":"Zwanenburg"}],"oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"Advanced Materials","day":"02","year":"2018","isi":1,"date_created":"2019-02-14T12:14:26Z","date_published":"2018-11-02T00:00:00Z","doi":"10.1002/adma.201802257"},{"oa_version":"None","abstract":[{"text":"The problem of private set-intersection (PSI) has been traditionally treated as an instance of the more general problem of multi-party computation (MPC). Consequently, in order to argue security, or compose these protocols one has to rely on the general theory that was developed for the purpose of MPC. The pursuit of efficient protocols, however, has resulted in designs that exploit properties pertaining to PSI. In almost all practical applications where a PSI protocol is deployed, it is expected to be executed multiple times, possibly on related inputs. In this work we initiate a dedicated study of PSI in the multi-interaction (MI) setting. In this model a server sets up the common system parameters and executes set-intersection multiple times with potentially different clients. We discuss a few attacks that arise when protocols are naïvely composed in this manner and, accordingly, craft security definitions for the MI setting and study their inter-relation. Finally, we suggest a set of protocols that are MI-secure, at the same time almost as efficient as their parent, stand-alone, protocols.","lang":"eng"}],"intvolume":" 12","month":"02","publisher":"AIMS","scopus_import":"1","quality_controlled":"1","publication":"American Institute of Mathematical Sciences","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2018","isi":1,"date_created":"2019-02-13T13:49:41Z","issue":"1","date_published":"2018-02-01T00:00:00Z","doi":"10.3934/amc.2018002","volume":12,"page":"17-47","_id":"5980","status":"public","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-19T14:27:59Z","citation":{"ama":"Chatterjee S, Kamath Hosdurg C, Kumar V. Private set-intersection with common set-up. American Institute of Mathematical Sciences. 2018;12(1):17-47. doi:10.3934/amc.2018002","apa":"Chatterjee, S., Kamath Hosdurg, C., & Kumar, V. (2018). Private set-intersection with common set-up. American Institute of Mathematical Sciences. AIMS. https://doi.org/10.3934/amc.2018002","short":"S. Chatterjee, C. Kamath Hosdurg, V. Kumar, American Institute of Mathematical Sciences 12 (2018) 17–47.","ieee":"S. Chatterjee, C. Kamath Hosdurg, and V. Kumar, “Private set-intersection with common set-up,” American Institute of Mathematical Sciences, vol. 12, no. 1. AIMS, pp. 17–47, 2018.","mla":"Chatterjee, Sanjit, et al. “Private Set-Intersection with Common Set-Up.” American Institute of Mathematical Sciences, vol. 12, no. 1, AIMS, 2018, pp. 17–47, doi:10.3934/amc.2018002.","ista":"Chatterjee S, Kamath Hosdurg C, Kumar V. 2018. Private set-intersection with common set-up. American Institute of Mathematical Sciences. 12(1), 17–47.","chicago":"Chatterjee, Sanjit, Chethan Kamath Hosdurg, and Vikas Kumar. “Private Set-Intersection with Common Set-Up.” American Institute of Mathematical Sciences. AIMS, 2018. https://doi.org/10.3934/amc.2018002."},"department":[{"_id":"KrPi"}],"title":"Private set-intersection with common set-up","article_processing_charge":"No","external_id":{"isi":["000430950400002"]},"author":[{"full_name":"Chatterjee, Sanjit","last_name":"Chatterjee","first_name":"Sanjit"},{"full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan"},{"full_name":"Kumar, Vikas","last_name":"Kumar","first_name":"Vikas"}]},{"has_accepted_license":"1","isi":1,"year":"2018","day":"12","publication":"PLOS Genetics","date_published":"2018-10-12T00:00:00Z","doi":"10.1371/journal.pgen.1007698","date_created":"2019-02-14T13:07:45Z","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"citation":{"chicago":"Velicky, Philipp, Gudrun Meinhardt, Kerstin Plessl, Sigrid Vondra, Tamara Weiss, Peter Haslinger, Thomas Lendl, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007698.","ista":"Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. 2018. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 14(10), e1007698.","mla":"Velicky, Philipp, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics, vol. 14, no. 10, e1007698, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007698.","apa":"Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., … Pollheimer, J. (2018). Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007698","ama":"Velicky P, Meinhardt G, Plessl K, et al. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 2018;14(10). doi:10.1371/journal.pgen.1007698","ieee":"P. Velicky et al., “Genome amplification and cellular senescence are hallmarks of human placenta development,” PLOS Genetics, vol. 14, no. 10. Public Library of Science, 2018.","short":"P. Velicky, G. Meinhardt, K. Plessl, S. Vondra, T. Weiss, P. Haslinger, T. Lendl, K. Aumayr, M. Mairhofer, X. Zhu, B. Schütz, R.L. Hannibal, R. Lindau, B. Weil, J. Ernerudh, J. Neesen, G. Egger, M. Mikula, C. Röhrl, A.E. Urban, J. Baker, M. Knöfler, J. Pollheimer, PLOS Genetics 14 (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"last_name":"Meinhardt","full_name":"Meinhardt, Gudrun","first_name":"Gudrun"},{"first_name":"Kerstin","last_name":"Plessl","full_name":"Plessl, Kerstin"},{"first_name":"Sigrid","full_name":"Vondra, Sigrid","last_name":"Vondra"},{"full_name":"Weiss, Tamara","last_name":"Weiss","first_name":"Tamara"},{"first_name":"Peter","full_name":"Haslinger, Peter","last_name":"Haslinger"},{"first_name":"Thomas","last_name":"Lendl","full_name":"Lendl, Thomas"},{"first_name":"Karin","full_name":"Aumayr, Karin","last_name":"Aumayr"},{"full_name":"Mairhofer, Mario","last_name":"Mairhofer","first_name":"Mario"},{"first_name":"Xiaowei","full_name":"Zhu, Xiaowei","last_name":"Zhu"},{"full_name":"Schütz, Birgit","last_name":"Schütz","first_name":"Birgit"},{"first_name":"Roberta L.","last_name":"Hannibal","full_name":"Hannibal, Roberta L."},{"first_name":"Robert","full_name":"Lindau, Robert","last_name":"Lindau"},{"first_name":"Beatrix","full_name":"Weil, Beatrix","last_name":"Weil"},{"full_name":"Ernerudh, Jan","last_name":"Ernerudh","first_name":"Jan"},{"first_name":"Jürgen","full_name":"Neesen, Jürgen","last_name":"Neesen"},{"last_name":"Egger","full_name":"Egger, Gerda","first_name":"Gerda"},{"first_name":"Mario","full_name":"Mikula, Mario","last_name":"Mikula"},{"last_name":"Röhrl","full_name":"Röhrl, Clemens","first_name":"Clemens"},{"first_name":"Alexander E.","last_name":"Urban","full_name":"Urban, Alexander E."},{"full_name":"Baker, Julie","last_name":"Baker","first_name":"Julie"},{"last_name":"Knöfler","full_name":"Knöfler, Martin","first_name":"Martin"},{"last_name":"Pollheimer","full_name":"Pollheimer, Jürgen","first_name":"Jürgen"}],"article_processing_charge":"No","external_id":{"isi":["000449328500025"]},"title":"Genome amplification and cellular senescence are hallmarks of human placenta development","article_number":"e1007698","publication_identifier":{"issn":["1553-7404"]},"publication_status":"published","file":[{"file_name":"2018_PLOS_Velicky.pdf","date_created":"2019-02-14T13:14:35Z","file_size":4592947,"date_updated":"2020-07-14T12:47:15Z","creator":"kschuh","file_id":"6000","checksum":"34aa9a5972f61889c19f18be8ee787a0","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":14,"issue":"10","abstract":[{"lang":"eng","text":"Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM."}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 14","date_updated":"2023-09-19T14:31:43Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:15Z","department":[{"_id":"JoDa"}],"_id":"5998","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"publication":"Bioinformatics","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2019-02-14T12:48:00Z","doi":"10.1093/bioinformatics/bty340","date_published":"2018-11-01T00:00:00Z","page":"3653-3658","oa":1,"publisher":"Oxford University Press ","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340","ama":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340","ieee":"D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.","short":"D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658.","mla":"Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.","ista":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.","chicago":"Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340."},"title":"Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation","article_processing_charge":"No","external_id":{"pmid":["29722803"],"isi":["000450038900008"]},"author":[{"last_name":"Usmanova","full_name":"Usmanova, Dinara R","first_name":"Dinara R"},{"full_name":"Bogatyreva, Natalya S","last_name":"Bogatyreva","first_name":"Natalya S"},{"first_name":"Joan","full_name":"Ariño Bernad, Joan","last_name":"Ariño Bernad"},{"first_name":"Aleksandra A","full_name":"Eremina, Aleksandra A","last_name":"Eremina"},{"last_name":"Gorshkova","full_name":"Gorshkova, Anastasiya A","first_name":"Anastasiya A"},{"first_name":"German M","last_name":"Kanevskiy","full_name":"Kanevskiy, German M"},{"first_name":"Lyubov R","full_name":"Lonishin, Lyubov R","last_name":"Lonishin"},{"last_name":"Meister","full_name":"Meister, Alexander V","first_name":"Alexander V"},{"first_name":"Alisa G","last_name":"Yakupova","full_name":"Yakupova, Alisa G"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","full_name":"Ivankov, Dmitry","last_name":"Ivankov"}],"project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution"}],"language":[{"iso":"eng"}],"file":[{"file_size":291969,"date_updated":"2020-07-14T12:47:15Z","creator":"kschuh","file_name":"2018_Oxford_Usmanova.pdf","date_created":"2019-02-14T13:00:55Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5997","checksum":"7e0495153f44211479674601d7f6ee03"}],"publication_status":"published","publication_identifier":{"issn":["1367-4803","1460-2059"]},"ec_funded":1,"issue":"21","volume":34,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here.","lang":"eng"}],"intvolume":" 34","month":"11","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-19T14:31:13Z","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:47:15Z","_id":"5995","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article"},{"citation":{"chicago":"Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner, Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell. American Society for Cell Biology , 2018. https://doi.org/10.1091/mbc.e18-02-0082.","ista":"Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner K, Falcke M. 2018. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 29(22), 2674–2686.","mla":"Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell, vol. 29, no. 22, American Society for Cell Biology , 2018, pp. 2674–86, doi:10.1091/mbc.e18-02-0082.","apa":"Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., … Falcke, M. (2018). On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. American Society for Cell Biology . https://doi.org/10.1091/mbc.e18-02-0082","ama":"Dolati S, Kage F, Mueller J, et al. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 2018;29(22):2674-2686. doi:10.1091/mbc.e18-02-0082","short":"S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K. Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686.","ieee":"S. Dolati et al., “On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility,” Molecular Biology of the Cell, vol. 29, no. 22. American Society for Cell Biology , pp. 2674–2686, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["30156465"],"isi":["000455641000011"]},"article_processing_charge":"No","author":[{"full_name":"Dolati, Setareh","last_name":"Dolati","first_name":"Setareh"},{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"first_name":"Jan","last_name":"Mueller","full_name":"Mueller, Jan"},{"first_name":"Mathias","full_name":"Müsken, Mathias","last_name":"Müsken"},{"first_name":"Marieluise","last_name":"Kirchner","full_name":"Kirchner, Marieluise"},{"first_name":"Gunnar","full_name":"Dittmar, Gunnar","last_name":"Dittmar"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"first_name":"Martin","full_name":"Falcke, Martin","last_name":"Falcke"}],"title":"On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility","oa":1,"quality_controlled":"1","publisher":"American Society for Cell Biology ","year":"2018","isi":1,"has_accepted_license":"1","publication":"Molecular Biology of the Cell","day":"01","page":"2674-2686","date_created":"2019-02-14T12:25:47Z","doi":"10.1091/mbc.e18-02-0082","date_published":"2018-11-01T00:00:00Z","_id":"5992","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-09-19T14:30:23Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:15Z","abstract":[{"lang":"eng","text":"Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 29","month":"11","publication_status":"published","publication_identifier":{"eissn":["1939-4586"]},"language":[{"iso":"eng"}],"file":[{"checksum":"e98465b4416b3e804c47f40086932af2","file_id":"5994","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-02-14T12:34:29Z","file_name":"2018_ASCB_Dolati.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:15Z","file_size":6668971}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","volume":29,"issue":"22"},{"_id":"6010","type":"journal_article","status":"public","date_updated":"2023-09-19T14:35:36Z","department":[{"_id":"MaJö"}],"abstract":[{"lang":"eng","text":"The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity."}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30026198","open_access":"1"}],"scopus_import":"1","intvolume":" 115","month":"08","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"issue":"32","volume":115,"citation":{"ama":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 2018;115(32):E7615-E7623. doi:10.1073/pnas.1804517115","apa":"Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P., López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1804517115","short":"F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L. López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings of the National Academy of Sciences 115 (2018) E7615–E7623.","ieee":"F. Garrido-Charad et al., ““Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network,” Proceedings of the National Academy of Sciences, vol. 115, no. 32. National Academy of Sciences, pp. E7615–E7623, 2018.","mla":"Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences, vol. 115, no. 32, National Academy of Sciences, 2018, pp. E7615–23, doi:10.1073/pnas.1804517115.","ista":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 115(32), E7615–E7623.","chicago":"Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez, Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten, Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1804517115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000440982000020"],"pmid":["30026198"]},"author":[{"first_name":"Florencia","last_name":"Garrido-Charad","full_name":"Garrido-Charad, Florencia"},{"id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A","last_name":"Vega Zuniga","full_name":"Vega Zuniga, Tomas A"},{"first_name":"Cristián","last_name":"Gutiérrez-Ibáñez","full_name":"Gutiérrez-Ibáñez, Cristián"},{"full_name":"Fernandez, Pedro","last_name":"Fernandez","first_name":"Pedro"},{"first_name":"Luciana","full_name":"López-Jury, Luciana","last_name":"López-Jury"},{"last_name":"González-Cabrera","full_name":"González-Cabrera, Cristian","first_name":"Cristian"},{"first_name":"Harvey J.","last_name":"Karten","full_name":"Karten, Harvey J."},{"full_name":"Luksch, Harald","last_name":"Luksch","first_name":"Harald"},{"last_name":"Marín","full_name":"Marín, Gonzalo J.","first_name":"Gonzalo J."}],"title":"“Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","year":"2018","isi":1,"publication":"Proceedings of the National Academy of Sciences","day":"07","page":"E7615-E7623","date_created":"2019-02-14T14:33:34Z","date_published":"2018-08-07T00:00:00Z","doi":"10.1073/pnas.1804517115"},{"volume":37,"issue":"6","ec_funded":1,"publication_identifier":{"issn":["0167-7055"]},"publication_status":"published","file":[{"date_created":"2019-02-14T14:09:28Z","file_name":"StylizedFabricationSTAR-Personal.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:15Z","file_size":6209349,"file_id":"6004","checksum":"d2bbe5c658d8159fbe9016a4f5e82b19","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"09","intvolume":" 37","abstract":[{"text":"Digital fabrication devices are powerful tools for creating tangible reproductions of 3D digital models. Most available printing technologies aim at producing an accurate copy of a tridimensional shape. However, fabrication technologies can also be used to create a stylistic representation of a digital shape. We refer to this class of methods as ‘stylized fabrication methods’. These methods abstract geometric and physical features of a given shape to create an unconventional representation, to produce an optical illusion or to devise a particular interaction with the fabricated model. In this state‐of‐the‐art report, we classify and overview this broad and emerging class of approaches and also propose possible directions for future research.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:47:15Z","date_updated":"2023-09-19T14:33:40Z","ddc":["004"],"type":"journal_article","status":"public","pubrep_id":"1051","_id":"6003","page":"325-342","doi":"10.1111/cgf.13327","date_published":"2018-09-01T00:00:00Z","date_created":"2019-02-14T13:52:25Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Computer Graphics Forum","publisher":"Wiley","quality_controlled":"1","oa":1,"author":[{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cignoni","full_name":"Cignoni, Paolo","first_name":"Paolo"},{"first_name":"Luigi","full_name":"Malomo, Luigi","last_name":"Malomo"},{"last_name":"Pietroni","full_name":"Pietroni, Nico","first_name":"Nico"}],"external_id":{"isi":["000437272800019"]},"article_processing_charge":"No","title":"State of the art on stylized fabrication","citation":{"mla":"Bickel, Bernd, et al. “State of the Art on Stylized Fabrication.” Computer Graphics Forum, vol. 37, no. 6, Wiley, 2018, pp. 325–42, doi:10.1111/cgf.13327.","ama":"Bickel B, Cignoni P, Malomo L, Pietroni N. State of the art on stylized fabrication. Computer Graphics Forum. 2018;37(6):325-342. doi:10.1111/cgf.13327","apa":"Bickel, B., Cignoni, P., Malomo, L., & Pietroni, N. (2018). State of the art on stylized fabrication. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13327","ieee":"B. Bickel, P. Cignoni, L. Malomo, and N. Pietroni, “State of the art on stylized fabrication,” Computer Graphics Forum, vol. 37, no. 6. Wiley, pp. 325–342, 2018.","short":"B. Bickel, P. Cignoni, L. Malomo, N. Pietroni, Computer Graphics Forum 37 (2018) 325–342.","chicago":"Bickel, Bernd, Paolo Cignoni, Luigi Malomo, and Nico Pietroni. “State of the Art on Stylized Fabrication.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13327.","ista":"Bickel B, Cignoni P, Malomo L, Pietroni N. 2018. State of the art on stylized fabrication. Computer Graphics Forum. 37(6), 325–342."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}]},{"abstract":[{"lang":"eng","text":"The Bogoliubov free energy functional is analysed. The functional serves as a model of a translation-invariant Bose gas at positive temperature. We prove the existence of minimizers in the case of repulsive interactions given by a sufficiently regular two-body potential. Furthermore, we prove the existence of a phase transition in this model and provide its phase diagram."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1511.05935","open_access":"1"}],"scopus_import":"1","intvolume":" 229","month":"09","publication_status":"published","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"language":[{"iso":"eng"}],"issue":"3","volume":229,"_id":"6002","type":"journal_article","status":"public","date_updated":"2023-09-19T14:33:12Z","department":[{"_id":"RoSe"}],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2018","isi":1,"publication":"Archive for Rational Mechanics and Analysis","day":"01","page":"1037-1090","date_created":"2019-02-14T13:40:53Z","date_published":"2018-09-01T00:00:00Z","doi":"10.1007/s00205-018-1232-6","project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"citation":{"ama":"Napiórkowski MM, Reuvers R, Solovej JP. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 2018;229(3):1037-1090. doi:10.1007/s00205-018-1232-6","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. P. (2018). The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-018-1232-6","short":"M.M. Napiórkowski, R. Reuvers, J.P. Solovej, Archive for Rational Mechanics and Analysis 229 (2018) 1037–1090.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. P. Solovej, “The Bogoliubov free energy functional I: Existence of minimizers and phase diagram,” Archive for Rational Mechanics and Analysis, vol. 229, no. 3. Springer Nature, pp. 1037–1090, 2018.","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis, vol. 229, no. 3, Springer Nature, 2018, pp. 1037–90, doi:10.1007/s00205-018-1232-6.","ista":"Napiórkowski MM, Reuvers R, Solovej JP. 2018. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 229(3), 1037–1090.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Philip Solovej. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00205-018-1232-6."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1511.05935"],"isi":["000435367300003"]},"article_processing_charge":"No","author":[{"last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reuvers, Robin","last_name":"Reuvers","first_name":"Robin"},{"last_name":"Solovej","full_name":"Solovej, Jan Philip","first_name":"Jan Philip"}],"title":"The Bogoliubov free energy functional I: Existence of minimizers and phase diagram"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"publication_status":"published","volume":839,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In pipes, turbulence sets in despite the linear stability of the laminar Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears in a given experiment – the ‘natural transition point’ – depends on imperfections of the set-up, or, more precisely, on the magnitude of finite amplitude perturbations. At onset, turbulence typically only occupies a certain fraction of the flow, and this fraction equally is found to differ from experiment to experiment. Despite these findings, Reynolds proposed that after sufficiently long times, flows may settle to steady conditions: below a critical velocity, flows should (regardless of initial conditions) always return to laminar, while above this velocity, eddying motion should persist. As will be shown, even in pipes several thousand diameters long, the spatio-temporal intermittent flow patterns observed at the end of the pipe strongly depend on the initial conditions, and there is no indication that different flow patterns would eventually settle to a (statistical) steady state. Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless), we continuously recreate the puff sequence exiting the pipe at the pipe entrance, and in doing so introduce periodic boundary conditions for the puff pattern. This procedure allows us to study the evolution of the flow patterns for arbitrary long times, and we find that after times in excess of advective time units, indeed a statistical steady state is reached. Although the resulting flows remain spatio-temporally intermittent, puff splitting and decay rates eventually reach a balance, so that the turbulent fraction fluctuates around a well-defined level which only depends on . In accordance with Reynolds’ proposition, we find that at lower (here 2020), flows eventually always resume to laminar, while for higher ( ), turbulence persists. The critical point for pipe flow hence falls in the interval of $2020 , which is in very good agreement with the recently proposed value of . The latter estimate was based on single-puff statistics and entirely neglected puff interactions. Unlike in typical contact processes where such interactions strongly affect the percolation threshold, in pipe flow, the critical point is only marginally influenced. Interactions, on the other hand, are responsible for the approach to the statistical steady state. As shown, they strongly affect the resulting flow patterns, where they cause ‘puff clustering’, and these regions of large puff densities are observed to travel across the puff pattern in a wave-like fashion."}],"month":"03","intvolume":" 839","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1709.06372","open_access":"1"}],"date_updated":"2023-09-19T14:37:49Z","department":[{"_id":"BjHo"}],"_id":"5996","status":"public","article_type":"original","type":"journal_article","day":"25","publication":"Journal of Fluid Mechanics","isi":1,"year":"2018","doi":"10.1017/jfm.2017.923","date_published":"2018-03-25T00:00:00Z","date_created":"2019-02-14T12:50:50Z","page":"76-94","acknowledgement":" We also thank Philipp Maier and the IST Austria workshop for theirdedicated technical support","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Vasudevan M, Hof B. 2018. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 839, 76–94.","chicago":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2018. https://doi.org/10.1017/jfm.2017.923.","ieee":"M. Vasudevan and B. Hof, “The critical point of the transition to turbulence in pipe flow,” Journal of Fluid Mechanics, vol. 839. Cambridge University Press, pp. 76–94, 2018.","short":"M. Vasudevan, B. Hof, Journal of Fluid Mechanics 839 (2018) 76–94.","ama":"Vasudevan M, Hof B. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 2018;839:76-94. doi:10.1017/jfm.2017.923","apa":"Vasudevan, M., & Hof, B. (2018). The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.923","mla":"Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics, vol. 839, Cambridge University Press, 2018, pp. 76–94, doi:10.1017/jfm.2017.923."},"title":"The critical point of the transition to turbulence in pipe flow","author":[{"id":"3C5A959A-F248-11E8-B48F-1D18A9856A87","first_name":"Mukund","last_name":"Vasudevan","full_name":"Vasudevan, Mukund"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"external_id":{"isi":["000437858300003"],"arxiv":["1709.06372"]},"article_processing_charge":"No","project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin"}]},{"date_published":"2018-06-01T00:00:00Z","doi":"10.1145/3174800","date_created":"2019-02-14T12:29:10Z","day":"01","publication":"ACM Transactions on Programming Languages and Systems","isi":1,"year":"2018","publisher":"Association for Computing Machinery (ACM)","quality_controlled":"1","oa":1,"title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","full_name":"Fu, Hongfei"},{"full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rouzbeh","full_name":"Hasheminezhad, Rouzbeh","last_name":"Hasheminezhad"}],"external_id":{"arxiv":["1510.08517"],"isi":["000434634500003"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2018. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 40(2), 7.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3174800.","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, ACM Transactions on Programming Languages and Systems 40 (2018).","ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2. Association for Computing Machinery (ACM), 2018.","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 2018;40(2). doi:10.1145/3174800","apa":"Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2018). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3174800","mla":"Chatterjee, Krishnendu, et al. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2, 7, Association for Computing Machinery (ACM), 2018, doi:10.1145/3174800."},"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"7","volume":40,"issue":"2","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1438"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0164-0925"]},"publication_status":"published","month":"06","intvolume":" 40","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.08517"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In this article, we consider the termination problem of probabilistic programs with real-valued variables. Thequestions concerned are: qualitative ones that ask (i) whether the program terminates with probability 1(almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); andquantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) tocompute a boundBsuch that the probability not to terminate afterBsteps decreases exponentially (con-centration problem). To solve these questions, we utilize the notion of ranking supermartingales, which isa powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmicsynthesis of linear ranking-supermartingales over affine probabilistic programs (Apps) with both angelic anddemonic non-determinism. An important subclass of Apps is LRApp which is defined as the class of all Appsover which a linear ranking-supermartingale exists.Our main contributions are as follows. Firstly, we show that the membership problem of LRApp (i) canbe decided in polynomial time for Apps with at most demonic non-determinism, and (ii) isNP-hard and inPSPACEfor Apps with angelic non-determinism. Moreover, theNP-hardness result holds already for Appswithout probability and demonic non-determinism. Secondly, we show that the concentration problem overLRApp can be solved in the same complexity as for the membership problem of LRApp. Finally, we show thatthe expectation problem over LRApp can be solved in2EXPTIMEand isPSPACE-hard even for Apps withoutprobability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate theeffectiveness of our approach to answer the qualitative and quantitative questions over Apps with at mostdemonic non-determinism."}],"department":[{"_id":"KrCh"}],"date_updated":"2023-09-19T14:38:42Z","status":"public","type":"journal_article","_id":"5993"},{"date_published":"2018-05-01T00:00:00Z","doi":"10.1112/plms.12111","date_created":"2019-02-14T13:14:22Z","page":"1029-1074","day":"01","publication":"Proceedings of the London Mathematical Society","isi":1,"year":"2018","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"title":"The cohomological Hall algebra of a preprojective algebra","author":[{"full_name":"Yang, Yaping","last_name":"Yang","first_name":"Yaping"},{"full_name":"Zhao, Gufang","last_name":"Zhao","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang"}],"article_processing_charge":"No","external_id":{"arxiv":["1407.7994"],"isi":["000431506400001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society, vol. 116, no. 5, Oxford University Press, 2018, pp. 1029–74, doi:10.1112/plms.12111.","short":"Y. Yang, G. Zhao, Proceedings of the London Mathematical Society 116 (2018) 1029–1074.","ieee":"Y. Yang and G. Zhao, “The cohomological Hall algebra of a preprojective algebra,” Proceedings of the London Mathematical Society, vol. 116, no. 5. Oxford University Press, pp. 1029–1074, 2018.","ama":"Yang Y, Zhao G. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 2018;116(5):1029-1074. doi:10.1112/plms.12111","apa":"Yang, Y., & Zhao, G. (2018). The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms.12111","chicago":"Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society. Oxford University Press, 2018. https://doi.org/10.1112/plms.12111.","ista":"Yang Y, Zhao G. 2018. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 116(5), 1029–1074."},"volume":116,"issue":"5","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0024-6115"]},"publication_status":"published","month":"05","intvolume":" 116","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1407.7994","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We introduce for each quiver Q and each algebraic oriented cohomology theory A, the cohomological Hall algebra (CoHA) of Q, as the A-homology of the moduli of representations of the preprojective algebra of Q. This generalizes the K-theoretic Hall algebra of commuting varieties defined by Schiffmann-Vasserot. When A is the Morava K-theory, we show evidence that this algebra is a candidate for Lusztig's reformulated conjecture on modular representations of algebraic groups.\r\nWe construct an action of the preprojective CoHA on the A-homology of Nakajima quiver varieties. We compare this with the action of the Borel subalgebra of Yangian when A is the intersection theory. We also give a shuffle algebra description of this CoHA in terms of the underlying formal group law of A. As applications, we obtain a shuffle description of the Yangian. ","lang":"eng"}],"department":[{"_id":"TaHa"}],"date_updated":"2023-09-19T14:37:19Z","status":"public","type":"journal_article","_id":"5999"},{"publisher":"Oxford University Press","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Genome Biology and Evolution","page":"840-856","date_published":"2018-03-01T00:00:00Z","doi":"10.1093/gbe/evy037","date_created":"2019-02-14T12:13:52Z","citation":{"chicago":"Kincaid-Smith, Julien, Marion A L Picard, Céline Cosseau, Jérôme Boissier, Dany Severac, Christoph Grunau, and Eve Toulza. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy037.","ista":"Kincaid-Smith J, Picard MAL, Cosseau C, Boissier J, Severac D, Grunau C, Toulza E. 2018. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. 10(3), 840–856.","mla":"Kincaid-Smith, Julien, et al. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 840–56, doi:10.1093/gbe/evy037.","short":"J. Kincaid-Smith, M.A.L. Picard, C. Cosseau, J. Boissier, D. Severac, C. Grunau, E. Toulza, Genome Biology and Evolution 10 (2018) 840–856.","ieee":"J. Kincaid-Smith et al., “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 840–856, 2018.","ama":"Kincaid-Smith J, Picard MAL, Cosseau C, et al. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. 2018;10(3):840-856. doi:10.1093/gbe/evy037","apa":"Kincaid-Smith, J., Picard, M. A. L., Cosseau, C., Boissier, J., Severac, D., Grunau, C., & Toulza, E. (2018). Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy037"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Kincaid-Smith","full_name":"Kincaid-Smith, Julien","first_name":"Julien"},{"full_name":"Picard, Marion A L","orcid":"0000-0002-8101-2518","last_name":"Picard","first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cosseau","full_name":"Cosseau, Céline","first_name":"Céline"},{"first_name":"Jérôme","last_name":"Boissier","full_name":"Boissier, Jérôme"},{"first_name":"Dany","last_name":"Severac","full_name":"Severac, Dany"},{"last_name":"Grunau","full_name":"Grunau, Christoph","first_name":"Christoph"},{"first_name":"Eve","last_name":"Toulza","full_name":"Toulza, Eve"}],"external_id":{"isi":["000429483700013"]},"article_processing_charge":"No","title":"Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites","abstract":[{"text":"Schistosomes are the causative agents of schistosomiasis, a neglected tropical disease affecting over 230 million people worldwide.Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatwormsare unique among the common hermaphroditic trematodes as they have separate sexes. This so-called “evolutionary scandal”displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexualdimorphism. These phenotypic differences are determined by a shared set of genes in both sexes, potentially leading to intralocussexual conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms such as sex-biased gene expression couldoccur, but parent-of-origin gene expression also provides an alternative. In this work we investigated the latter mechanism, that is,genes expressed preferentially from either the maternal or the paternal allele, inSchistosoma mansonispecies. To this end, tran-scriptomes from male and female hybrid adults obtained by strain crosses were sequenced. Strain-specific single nucleotide poly-morphism (SNP) markers allowed us to discriminate the parental origin, while reciprocal crosses helped to differentiate parentalexpression from strain-specific expression. We identified genes containing SNPs expressed in a parent-of-origin manner consistentwith paternal and maternal imprints. Although the majority of the SNPs was identified in mitochondrial and Z-specific loci, theremaining SNPs found in male and female transcriptomes were situated in genes that have the potential to explain sexual differencesin schistosome parasites. Furthermore, we identified and validated four new Z-specific scaffolds.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 10","publication_identifier":{"issn":["1759-6653"]},"publication_status":"published","file":[{"checksum":"736a459cb77de5824354466bb0331caf","file_id":"5991","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-02-14T12:20:01Z","file_name":"2018_GBE_Kincaid_Smith.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:15Z","file_size":529755}],"language":[{"iso":"eng"}],"issue":"3","volume":10,"_id":"5989","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","date_updated":"2023-09-19T14:39:08Z","ddc":["570"],"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:15Z"},{"day":"31","publication":"2018 IEEE International Workshop on Signal Processing Systems","language":[{"iso":"eng"}],"isi":1,"publication_status":"published","year":"2018","date_published":"2018-12-31T00:00:00Z","doi":"10.1109/SiPS.2018.8598402","volume":"2018-October","date_created":"2019-02-17T22:59:25Z","oa_version":"None","abstract":[{"lang":"eng","text":"We introduce Clover, a new library for efficient computation using low-precision data, providing mathematical routines required by fundamental methods in optimization and sparse recovery. Our library faithfully implements variants of stochastic quantization that guarantee convergence at low precision, and supports data formats from 4-bit quantized to 32-bit IEEE-754 on current Intel processors. In particular, we show that 4-bit can be implemented efficiently using Intel AVX despite the lack of native support for this data format. Experimental results with dot product, matrix-vector multiplication (MVM), gradient descent (GD), and iterative hard thresholding (IHT) demonstrate that the attainable speedups are in many cases close to linear with respect to the reduction of precision due to reduced data movement. Finally, for GD and IHT, we show examples of absolute speedup achieved by 4-bit versus 32-bit, by iterating until a given target error is achieved."}],"month":"12","scopus_import":"1","quality_controlled":"1","publisher":"IEEE","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Stojanov, Alen, et al. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” 2018 IEEE International Workshop on Signal Processing Systems, vol. 2018–October, 8598402, IEEE, 2018, doi:10.1109/SiPS.2018.8598402.","apa":"Stojanov, A., Smith, T. M., Alistarh, D.-A., & Puschel, M. (2018). Fast quantized arithmetic on x86: Trading compute for data movement. In 2018 IEEE International Workshop on Signal Processing Systems (Vol. 2018–October). Cape Town, South Africa: IEEE. https://doi.org/10.1109/SiPS.2018.8598402","ama":"Stojanov A, Smith TM, Alistarh D-A, Puschel M. Fast quantized arithmetic on x86: Trading compute for data movement. In: 2018 IEEE International Workshop on Signal Processing Systems. Vol 2018-October. IEEE; 2018. doi:10.1109/SiPS.2018.8598402","short":"A. Stojanov, T.M. Smith, D.-A. Alistarh, M. Puschel, in:, 2018 IEEE International Workshop on Signal Processing Systems, IEEE, 2018.","ieee":"A. Stojanov, T. M. Smith, D.-A. Alistarh, and M. Puschel, “Fast quantized arithmetic on x86: Trading compute for data movement,” in 2018 IEEE International Workshop on Signal Processing Systems, Cape Town, South Africa, 2018, vol. 2018–October.","chicago":"Stojanov, Alen, Tyler Michael Smith, Dan-Adrian Alistarh, and Markus Puschel. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” In 2018 IEEE International Workshop on Signal Processing Systems, Vol. 2018–October. IEEE, 2018. https://doi.org/10.1109/SiPS.2018.8598402.","ista":"Stojanov A, Smith TM, Alistarh D-A, Puschel M. 2018. Fast quantized arithmetic on x86: Trading compute for data movement. 2018 IEEE International Workshop on Signal Processing Systems. SiPS: Workshop on Signal Processing Systems vol. 2018–October, 8598402."},"date_updated":"2023-09-19T14:41:51Z","title":"Fast quantized arithmetic on x86: Trading compute for data movement","department":[{"_id":"DaAl"}],"author":[{"first_name":"Alen","last_name":"Stojanov","full_name":"Stojanov, Alen"},{"first_name":"Tyler Michael","last_name":"Smith","full_name":"Smith, Tyler Michael"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Puschel","full_name":"Puschel, Markus","first_name":"Markus"}],"article_processing_charge":"No","external_id":{"isi":["000465106800060"]},"article_number":"8598402","_id":"6031","status":"public","type":"conference","conference":{"location":"Cape Town, South Africa","end_date":"2018-10-24","start_date":"2018-10-21","name":"SiPS: Workshop on Signal Processing Systems"}},{"language":[{"iso":"eng"}],"publication_status":"published","volume":"2018-July","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Partially observable Markov decision processes (POMDPs) are the standard models for planning under uncertainty with both finite and infinite horizon. Besides the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs) is another classical objective for POMDPs. In this case, given a set of target states and a positive cost for each transition, the optimization objective is to minimize the expected total cost until a target state is reached. In the literature, RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees, and HSVI may even fail to terminate its trials. We give the following contributions: (1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they prevent the original HSVI from converging. (2) We present a novel algorithm inspired by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees. (3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples."}],"month":"07","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.24963/ijcai.2018/662"}],"date_updated":"2023-09-19T14:44:59Z","department":[{"_id":"KrCh"}],"_id":"25","status":"public","type":"conference","conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","location":"Stockholm, Sweden","end_date":"2018-07-19","start_date":"2018-07-13"},"day":"01","publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","isi":1,"year":"2018","date_published":"2018-07-01T00:00:00Z","doi":"10.24963/ijcai.2018/662","date_created":"2018-12-11T11:44:13Z","page":"4764 - 4770","acknowledgement":"∗This work has been supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games). This research was sponsored by the Army Research Laboratory and was accomplished under Cooperative Agreement Number W911NF-13-2-0045 (ARL Cyber Security CRA). ","publisher":"IJCAI","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018–July, 4764–4770.","chicago":"Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018–July:4764–70. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/662.","ama":"Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. Vol 2018-July. IJCAI; 2018:4764-4770. doi:10.24963/ijcai.2018/662","apa":"Horák, K., Bošanský, B., & Chatterjee, K. (2018). Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence (Vol. 2018–July, pp. 4764–4770). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/662","ieee":"K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value iteration for goal-POMDPs,” in Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018–July, pp. 4764–4770.","short":"K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.","mla":"Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:10.24963/ijcai.2018/662."},"title":"Goal-HSVI: Heuristic search value iteration for goal-POMDPs","publist_id":"8030","author":[{"first_name":"Karel","last_name":"Horák","full_name":"Horák, Karel"},{"first_name":"Branislav","last_name":"Bošanský","full_name":"Bošanský, Branislav"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"external_id":{"isi":["000764175404127"]},"article_processing_charge":"No","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}]},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":2018,"abstract":[{"lang":"eng","text":"Partially-observable Markov decision processes (POMDPs) with discounted-sum payoff are a standard framework to model a wide range of problems related to decision making under uncertainty. Traditionally, the goal has been to obtain policies that optimize the expectation of the discounted-sum payoff. A key drawback of the expectation measure is that even low probability events with extreme payoff can significantly affect the expectation, and thus the obtained policies are not necessarily risk-averse. An alternate approach is to optimize the probability that the payoff is above a certain threshold, which allows obtaining risk-averse policies, but ignores optimization of the expectation. We consider the expectation optimization with probabilistic guarantee (EOPG) problem, where the goal is to optimize the expectation ensuring that the payoff is above a given threshold with at least a specified probability. We present several results on the EOPG problem, including the first algorithm to solve it."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1804.10601","open_access":"1"}],"scopus_import":"1","intvolume":" 2018","month":"07","date_updated":"2023-09-19T14:45:48Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"24","conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","start_date":"2018-07-13","end_date":"2018-07-19","location":"Stockholm, Sweden"},"type":"conference","status":"public","year":"2018","isi":1,"day":"01","page":"4692 - 4699","date_created":"2018-12-11T11:44:13Z","date_published":"2018-07-01T00:00:00Z","doi":"10.24963/ijcai.2018/652","acknowledgement":"This research was supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and an ERC Start Grant (279307:Graph Games).\r\n","oa":1,"publisher":"IJCAI","quality_controlled":"1","citation":{"short":"K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp. 4692–4699.","ieee":"K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4692–4699.","apa":"Chatterjee, K., Elgyütt, A., Novotný, P., & Rouillé, O. (2018). Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives (Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/652","ama":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018. IJCAI; 2018:4692-4699. doi:10.24963/ijcai.2018/652","mla":"Chatterjee, Krishnendu, et al. Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives. Vol. 2018, IJCAI, 2018, pp. 4692–99, doi:10.24963/ijcai.2018/652.","ista":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699.","chicago":"Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé. “Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives,” 2018:4692–99. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/652."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1804.10601"],"isi":["000764175404117"]},"article_processing_charge":"No","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Elgyütt","full_name":"Elgyütt, Adrian","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian"},{"full_name":"Novotny, Petr","last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"last_name":"Rouillé","full_name":"Rouillé, Owen","first_name":"Owen"}],"publist_id":"8031","title":"Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}]},{"citation":{"mla":"Chatterjee, Krishnendu, et al. Sensor Synthesis for POMDPs with Reachability Objectives. Vol. 2018, AAAI Press, 2018, pp. 47–55.","ama":"Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability objectives. In: Vol 2018. AAAI Press; 2018:47-55.","apa":"Chatterjee, K., Chemlík, M., & Topcu, U. (2018). Sensor synthesis for POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands: AAAI Press.","ieee":"K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with reachability objectives,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.","short":"K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55.","chicago":"Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018.","ista":"Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with reachability objectives. ICAPS: International Conference on Automated Planning and Scheduling, ICAPS, vol. 2018, 47–55."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chemlík, Martin","last_name":"Chemlík","first_name":"Martin"},{"first_name":"Ufuk","last_name":"Topcu","full_name":"Topcu, Ufuk"}],"publist_id":"8021","external_id":{"arxiv":["1710.00675"],"isi":["000492986200006"]},"article_processing_charge":"No","title":"Sensor synthesis for POMDPs with reachability objectives","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"isi":1,"year":"2018","day":"01","page":"47 - 55","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:44:16Z","quality_controlled":"1","publisher":"AAAI Press","oa":1,"date_updated":"2023-09-19T14:44:14Z","department":[{"_id":"KrCh"}],"_id":"34","type":"conference","conference":{"location":"Delft, Netherlands","end_date":"2018-06-29","start_date":"2018-06-24","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":2018,"ec_funded":1,"abstract":[{"text":"Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies.","lang":"eng"}],"oa_version":"Preprint","alternative_title":["ICAPS"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1710.00675","open_access":"1"}],"month":"06","intvolume":" 2018"},{"publication":"Ars Combinatoria","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:44:11Z","date_published":"2018-10-01T00:00:00Z","page":"269 - 304","oa":1,"publisher":"Charles Babbage Research Centre","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Kolmogorov V, Rolinek M. Superconcentrators of density 25.3. Ars Combinatoria. 2018;141(10):269-304.","apa":"Kolmogorov, V., & Rolinek, M. (2018). Superconcentrators of density 25.3. Ars Combinatoria. Charles Babbage Research Centre.","ieee":"V. Kolmogorov and M. Rolinek, “Superconcentrators of density 25.3,” Ars Combinatoria, vol. 141, no. 10. Charles Babbage Research Centre, pp. 269–304, 2018.","short":"V. Kolmogorov, M. Rolinek, Ars Combinatoria 141 (2018) 269–304.","mla":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” Ars Combinatoria, vol. 141, no. 10, Charles Babbage Research Centre, 2018, pp. 269–304.","ista":"Kolmogorov V, Rolinek M. 2018. Superconcentrators of density 25.3. Ars Combinatoria. 141(10), 269–304.","chicago":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” Ars Combinatoria. Charles Babbage Research Centre, 2018."},"title":"Superconcentrators of density 25.3","article_processing_charge":"No","external_id":{"isi":["000446809500022"],"arxiv":["1405.7828"]},"publist_id":"8037","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"last_name":"Rolinek","full_name":"Rolinek, Michal","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0381-7032"]},"volume":141,"issue":"10","oa_version":"Preprint","abstract":[{"text":"An N-superconcentrator is a directed, acyclic graph with N input nodes and N output nodes such that every subset of the inputs and every subset of the outputs of same cardinality can be connected by node-disjoint paths. It is known that linear-size and bounded-degree superconcentrators exist. We prove the existence of such superconcentrators with asymptotic density 25.3 (where the density is the number of edges divided by N). The previously best known densities were 28 [12] and 27.4136 [17].","lang":"eng"}],"intvolume":" 141","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1405.7828","open_access":"1"}],"scopus_import":"1","date_updated":"2023-09-19T14:46:18Z","department":[{"_id":"VlKo"}],"_id":"18","status":"public","type":"journal_article"},{"publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"doi":"10.1017/fms.2018.7","date_published":"2018-05-31T00:00:00Z","date_created":"2019-04-30T06:09:57Z","day":"31","publication":"Forum of Mathematics, Sigma","isi":1,"has_accepted_license":"1","year":"2018","project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e7","title":"Any cyclic quadrilateral can be inscribed in any closed convex smooth curve","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"}],"article_processing_charge":"No","external_id":{"arxiv":["1712.10205"],"isi":["000433915500001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"A. Akopyan and S. Avvakumov, “Any cyclic quadrilateral can be inscribed in any closed convex smooth curve,” Forum of Mathematics, Sigma, vol. 6. Cambridge University Press, 2018.","short":"A. Akopyan, S. Avvakumov, Forum of Mathematics, Sigma 6 (2018).","ama":"Akopyan A, Avvakumov S. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 2018;6. doi:10.1017/fms.2018.7","apa":"Akopyan, A., & Avvakumov, S. (2018). Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2018.7","mla":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma, vol. 6, e7, Cambridge University Press, 2018, doi:10.1017/fms.2018.7.","ista":"Akopyan A, Avvakumov S. 2018. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 6, e7.","chicago":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma. Cambridge University Press, 2018. https://doi.org/10.1017/fms.2018.7."},"month":"05","intvolume":" 6","oa_version":"Published Version","abstract":[{"text":"We prove that any cyclic quadrilateral can be inscribed in any closed convex C1-curve. The smoothness condition is not required if the quadrilateral is a rectangle.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"8156","relation":"dissertation_contains"}]},"volume":6,"ec_funded":1,"file":[{"date_updated":"2020-07-14T12:47:28Z","file_size":249246,"creator":"dernst","date_created":"2019-04-30T06:14:58Z","file_name":"2018_ForumMahtematics_Akopyan.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5a71b24ba712a3eb2e46165a38fbc30a","file_id":"6356"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050-5094"]},"publication_status":"published","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6355","department":[{"_id":"UlWa"},{"_id":"HeEd"},{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:28Z","ddc":["510"],"date_updated":"2023-09-19T14:50:12Z"},{"month":"09","scopus_import":"1","publisher":"IEEE","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"In the context of robotic manipulation and grasping, the shift from a view that is static (force closure of a single posture) and contact-deprived (only contact for force closure is allowed, everything else is obstacle) towards a view that is dynamic and contact-rich (soft manipulation) has led to an increased interest in soft hands. These hands can easily exploit environmental constraints and object surfaces without risk, and safely interact with humans, but present also some challenges. Designing them is difficult, as well as predicting, modelling, and “programming” their interactions with the objects and the environment. This paper tackles the problem of simulating them in a fast and effective way, leveraging on novel and existing simulation technologies. We present a triple-layered simulation framework where dynamic properties such as stiffness are determined from slow but accurate FEM simulation data once, and then condensed into a lumped parameter model that can be used to fast simulate soft fingers and soft hands. We apply our approach to the simulation of soft pneumatic fingers."}],"date_published":"2018-09-10T00:00:00Z","doi":"10.1109/icra.2018.8461106","date_created":"2019-04-04T09:50:38Z","day":"10","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781538630815"]},"isi":1,"publication_status":"published","year":"2018","status":"public","type":"conference","conference":{"name":"ICRA: International Conference on Robotics and Automation","location":"Brisbane, Australia","end_date":"2018-05-25","start_date":"2018-05-21"},"article_number":"8461106","_id":"6195","department":[{"_id":"BeBi"}],"title":"Efficient FEM-based simulation of soft robots modeled as kinematic chains","author":[{"first_name":"Maria","last_name":"Pozzi","full_name":"Pozzi, Maria"},{"orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder"},{"first_name":"Raphael","full_name":"Deimel, Raphael","last_name":"Deimel"},{"full_name":"Malvezzi, Monica","last_name":"Malvezzi","first_name":"Monica"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"},{"first_name":"Oliver","full_name":"Brock, Oliver","last_name":"Brock"},{"full_name":"Prattichizzo, Domenico","last_name":"Prattichizzo","first_name":"Domenico"}],"article_processing_charge":"No","external_id":{"isi":["000446394503031"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-19T14:49:03Z","citation":{"chicago":"Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. https://doi.org/10.1109/icra.2018.8461106.","ista":"Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains. ICRA: International Conference on Robotics and Automation, 8461106.","mla":"Pozzi, Maria, et al. Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains. 8461106, IEEE, 2018, doi:10.1109/icra.2018.8461106.","ieee":"M. Pozzi et al., “Efficient FEM-based simulation of soft robots modeled as kinematic chains,” presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia, 2018.","short":"M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock, D. Prattichizzo, in:, IEEE, 2018.","ama":"Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:10.1109/icra.2018.8461106","apa":"Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock, O., & Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots modeled as kinematic chains. Presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia: IEEE. https://doi.org/10.1109/icra.2018.8461106"}},{"type":"conference","conference":{"start_date":"2018-02-26","location":"Nieuwpoort, Curacao","end_date":"2018-03-02","name":"FC: Financial Cryptography and Data Security"},"status":"public","_id":"6941","department":[{"_id":"KrPi"}],"date_updated":"2023-09-19T15:02:13Z","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://eprint.iacr.org/2015/528","open_access":"1"}],"month":"12","intvolume":" 10957","abstract":[{"lang":"eng","text":"Bitcoin has become the most successful cryptocurrency ever deployed, and its most distinctive feature is that it is decentralized. Its underlying protocol (Nakamoto consensus) achieves this by using proof of work, which has the drawback that it causes the consumption of vast amounts of energy to maintain the ledger. Moreover, Bitcoin mining dynamics have become less distributed over time.\r\n\r\nTowards addressing these issues, we propose SpaceMint, a cryptocurrency based on proofs of space instead of proofs of work. Miners in SpaceMint dedicate disk space rather than computation. We argue that SpaceMint’s design solves or alleviates several of Bitcoin’s issues: most notably, its large energy consumption. SpaceMint also rewards smaller miners fairly according to their contribution to the network, thus incentivizing more distributed participation.\r\n\r\nThis paper adapts proof of space to enable its use in cryptocurrency, studies the attacks that can arise against a Bitcoin-like blockchain that uses proof of space, and proposes a new blockchain format and transaction types to address these attacks. Our prototype shows that initializing 1 TB for mining takes about a day (a one-off setup cost), and miners spend on average just a fraction of a second per block mined. Finally, we provide a game-theoretic analysis modeling SpaceMint as an extensive game (the canonical game-theoretic notion for games that take place over time) and show that this stylized game satisfies a strong equilibrium notion, thereby arguing for SpaceMint ’s stability and consensus."}],"oa_version":"Submitted Version","volume":10957,"ec_funded":1,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783662583869","9783662583876"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"last_name":"Park","full_name":"Park, Sunoo","first_name":"Sunoo"},{"full_name":"Kwon, Albert","last_name":"Kwon","first_name":"Albert"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer"},{"full_name":"Gazi, Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"article_processing_charge":"No","external_id":{"isi":["000540656400026"]},"title":"SpaceMint: A cryptocurrency based on proofs of space","citation":{"ista":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. 2018. SpaceMint: A cryptocurrency based on proofs of space. 22nd International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 10957, 480–499.","chicago":"Park, Sunoo, Albert Kwon, Georg Fuchsbauer, Peter Gazi, Joel F Alwen, and Krzysztof Z Pietrzak. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” In 22nd International Conference on Financial Cryptography and Data Security, 10957:480–99. Springer Nature, 2018. https://doi.org/10.1007/978-3-662-58387-6_26.","apa":"Park, S., Kwon, A., Fuchsbauer, G., Gazi, P., Alwen, J. F., & Pietrzak, K. Z. (2018). SpaceMint: A cryptocurrency based on proofs of space. In 22nd International Conference on Financial Cryptography and Data Security (Vol. 10957, pp. 480–499). Nieuwpoort, Curacao: Springer Nature. https://doi.org/10.1007/978-3-662-58387-6_26","ama":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. SpaceMint: A cryptocurrency based on proofs of space. In: 22nd International Conference on Financial Cryptography and Data Security. Vol 10957. Springer Nature; 2018:480-499. doi:10.1007/978-3-662-58387-6_26","ieee":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J. F. Alwen, and K. Z. Pietrzak, “SpaceMint: A cryptocurrency based on proofs of space,” in 22nd International Conference on Financial Cryptography and Data Security, Nieuwpoort, Curacao, 2018, vol. 10957, pp. 480–499.","short":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J.F. Alwen, K.Z. Pietrzak, in:, 22nd International Conference on Financial Cryptography and Data Security, Springer Nature, 2018, pp. 480–499.","mla":"Park, Sunoo, et al. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” 22nd International Conference on Financial Cryptography and Data Security, vol. 10957, Springer Nature, 2018, pp. 480–99, doi:10.1007/978-3-662-58387-6_26."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"480-499","date_published":"2018-12-07T00:00:00Z","doi":"10.1007/978-3-662-58387-6_26","date_created":"2019-10-14T06:35:38Z","isi":1,"year":"2018","day":"07","publication":"22nd International Conference on Financial Cryptography and Data Security"},{"publisher":"Rockefeller University Press","quality_controlled":"1","oa":1,"page":"1869–1890","doi":"10.1084/jem.20170896","date_published":"2018-06-06T00:00:00Z","date_created":"2019-05-28T12:36:47Z","isi":1,"has_accepted_license":"1","year":"2018","day":"06","publication":"The Journal of Experimental Medicine","author":[{"first_name":"Federica","last_name":"Moalli","full_name":"Moalli, Federica"},{"last_name":"Ficht","full_name":"Ficht, Xenia","first_name":"Xenia"},{"last_name":"Germann","full_name":"Germann, Philipp","first_name":"Philipp"},{"first_name":"Mykhailo","full_name":"Vladymyrov, Mykhailo","last_name":"Vladymyrov"},{"first_name":"Bettina","full_name":"Stolp, Bettina","last_name":"Stolp"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"de Vries, Ingrid","last_name":"de Vries"},{"first_name":"Ruth","last_name":"Lyck","full_name":"Lyck, Ruth"},{"first_name":"Jasmin","last_name":"Balmer","full_name":"Balmer, Jasmin"},{"full_name":"Fiocchi, Amleto","last_name":"Fiocchi","first_name":"Amleto"},{"last_name":"Kreutzfeldt","full_name":"Kreutzfeldt, Mario","first_name":"Mario"},{"last_name":"Merkler","full_name":"Merkler, Doron","first_name":"Doron"},{"last_name":"Iannacone","full_name":"Iannacone, Matteo","first_name":"Matteo"},{"first_name":"Akitaka","full_name":"Ariga, Akitaka","last_name":"Ariga"},{"full_name":"Stoffel, Michael H.","last_name":"Stoffel","first_name":"Michael H."},{"first_name":"James","last_name":"Sharpe","full_name":"Sharpe, James"},{"first_name":"Martin","last_name":"Bähler","full_name":"Bähler, Martin"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, Alba","first_name":"Alba"},{"first_name":"Jens V.","last_name":"Stein","full_name":"Stein, Jens V."}],"article_processing_charge":"No","external_id":{"isi":["000440822900011"]},"title":"The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells","citation":{"ista":"Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2015(7), 1869–1890.","chicago":"Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20170896.","short":"F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R. Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga, M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal of Experimental Medicine 2015 (2018) 1869–1890.","ieee":"F. Moalli et al., “The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells,” The Journal of Experimental Medicine, vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018.","ama":"Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2018;2015(7):1869–1890. doi:10.1084/jem.20170896","apa":"Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I., … Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20170896","mla":"Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine, vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:10.1084/jem.20170896."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"06","intvolume":" 2015","abstract":[{"lang":"eng","text":"T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations."}],"oa_version":"Published Version","issue":"7","volume":2015,"publication_identifier":{"issn":["0022-1007"],"eissn":["1540-9538"]},"publication_status":"published","file":[{"checksum":"86ae5331f9bfced9a6358a790a04bef4","file_id":"6498","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-05-28T12:40:05Z","file_name":"2018_rupress_Moalli.pdf","date_updated":"2020-07-14T12:47:32Z","file_size":3841660,"creator":"kschuh"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","_id":"6497","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:32Z","date_updated":"2023-09-19T14:52:08Z","ddc":["570"]},{"day":"01","publication":"EMBO reports","isi":1,"has_accepted_license":"1","year":"2018","date_published":"2018-09-01T00:00:00Z","doi":"10.15252/embr.201845836","date_created":"2019-05-28T13:16:08Z","publisher":"EMBO","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 2018;19(9). doi:10.15252/embr.201845836","apa":"Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., & Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO Reports. EMBO. https://doi.org/10.15252/embr.201845836","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” EMBO reports, vol. 19, no. 9. EMBO, 2018.","mla":"Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports, vol. 19, no. 9, e45836, EMBO, 2018, doi:10.15252/embr.201845836.","ista":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836.","chicago":"Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports. EMBO, 2018. https://doi.org/10.15252/embr.201845836."},"title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","author":[{"first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt"},{"full_name":"Maidorn, Manuel","last_name":"Maidorn","first_name":"Manuel"},{"last_name":"Crzan","full_name":"Crzan, Dagmar","first_name":"Dagmar"},{"full_name":"Wildhagen, Hanna","last_name":"Wildhagen","first_name":"Hanna"},{"first_name":"Selda","full_name":"Kabatas, Selda","last_name":"Kabatas"},{"first_name":"Silvio O","last_name":"Rizzoli","full_name":"Rizzoli, Silvio O"}],"external_id":{"isi":["000443682200009"]},"article_processing_charge":"No","article_number":"e45836","file":[{"file_size":2005572,"date_updated":"2020-07-14T12:47:32Z","creator":"kschuh","file_name":"2018_embo_Truckenbrodt.pdf","date_created":"2019-05-28T13:17:19Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6500","checksum":"6ec90abc637f09cca3a7b6424d7e7a26"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"publication_status":"published","volume":19,"issue":"9","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge."}],"month":"09","intvolume":" 19","scopus_import":"1","ddc":["580"],"date_updated":"2023-09-19T14:52:32Z","department":[{"_id":"JoDa"}],"file_date_updated":"2020-07-14T12:47:32Z","_id":"6499","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"quality_controlled":"1","publisher":"ACM","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.04947"}],"oa":1,"month":"01","abstract":[{"lang":"eng","text":"Population protocols are a popular model of distributed computing, in which n agents with limited local state interact randomly, and cooperate to collectively compute global predicates. Inspired by recent developments in DNA programming, an extensive series of papers, across different communities, has examined the computability and complexity characteristics of this model. Majority, or consensus, is a central task in this model, in which agents need to collectively reach a decision as to which one of two states A or B had a higher initial count. Two metrics are important: the time that a protocol requires to stabilize to an output decision, and the state space size that each agent requires to do so. It is known that majority requires Ω(log log n) states per agent to allow for fast (poly-logarithmic time) stabilization, and that O(log2 n) states are sufficient. Thus, there is an exponential gap between the space upper and lower bounds for this problem. This paper addresses this question.\r\n\r\nOn the negative side, we provide a new lower bound of Ω(log n) states for any protocol which stabilizes in O(n1–c) expected time, for any constant c > 0. This result is conditional on monotonicity and output assumptions, satisfied by all known protocols. Technically, it represents a departure from previous lower bounds, in that it does not rely on the existence of dense configurations. Instead, we introduce a new generalized surgery technique to prove the existence of incorrect executions for any algorithm which would contradict the lower bound. Subsequently, our lower bound also applies to general initial configurations, including ones with a leader. On the positive side, we give a new algorithm for majority which uses O(log n) states, and stabilizes in O(log2 n) expected time. Central to the algorithm is a new leaderless phase clock technique, which allows agents to synchronize in phases of Θ(n log n) consecutive interactions using O(log n) states per agent, exploiting a new connection between population protocols and power-of-two-choices load balancing mechanisms. We also employ our phase clock to build a leader election algorithm with a state space of size O(log n), which stabilizes in O(log2 n) expected time."}],"oa_version":"Preprint","page":"2221-2239","date_published":"2018-01-30T00:00:00Z","doi":"10.1137/1.9781611975031.144","date_created":"2019-11-26T15:10:55Z","isi":1,"publication_identifier":{"isbn":["9781611975031"]},"publication_status":"published","year":"2018","day":"30","publication":"Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms","language":[{"iso":"eng"}],"type":"conference","conference":{"start_date":"2018-01-07","location":"New Orleans, LA, United States","end_date":"2018-01-10","name":"SODA: Symposium on Discrete Algorithms"},"status":"public","_id":"7123","author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"}],"external_id":{"arxiv":["1704.04947"],"isi":["000483921200145"]},"article_processing_charge":"No","department":[{"_id":"DaAl"}],"title":"Space-optimal majority in population protocols","date_updated":"2023-09-19T15:03:16Z","citation":{"ama":"Alistarh D-A, Aspnes J, Gelashvili R. Space-optimal majority in population protocols. In: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms. ACM; 2018:2221-2239. doi:10.1137/1.9781611975031.144","apa":"Alistarh, D.-A., Aspnes, J., & Gelashvili, R. (2018). Space-optimal majority in population protocols. In Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 2221–2239). New Orleans, LA, United States: ACM. https://doi.org/10.1137/1.9781611975031.144","short":"D.-A. Alistarh, J. Aspnes, R. Gelashvili, in:, Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–2239.","ieee":"D.-A. Alistarh, J. Aspnes, and R. Gelashvili, “Space-optimal majority in population protocols,” in Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA, United States, 2018, pp. 2221–2239.","mla":"Alistarh, Dan-Adrian, et al. “Space-Optimal Majority in Population Protocols.” Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–39, doi:10.1137/1.9781611975031.144.","ista":"Alistarh D-A, Aspnes J, Gelashvili R. 2018. Space-optimal majority in population protocols. Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 2221–2239.","chicago":"Alistarh, Dan-Adrian, James Aspnes, and Rati Gelashvili. “Space-Optimal Majority in Population Protocols.” In Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, 2221–39. ACM, 2018. https://doi.org/10.1137/1.9781611975031.144."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"has_accepted_license":"1","isi":1,"year":"2018","day":"20","publication":"Evolution Letters","page":"297-309","doi":"10.1002/evl3.74","date_published":"2018-08-20T00:00:00Z","date_created":"2021-08-16T07:45:38Z","acknowledgement":"We are very grateful to people who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot and Irena Senčić. We would also like to thank Magnus Alm Rosenblad and Mats Töpel for their contribution to assembling the Littorina saxatilis genome, Carl André, Pasi Rastas, and Romain Villoutreix for discussion, and two anonymous reviewers for their helpful comments on the manuscript. We are grateful to RapidGenomics for library preparation and sequencing. We thank the Natural Environment Research Council, the European Research Council and the Swedish Research Councils VR and Formas (Linnaeus grant to the Centre for Marine Evolutionary Biology and Tage Erlander Guest Professorship) for funding. P.C. was funded by the University of Sheffield Vice-chancellor's India scholarship. R.F. is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 706376. M. Raf. was supported by the Adlerbert Research Foundation.","quality_controlled":"1","publisher":"Wiley","oa":1,"citation":{"ama":"Westram AM, Rafajlović M, Chaube P, et al. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. 2018;2(4):297-309. doi:10.1002/evl3.74","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.74","ieee":"A. M. Westram et al., “Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow,” Evolution Letters, vol. 2, no. 4. Wiley, pp. 297–309, 2018.","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, Evolution Letters 2 (2018) 297–309.","mla":"Westram, Anja M., et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Evolution Letters, vol. 2, no. 4, Wiley, 2018, pp. 297–309, doi:10.1002/evl3.74.","ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. 2(4), 297–309.","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Evolution Letters. Wiley, 2018. https://doi.org/10.1002/evl3.74."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"last_name":"Chaube","full_name":"Chaube, Pragya","first_name":"Pragya"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Larsson","full_name":"Larsson, Tomas","first_name":"Tomas"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"last_name":"Blomberg","full_name":"Blomberg, Anders","first_name":"Anders"},{"last_name":"Mehlig","full_name":"Mehlig, Bernhard","first_name":"Bernhard"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"article_processing_charge":"Yes","external_id":{"isi":["000446774400004"],"pmid":["30283683"]},"title":"Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow","publication_identifier":{"eissn":["2056-3744"],"issn":["2056-3744"]},"publication_status":"published","file":[{"date_created":"2021-08-16T07:48:03Z","file_name":"2018_EvolutionLetters_Westram.pdf","date_updated":"2021-08-16T07:48:03Z","file_size":764299,"creator":"asandaue","checksum":"8524e72507d521416be3f8ccfcd5e3f5","file_id":"9918","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"4","related_material":{"record":[{"status":"public","id":"9930","relation":"research_data"}]},"volume":2,"abstract":[{"text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","month":"08","intvolume":" 2","date_updated":"2023-09-19T15:08:25Z","ddc":["570"],"file_date_updated":"2021-08-16T07:48:03Z","department":[{"_id":"BeVi"}],"_id":"9917","type":"journal_article","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"citation":{"ieee":"J. Hollander et al., “Are assortative mating and genital divergence driven by reinforcement?,” Evolution Letters, vol. 2, no. 6. Wiley, pp. 557–566, 2018.","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, Evolution Letters 2 (2018) 557–566.","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. 2018;2(6):557-566. doi:10.1002/evl3.85","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. Wiley. https://doi.org/10.1002/evl3.85","mla":"Hollander, Johan, et al. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Evolution Letters, vol. 2, no. 6, Wiley, 2018, pp. 557–66, doi:10.1002/evl3.85.","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. 2(6), 557–566.","chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Evolution Letters. Wiley, 2018. https://doi.org/10.1002/evl3.85."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Johan","full_name":"Hollander, Johan","last_name":"Hollander"},{"first_name":"Mauricio","last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio"},{"full_name":"Bianco, Giuseppe","last_name":"Bianco","first_name":"Giuseppe"},{"last_name":"Yang","full_name":"Yang, Xi","first_name":"Xi"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Duvaux, Ludovic","last_name":"Duvaux","first_name":"Ludovic"},{"first_name":"David G.","last_name":"Reid","full_name":"Reid, David G."},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"article_processing_charge":"Yes","external_id":{"pmid":["30564439"],"isi":["000452990000002"]},"title":"Are assortative mating and genital divergence driven by reinforcement?","acknowledgement":"The authors express a special thanks to Dr Richard Willan at the Museum and Art Gallery of the Northern Territory for guidance and support in the field, and to Carole Smadja for reading and commenting on the manuscript. The authors thank the Government of Western Australia Department of Parks and Wildlife (license no. 009254) and Fishery Research Division (exemption no. 2262) for assistance with permits. Khalid Belkhir modified the coalescent sampler msnsam for the specific needs of this project and Martin Hirsch helped to set up the ABC pipeline and to modify the summary statistic calculator mscalc. The authors are grateful to the Crafoord Foundation for supporting this project. R.K.B., A.M.W., and L.D. were supported by grants from the Natural Environment Research Council, R.K.B. and A.M.W. were also supported by the European Research Council and R.K.B. and L.D. by the Leverhulme Trust. M.M.R. was supported by Consejo Nacional de Ciencia y Tecnología and Secretaría de Educación Pública, Mexico. G.B. was supported by the Centre for Animal Movement Research (CAnMove) financed by a Linnaeus grant (No. 349-2007-8690) from the Swedish Research Council and Lund University.","publisher":"Wiley","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"13","publication":"Evolution Letters","page":"557-566","date_published":"2018-12-13T00:00:00Z","doi":"10.1002/evl3.85","date_created":"2021-08-16T07:30:00Z","_id":"9915","type":"journal_article","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-19T15:08:53Z","ddc":["570"],"file_date_updated":"2021-08-16T07:37:28Z","department":[{"_id":"BeVi"}],"abstract":[{"text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","month":"12","intvolume":" 2","publication_identifier":{"eissn":["2056-3744"],"issn":[" 2056-3744"]},"publication_status":"published","file":[{"creator":"asandaue","file_size":584606,"date_updated":"2021-08-16T07:37:28Z","file_name":"2018_EvolutionLetters_Hollander.pdf","date_created":"2021-08-16T07:37:28Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"997a78ac41c809975ca69cbdea441f88","file_id":"9916"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9929","status":"public","relation":"research_data"}]},"volume":2,"issue":"6"},{"ddc":["570"],"date_updated":"2023-09-19T15:04:49Z","department":[{"_id":"JoDa"}],"file_date_updated":"2020-10-06T16:35:16Z","_id":"8618","status":"public","keyword":["Multidisciplinary"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"8619","checksum":"e642080fcbde9584c63544f587c74f03","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-06T16:35:16Z","file_name":"2018_ScientificReports_Gregor.pdf","date_updated":"2020-10-06T16:35:16Z","file_size":2818077,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2045-2322"]},"publication_status":"published","volume":8,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting.","lang":"eng"}],"month":"02","intvolume":" 8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” Scientific Reports. Springer Nature, 2018. https://doi.org/10.1038/s41598-018-19947-1.","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., & Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-018-19947-1","ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 2018;8. doi:10.1038/s41598-018-19947-1","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” Scientific Reports, vol. 8. Springer Nature, 2018.","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” Scientific Reports, vol. 8, 2724, Springer Nature, 2018, doi:10.1038/s41598-018-19947-1."},"title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","author":[{"first_name":"Carola","full_name":"Gregor, Carola","last_name":"Gregor"},{"first_name":"Sven C.","full_name":"Sidenstein, Sven C.","last_name":"Sidenstein"},{"first_name":"Martin","last_name":"Andresen","full_name":"Andresen, Martin"},{"first_name":"Steffen J.","full_name":"Sahl, Steffen J.","last_name":"Sahl"},{"last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan W.","last_name":"Hell","full_name":"Hell, Stefan W."}],"article_processing_charge":"No","external_id":{"isi":["000424630400037"],"pmid":["29426833"]},"article_number":"2724","day":"09","publication":"Scientific Reports","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-02-09T00:00:00Z","doi":"10.1038/s41598-018-19947-1","date_created":"2020-10-06T16:33:37Z","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"department":[{"_id":"JiFr"}],"date_updated":"2023-09-19T15:10:43Z","keyword":["Plant Science","Physiology"],"status":"public","article_type":"original","type":"journal_article","_id":"10881","ec_funded":1,"issue":"9","volume":69,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"intvolume":" 69","month":"04","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants.","lang":"eng"}],"title":"Molecular evolution and diversification of the SMXL gene family","article_processing_charge":"No","external_id":{"isi":["000430727000016"],"pmid":["29538714"]},"author":[{"first_name":"Taraka Ramji","last_name":"Moturu","full_name":"Moturu, Taraka Ramji"},{"full_name":"Thula, Sravankumar","last_name":"Thula","first_name":"Sravankumar"},{"first_name":"Ravi Kumar","full_name":"Singh, Ravi Kumar","last_name":"Singh"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Radka Svobodová","full_name":"Vařeková, Radka Svobodová","last_name":"Vařeková"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery097.","ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” Journal of Experimental Botany, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:10.1093/jxb/ery097.","ieee":"T. R. Moturu et al., “Molecular evolution and diversification of the SMXL gene family,” Journal of Experimental Botany, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.","apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., & Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery097","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 2018;69(9):2367-2378. doi:10.1093/jxb/ery097"},"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"date_created":"2022-03-18T12:43:22Z","date_published":"2018-04-13T00:00:00Z","doi":"10.1093/jxb/ery097","page":"2367-2378","publication":"Journal of Experimental Botany","day":"13","year":"2018","isi":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. "},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bfgp/ely007"}],"scopus_import":"1","intvolume":" 17","month":"09","abstract":[{"lang":"eng","text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation."}],"pmid":1,"oa_version":"Published Version","volume":17,"issue":"5","publication_status":"published","publication_identifier":{"eissn":["2041-2657"],"issn":["2041-2649"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"status":"public","_id":"10880","department":[{"_id":"CaHe"}],"date_updated":"2023-09-19T15:11:22Z","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","page":"329-338","date_created":"2022-03-18T12:40:35Z","doi":"10.1093/bfgp/ely007","date_published":"2018-09-01T00:00:00Z","year":"2018","isi":1,"publication":"Briefings in Functional Genomics","day":"01","external_id":{"pmid":["29579140"],"isi":["000456054400004"]},"article_processing_charge":"No","author":[{"last_name":"Yuuta","orcid":"0000-0002-2853-8051","full_name":"Yuuta, Moriyama","first_name":"Moriyama","id":"4968E7C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kazuko","last_name":"Koshiba-Takeuchi","full_name":"Koshiba-Takeuchi, Kazuko"}],"title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","citation":{"chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional Genomics. Oxford University Press, 2018. https://doi.org/10.1093/bfgp/ely007.","ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338.","mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional Genomics, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:10.1093/bfgp/ely007.","ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 2018;17(5):329-338. doi:10.1093/bfgp/ely007","apa":"Yuuta, M., & Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. Oxford University Press. https://doi.org/10.1093/bfgp/ely007","short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338.","ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” Briefings in Functional Genomics, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-19T15:08:24Z","citation":{"ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow, Dryad, 10.5061/dryad.bp25b65.","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018. https://doi.org/10.5061/dryad.bp25b65.","ama":"Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. 2018. doi:10.5061/dryad.bp25b65","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. Dryad. https://doi.org/10.5061/dryad.bp25b65","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018).","ieee":"A. M. Westram et al., “Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.","mla":"Westram, Anja M., et al. Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow. Dryad, 2018, doi:10.5061/dryad.bp25b65."},"title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","department":[{"_id":"BeVi"}],"author":[{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"first_name":"Pragya","full_name":"Chaube, Pragya","last_name":"Chaube"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Blomberg","full_name":"Blomberg, Anders","first_name":"Anders"},{"first_name":"Bernhard","last_name":"Mehlig","full_name":"Mehlig, Bernhard"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"article_processing_charge":"No","_id":"9930","status":"public","type":"research_data_reference","day":"23","year":"2018","date_published":"2018-07-23T00:00:00Z","doi":"10.5061/dryad.bp25b65","related_material":{"record":[{"relation":"used_in_publication","id":"9917","status":"public"}]},"date_created":"2021-08-17T08:58:47Z","oa_version":"Published Version","abstract":[{"text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.","lang":"eng"}],"month":"07","publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.bp25b65","open_access":"1"}]},{"related_material":{"record":[{"id":"9915","status":"public","relation":"used_in_publication"}]},"doi":"10.5061/dryad.51sd2p5","date_published":"2018-10-17T00:00:00Z","date_created":"2021-08-17T08:51:06Z","day":"17","year":"2018","month":"10","publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.51sd2p5","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favour reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence.","lang":"eng"}],"title":"Data from: Are assortative mating and genital divergence driven by reinforcement?","department":[{"_id":"BeVi"}],"author":[{"full_name":"Hollander, Johan","last_name":"Hollander","first_name":"Johan"},{"last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio","first_name":"Mauricio"},{"first_name":"Giuseppe","full_name":"Bianco, Giuseppe","last_name":"Bianco"},{"first_name":"Xi","last_name":"Yang","full_name":"Yang, Xi"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"},{"last_name":"Duvaux","full_name":"Duvaux, Ludovic","first_name":"Ludovic"},{"first_name":"David G.","full_name":"Reid, David G.","last_name":"Reid"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-19T15:08:53Z","citation":{"chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Dryad, 2018. https://doi.org/10.5061/dryad.51sd2p5.","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Data from: Are assortative mating and genital divergence driven by reinforcement?, Dryad, 10.5061/dryad.51sd2p5.","mla":"Hollander, Johan, et al. Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement? Dryad, 2018, doi:10.5061/dryad.51sd2p5.","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, (2018).","ieee":"J. Hollander et al., “Data from: Are assortative mating and genital divergence driven by reinforcement?” Dryad, 2018.","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Data from: Are assortative mating and genital divergence driven by reinforcement? 2018. doi:10.5061/dryad.51sd2p5","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Data from: Are assortative mating and genital divergence driven by reinforcement? Dryad. https://doi.org/10.5061/dryad.51sd2p5"},"status":"public","type":"research_data_reference","_id":"9929"},{"status":"public","conference":{"name":"CVF: Conference on Computer Vision and Pattern Recognition","start_date":"2018-06-18","end_date":"2018-06-23","location":"Salt Lake City, UT, United States"},"type":"conference","_id":"10882","department":[{"_id":"ChLa"}],"date_updated":"2023-09-19T15:11:49Z","month":"12","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1712.08087","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger."}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781538664209"],"eissn":["2575-7075"]},"title":"Learning intelligent dialogs for bounding box annotation","external_id":{"arxiv":["1712.08087"],"isi":["000457843609036"]},"article_processing_charge":"No","author":[{"full_name":"Uijlings, Jasper","last_name":"Uijlings","first_name":"Jasper"},{"first_name":"Ksenia","full_name":"Konyushkova, Ksenia","last_name":"Konyushkova"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"},{"first_name":"Vittorio","full_name":"Ferrari, Vittorio","last_name":"Ferrari"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, United States, 2018, pp. 9175–9184.","ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:9175-9184. doi:10.1109/cvpr.2018.00956","apa":"Uijlings, J., Konyushkova, K., Lampert, C., & Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. https://doi.org/10.1109/cvpr.2018.00956","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–84, doi:10.1109/cvpr.2018.00956.","ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 9175–84. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00956."},"oa":1,"quality_controlled":"1","publisher":"IEEE","date_created":"2022-03-18T12:45:09Z","date_published":"2018-12-17T00:00:00Z","doi":"10.1109/cvpr.2018.00956","page":"9175-9184","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","day":"17","year":"2018","isi":1},{"volume":2018,"language":[{"iso":"eng"}],"publication_status":"published","month":"12","intvolume":" 2018","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.08917","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of m machines which allegedly compute stochastic gradients every iteration, an α-fraction are Byzantine, and may behave adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations. In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sample complexity and time complexity.","lang":"eng"}],"department":[{"_id":"DaAl"}],"date_updated":"2023-09-19T15:12:45Z","status":"public","type":"conference","conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","start_date":"2018-12-02","end_date":"2018-12-08","location":"Montreal, Canada"},"_id":"6558","date_published":"2018-12-01T00:00:00Z","date_created":"2019-06-13T08:22:37Z","page":"4613-4623","day":"01","publication":"Advances in Neural Information Processing Systems","isi":1,"year":"2018","quality_controlled":"1","publisher":"Neural Information Processing Systems Foundation","oa":1,"title":"Byzantine stochastic gradient descent","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"Zeyuan","full_name":"Allen-Zhu, Zeyuan","last_name":"Allen-Zhu"},{"full_name":"Li, Jerry","last_name":"Li","first_name":"Jerry"}],"article_processing_charge":"No","external_id":{"isi":["000461823304061"],"arxiv":["1803.08917"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic Gradient Descent.” In Advances in Neural Information Processing Systems, 2018:4613–23. Neural Information Processing Systems Foundation, 2018.","ista":"Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 2018, 4613–4623.","mla":"Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” Advances in Neural Information Processing Systems, vol. 2018, Neural Information Processing Systems Foundation, 2018, pp. 4613–23.","apa":"Alistarh, D.-A., Allen-Zhu, Z., & Li, J. (2018). Byzantine stochastic gradient descent. In Advances in Neural Information Processing Systems (Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems Foundation.","ama":"Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In: Advances in Neural Information Processing Systems. Vol 2018. Neural Information Processing Systems Foundation; 2018:4613-4623.","ieee":"D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 2018, pp. 4613–4623.","short":"D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018, pp. 4613–4623."}},{"abstract":[{"lang":"eng","text":"The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, co-independent, compact, local, linear, and binary, with the following caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1602.03124","open_access":"1"}],"scopus_import":"1","intvolume":" 15","month":"12","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1192"}]},"volume":15,"issue":"2","_id":"6032","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-20T11:20:26Z","department":[{"_id":"VlKo"}],"oa":1,"publisher":"ACM","quality_controlled":"1","year":"2018","isi":1,"publication":"ACM Transactions on Algorithms","day":"01","date_created":"2019-02-17T22:59:25Z","doi":"10.1145/3230649","date_published":"2018-12-01T00:00:00Z","article_number":"22","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms. ACM, 2018. https://doi.org/10.1145/3230649.","ista":"Kazda A, Kolmogorov V, Rolinek M. 2018. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 15(2), 22.","mla":"Kazda, Alexandr, et al. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms, vol. 15, no. 2, 22, ACM, 2018, doi:10.1145/3230649.","ama":"Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 2018;15(2). doi:10.1145/3230649","apa":"Kazda, A., Kolmogorov, V., & Rolinek, M. (2018). Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3230649","ieee":"A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar boolean CSPs,” ACM Transactions on Algorithms, vol. 15, no. 2. ACM, 2018.","short":"A. Kazda, V. Kolmogorov, M. Rolinek, ACM Transactions on Algorithms 15 (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1602.03124"],"isi":["000468036500007"]},"author":[{"last_name":"Kazda","full_name":"Kazda, Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr"},{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rolinek, Michal","last_name":"Rolinek"}],"title":"Even delta-matroids and the complexity of planar boolean CSPs"},{"page":"146","date_published":"2018-02-21T00:00:00Z","doi":"10.15479/AT:ISTA:th_963","date_created":"2018-12-11T11:45:10Z","has_accepted_license":"1","year":"2018","day":"21","publisher":"Institute of Science and Technology Austria","oa":1,"publist_id":"7713","author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682"}],"article_processing_charge":"No","title":"Inferring recent demography from spatial genetic structure","citation":{"mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963","apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"563","status":"public","relation":"part_of_dissertation"},{"id":"1074","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"checksum":"8cc534d2b528ae017acf80874cce48c9","file_id":"5111","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:55Z","file_name":"IST-2018-963-v1+1_thesis.pdf","date_updated":"2020-07-14T12:45:23Z","file_size":5792935,"creator":"system"},{"checksum":"6af18d7e5a7e2728ceda2f41ee24f628","file_id":"6224","content_type":"application/zip","access_level":"closed","relation":"source_file","date_created":"2019-04-05T09:30:12Z","file_name":"2018_thesis_ringbauer_source.zip","date_updated":"2020-07-14T12:45:23Z","file_size":113365,"creator":"dernst"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"02","abstract":[{"lang":"eng","text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm."}],"oa_version":"Published Version","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:23Z","supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-20T12:00:56Z","ddc":["576"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","pubrep_id":"963","_id":"200"},{"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"first_name":"Alexey","last_name":"Balitskiy","full_name":"Balitskiy, Alexey"},{"first_name":"Mikhail","full_name":"Grigorev, Mikhail","last_name":"Grigorev"}],"publist_id":"6324","external_id":{"isi":["000432205500011"]},"article_processing_charge":"Yes (via OA deal)","title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","citation":{"ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 59(4), 1001–1009.","chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational Geometry. Springer, 2018. https://doi.org/10.1007/s00454-017-9883-x.","ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 2018;59(4):1001-1009. doi:10.1007/s00454-017-9883-x","apa":"Akopyan, A., Balitskiy, A., & Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9883-x","short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete & Computational Geometry 59 (2018) 1001–1009.","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” Discrete & Computational Geometry, vol. 59, no. 4. Springer, pp. 1001–1009, 2018.","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational Geometry, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:10.1007/s00454-017-9883-x."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"1001-1009","date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s00454-017-9883-x","date_created":"2018-12-11T11:49:57Z","isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Discrete & Computational Geometry","publisher":"Springer","quality_controlled":"1","oa":1,"department":[{"_id":"HeEd"}],"file_date_updated":"2019-01-18T09:27:36Z","date_updated":"2023-09-20T12:08:51Z","ddc":["516","000"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"1064","volume":59,"issue":"4","ec_funded":1,"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"publication_status":"published","file":[{"date_created":"2019-01-18T09:27:36Z","file_name":"2018_DiscreteComp_Akopyan.pdf","date_updated":"2019-01-18T09:27:36Z","file_size":482518,"creator":"dernst","file_id":"5844","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 59","abstract":[{"text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets.","lang":"eng"}],"oa_version":"Published Version"},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"08","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:46:22Z","date_published":"2018-01-08T00:00:00Z","doi":"10.15479/AT:ISTA:th_913","page":"107","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria.","chicago":"Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation and Survival .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_913.","short":"E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation and Survival , Institute of Science and Technology Austria, 2018.","ieee":"E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation and survival ,” Institute of Science and Technology Austria, 2018.","apa":"Gschaider-Reichhart, E. (2018). Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_913","ama":"Gschaider-Reichhart E. Optical and optogenetic control of proliferation and survival . 2018. doi:10.15479/AT:ISTA:th_913","mla":"Gschaider-Reichhart, Eva. Optical and Optogenetic Control of Proliferation and Survival . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_913."},"title":"Optical and optogenetic control of proliferation and survival ","article_processing_charge":"No","author":[{"id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart"}],"publist_id":"7405","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The aim of this thesis was the development of new strategies for optical and optogenetic control of proliferative and pro-survival signaling, and characterizing them from the molecular mechanism up to cellular effects. These new light-based methods have unique features, such as red light as an activator, or the avoidance of gene delivery, which enable to overcome current limitations, such as light delivery to target tissues and feasibility as therapeutic approach. A special focus was placed on implementing these new light-based approaches in pancreatic β-cells, as β-cells are the key players in diabetes and especially their loss in number negatively affects disease progression. Currently no treatment options are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn a first approach, red-light-activated growth factor receptors, in particular receptor tyrosine kinases were engineered and characterized. Receptor activation with light allows spatio-temporal control compared to ligand-based activation, and especially red light exhibits deeper tissue penetration than other wavelengths of the visible spectrum. Red-light-activated receptor tyrosine kinases robustly activated major growth factor related signaling pathways with a high temporal resolution. Moreover, the remote activation of the proliferative MAPK/Erk pathway by red-light-activated receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine kinases are particularly attractive for applications in animal models due to the deep tissue penetration of red light, a drawback, especially with regard to translation into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous light-sensitive mechanism was identified and its potential to promote proliferative and pro-survival signals was explored, towards light-based tissue regeneration without the need for gene transfer. Blue-green light illumination was found to be sufficient for the activation of proliferation and survival promoting signaling pathways in primary pancreatic murine and human islets. Blue-green light also led to an increase in proliferation of primary islet cells, an effect which was shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated that this approach of pancreatic β-cell expansion did not have any negative effect on the β-cell function, in particular on their insulin secretion capacity. In contrast, a trend for enhanced insulin secretion under high glucose conditions after illumination was detected. In order to unravel the detailed characteristics of this endogenous light-sensitive mechanism, the precise light requirements were determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin, was detected. The observed effects were found to be independent of handling effects such as temperature differences and cytochrome c oxidase dependent ATP increase, but they were found to be enhanced through the knockout of OPN3. The exact mechanism of how islets cells sense light and the identity of the photoreceptor remains unknown.\r\nSummarized two new light-based systems with unique features were established that enable the activation of proliferative and pro-survival signaling pathways. While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics research, by allowing non-invasive control of signaling in vivo, the identified endogenous light-sensitive mechanism has the potential to be the basis of a gene therapy-free therapeutical approach for light-based β-cell expansion."}],"month":"01","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","checksum":"697fa72ca36fb1b8ceabc133d58a73e5","file_id":"6222","date_updated":"2020-07-14T12:46:24Z","file_size":7012495,"creator":"dernst","date_created":"2019-04-05T09:28:03Z","file_name":"2018_THESIS_Gschaider-Reichhart_source.docx"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6223","checksum":"58d7d1e9e58aeb7f061ab686b1d8a48c","date_updated":"2020-07-14T12:46:24Z","file_size":6355280,"creator":"dernst","date_created":"2019-04-05T09:28:03Z","file_name":"2018_THESIS_Gschaider-Reichhart.pdf"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"1441","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1678"},{"relation":"part_of_dissertation","status":"public","id":"2084"},{"relation":"part_of_dissertation","id":"1028","status":"public"}]},"_id":"418","pubrep_id":"913","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["571","570"],"date_updated":"2023-09-22T09:20:10Z","supervisor":[{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"}],"department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:46:24Z"},{"main_file_link":[{"url":"https://arxiv.org/abs/1608.05163","open_access":"1"}],"scopus_import":"1","intvolume":" 2018","month":"05","abstract":[{"lang":"eng","text":"We prove a new central limit theorem (CLT) for the difference of linear eigenvalue statistics of a Wigner random matrix H and its minor H and find that the fluctuation is much smaller than the fluctuations of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of H and H. In particular, our theorem identifies the fluctuation of Kerov's rectangular Young diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel measure follow the same limiting shape. For this, algebraically motivated, ensemble a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar to our result but the variance is different, indicating that the analogy between the two models has its limitations. Moreover, our theorem shows that Borodin's result [7] on the convergence of the spectral distribution of Wigner matrices to a Gaussian free field also holds in derivative sense."}],"oa_version":"Preprint","ec_funded":1,"volume":2018,"issue":"10","related_material":{"record":[{"status":"public","id":"6179","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"issn":["10737928"]},"language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1012","department":[{"_id":"LaEr"}],"date_updated":"2023-09-22T09:44:21Z","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","page":"3255-3298","date_created":"2018-12-11T11:49:41Z","date_published":"2018-05-18T00:00:00Z","doi":"10.1093/imrn/rnw330","year":"2018","isi":1,"publication":"International Mathematics Research Notices","day":"18","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"external_id":{"arxiv":["1608.05163"],"isi":["000441668300009"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"}],"publist_id":"6383","title":"Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues","citation":{"chicago":"Erdös, László, and Dominik J Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research Notices. Oxford University Press, 2018. https://doi.org/10.1093/imrn/rnw330.","ista":"Erdös L, Schröder DJ. 2018. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. 2018(10), 3255–3298.","mla":"Erdös, László, and Dominik J. Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research Notices, vol. 2018, no. 10, Oxford University Press, 2018, pp. 3255–98, doi:10.1093/imrn/rnw330.","short":"L. Erdös, D.J. Schröder, International Mathematics Research Notices 2018 (2018) 3255–3298.","ieee":"L. Erdös and D. J. Schröder, “Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues,” International Mathematics Research Notices, vol. 2018, no. 10. Oxford University Press, pp. 3255–3298, 2018.","apa":"Erdös, L., & Schröder, D. J. (2018). Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnw330","ama":"Erdös L, Schröder DJ. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. 2018;2018(10):3255-3298. doi:10.1093/imrn/rnw330"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"title":"An abstraction-refinement methodology for reasoning about network games","author":[{"last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Avni G, Guha S, Kupferman O. 2018. An abstraction-refinement methodology for reasoning about network games. Games. 9(3), 39.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” Games. MDPI AG, 2018. https://doi.org/10.3390/g9030039.","short":"G. Avni, S. Guha, O. Kupferman, Games 9 (2018).","ieee":"G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology for reasoning about network games,” Games, vol. 9, no. 3. MDPI AG, 2018.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). An abstraction-refinement methodology for reasoning about network games. Games. MDPI AG. https://doi.org/10.3390/g9030039","ama":"Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning about network games. Games. 2018;9(3). doi:10.3390/g9030039","mla":"Avni, Guy, et al. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” Games, vol. 9, no. 3, 39, MDPI AG, 2018, doi:10.3390/g9030039."},"project":[{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"article_number":"39","date_created":"2019-02-14T14:17:54Z","date_published":"2018-09-01T00:00:00Z","doi":"10.3390/g9030039","publication":"Games","day":"01","year":"2018","has_accepted_license":"1","oa":1,"publisher":"MDPI AG","quality_controlled":"1","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:16Z","ddc":["004"],"date_updated":"2023-09-22T09:48:59Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"6006","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1003"}]},"issue":"3","volume":9,"language":[{"iso":"eng"}],"file":[{"file_name":"2018_MDPI_Avni.pdf","date_created":"2019-02-14T14:20:31Z","file_size":505155,"date_updated":"2020-07-14T12:47:16Z","creator":"kschuh","file_id":"6008","checksum":"749d65ca4ce74256a029d9644a1b1cb0","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["2073-4336"]},"intvolume":" 9","month":"09","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Network games (NGs) are played on directed graphs and are extensively used in network design and analysis. Search problems for NGs include finding special strategy profiles such as a Nash equilibrium and a globally-optimal solution. The networks modeled by NGs may be huge. In formal verification, abstraction has proven to be an extremely effective technique for reasoning about systems with big and even infinite state spaces. We describe an abstraction-refinement methodology for reasoning about NGs. Our methodology is based on an abstraction function that maps the state space of an NG to a much smaller state space. We search for a global optimum and a Nash equilibrium by reasoning on an under- and an over-approximation defined on top of this smaller state space. When the approximations are too coarse to find such profiles, we refine the abstraction function. We extend the abstraction-refinement methodology to labeled networks, where the objectives of the players are regular languages. Our experimental results demonstrate the effectiveness of the methodology. "}]},{"date_created":"2018-12-11T11:44:17Z","date_published":"2018-06-01T00:00:00Z","year":"2018","isi":1,"publication":"28th International Conference on Automated Planning and Scheduling ","day":"01","oa":1,"quality_controlled":"1","publisher":"AAAI Press","article_processing_charge":"No","external_id":{"isi":["000492986200007"],"arxiv":["1804.07031"]},"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wolfgang","last_name":"Dvorák","full_name":"Dvorák, Wolfgang"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Svozil","full_name":"Svozil, Alexander","first_name":"Alexander"}],"publist_id":"8020","title":"Algorithms and conditional lower bounds for planning problems","citation":{"mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” in 28th International Conference on Automated Planning and Scheduling , Delft, Netherlands, 2018.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2018). Algorithms and conditional lower bounds for planning problems. In 28th International Conference on Automated Planning and Scheduling . Delft, Netherlands: AAAI Press.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Algorithms and conditional lower bounds for planning problems. In: 28th International Conference on Automated Planning and Scheduling . AAAI Press; 2018.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” In 28th International Conference on Automated Planning and Scheduling . AAAI Press, 2018.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2018. Algorithms and conditional lower bounds for planning problems. 28th International Conference on Automated Planning and Scheduling . ICAPS: International Conference on Automated Planning and Scheduling."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"9293"}]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07031"}],"scopus_import":"1","month":"06","abstract":[{"text":"We consider planning problems for graphs, Markov decision processes (MDPs), and games on graphs. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems where there are k different target sets, and the problems are as follows: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) objective-separation results showing that for MDPs the coverage problem is harder than the sequential target problem.","lang":"eng"}],"oa_version":"None","department":[{"_id":"KrCh"}],"date_updated":"2023-09-26T10:41:41Z","conference":{"start_date":"2018-06-24","end_date":"2018-06-29","location":"Delft, Netherlands","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"type":"conference","status":"public","_id":"35"},{"publisher":"Springer","quality_controlled":"1","oa":1,"date_published":"2018-01-01T00:00:00Z","doi":"10.1007/s11241-017-9293-4","date_created":"2018-12-11T11:48:14Z","page":"166 - 207","day":"01","publication":"Real-Time Systems","isi":1,"has_accepted_license":"1","year":"2018","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"title":"Automated competitive analysis of real time scheduling with graph games","publist_id":"6929","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kößler, Alexander","last_name":"Kößler","first_name":"Alexander"},{"full_name":"Schmid, Ulrich","last_name":"Schmid","first_name":"Ulrich"}],"article_processing_charge":"No","external_id":{"isi":["000419955500006"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Chatterjee, Krishnendu, et al. “Automated Competitive Analysis of Real Time Scheduling with Graph Games.” Real-Time Systems, vol. 54, no. 1, Springer, 2018, pp. 166–207, doi:10.1007/s11241-017-9293-4.","ieee":"K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “Automated competitive analysis of real time scheduling with graph games,” Real-Time Systems, vol. 54, no. 1. Springer, pp. 166–207, 2018.","short":"K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, Real-Time Systems 54 (2018) 166–207.","apa":"Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2018). Automated competitive analysis of real time scheduling with graph games. Real-Time Systems. Springer. https://doi.org/10.1007/s11241-017-9293-4","ama":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. Automated competitive analysis of real time scheduling with graph games. Real-Time Systems. 2018;54(1):166-207. doi:10.1007/s11241-017-9293-4","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “Automated Competitive Analysis of Real Time Scheduling with Graph Games.” Real-Time Systems. Springer, 2018. https://doi.org/10.1007/s11241-017-9293-4.","ista":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2018. Automated competitive analysis of real time scheduling with graph games. Real-Time Systems. 54(1), 166–207."},"month":"01","intvolume":" 54","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"This paper is devoted to automatic competitive analysis of real-time scheduling algorithms for firm-deadline tasksets, where only completed tasks con- tribute some utility to the system. Given such a taskset T , the competitive ratio of an on-line scheduling algorithm A for T is the worst-case utility ratio of A over the utility achieved by a clairvoyant algorithm. We leverage the theory of quantitative graph games to address the competitive analysis and competitive synthesis problems. For the competitive analysis case, given any taskset T and any finite-memory on- line scheduling algorithm A , we show that the competitive ratio of A in T can be computed in polynomial time in the size of the state space of A . Our approach is flexible as it also provides ways to model meaningful constraints on the released task sequences that determine the competitive ratio. We provide an experimental study of many well-known on-line scheduling algorithms, which demonstrates the feasibility of our competitive analysis approach that effectively replaces human ingenuity (required Preliminary versions of this paper have appeared in Chatterjee et al. ( 2013 , 2014 ). B Andreas Pavlogiannis pavlogiannis@ist.ac.at Krishnendu Chatterjee krish.chat@ist.ac.at Alexander Kößler koe@ecs.tuwien.ac.at Ulrich Schmid s@ecs.tuwien.ac.at 1 IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400 Klosterneuburg, Austria 2 Embedded Computing Systems Group, Vienna University of Technology, Treitlstrasse 3, 1040 Vienna, Austria 123 Real-Time Syst for finding worst-case scenarios) by computing power. For the competitive synthesis case, we are just given a taskset T , and the goal is to automatically synthesize an opti- mal on-line scheduling algorithm A , i.e., one that guarantees the largest competitive ratio possible for T . We show how the competitive synthesis problem can be reduced to a two-player graph game with partial information, and establish that the compu- tational complexity of solving this game is Np -complete. The competitive synthesis problem is hence in Np in the size of the state space of the non-deterministic labeled transition system encoding the taskset. Overall, the proposed framework assists in the selection of suitable scheduling algorithms for a given taskset, which is in fact the most common situation in real-time systems design. ","lang":"eng"}],"volume":54,"related_material":{"record":[{"relation":"earlier_version","id":"2820","status":"public"}]},"issue":"1","ec_funded":1,"file":[{"date_updated":"2020-07-14T12:47:56Z","file_size":1163507,"creator":"system","date_created":"2018-12-12T10:17:14Z","file_name":"IST-2018-960-v1+1_2017_Chatterjee_Automated_competetive.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c2590ef160709d8054cf29ee173f1454","file_id":"5267"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"960","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"738","file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-09-27T12:52:38Z"},{"project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"title":"Point interactions in systems of fermions","article_processing_charge":"No","publist_id":"8002","author":[{"last_name":"Moser","full_name":"Moser, Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Moser, Thomas. “Point Interactions in Systems of Fermions.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1043.","ista":"Moser T. 2018. Point interactions in systems of fermions. Institute of Science and Technology Austria.","mla":"Moser, Thomas. Point Interactions in Systems of Fermions. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1043.","apa":"Moser, T. (2018). Point interactions in systems of fermions. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1043","ama":"Moser T. Point interactions in systems of fermions. 2018. doi:10.15479/AT:ISTA:th_1043","short":"T. Moser, Point Interactions in Systems of Fermions, Institute of Science and Technology Austria, 2018.","ieee":"T. Moser, “Point interactions in systems of fermions,” Institute of Science and Technology Austria, 2018."},"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:44:22Z","date_published":"2018-09-04T00:00:00Z","doi":"10.15479/AT:ISTA:th_1043","page":"115","day":"04","year":"2018","has_accepted_license":"1","pubrep_id":"1043","status":"public","type":"dissertation","_id":"52","file_date_updated":"2020-07-14T12:46:37Z","department":[{"_id":"RoSe"}],"ddc":["515","530","519"],"date_updated":"2023-09-27T12:34:14Z","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this thesis we will discuss systems of point interacting fermions, their stability and other spectral properties. Whereas for bosons a point interacting system is always unstable this ques- tion is more subtle for a gas of two species of fermions. In particular the answer depends on the mass ratio between these two species. Most of this work will be focused on the N + M model which consists of two species of fermions with N, M particles respectively which interact via point interactions. We will introduce this model using a formal limit and discuss the N + 1 system in more detail. In particular, we will show that for mass ratios above a critical one, which does not depend on the particle number, the N + 1 system is stable. In the context of this model we will prove rigorous versions of Tan relations which relate various quantities of the point-interacting model. By restricting the N + 1 system to a box we define a finite density model with point in- teractions. In the context of this system we will discuss the energy change when introducing a point-interacting impurity into a system of non-interacting fermions. We will see that this change in energy is bounded independently of the particle number and in particular the bound only depends on the density and the scattering length. As another special case of the N + M model we will show stability of the 2 + 2 model for mass ratios in an interval around one. Further we will investigate a different model of point interactions which was discussed before in the literature and which is, contrary to the N + M model, not given by a limiting procedure but is based on a Dirichlet form. We will show that this system behaves trivially in the thermodynamic limit, i.e. the free energy per particle is the same as the one of the non-interacting system."}],"related_material":{"record":[{"id":"5856","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"154"},{"relation":"part_of_dissertation","status":"public","id":"1198"},{"status":"public","id":"741","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:37Z","file_size":851164,"creator":"dernst","date_created":"2019-04-09T07:45:38Z","file_name":"2018_Thesis_Moser.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"fbd8c747d148b468a21213b7cf175225","file_id":"6256"},{"content_type":"application/zip","relation":"source_file","access_level":"closed","file_id":"6257","checksum":"c28e16ecfc1126d3ce324ec96493c01e","file_size":1531516,"date_updated":"2020-07-14T12:46:37Z","creator":"dernst","file_name":"2018_Thesis_Moser_Source.zip","date_created":"2019-04-09T07:45:38Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]}},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis."}],"month":"01","intvolume":" 131","scopus_import":"1","file":[{"creator":"dernst","file_size":14925985,"date_updated":"2020-07-14T12:48:15Z","file_name":"2017_adamowski_PATELLINS_are.pdf","date_created":"2019-04-12T08:46:32Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"bf156c20a4f117b4b932370d54cbac8c","file_id":"6299"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00219533"]},"publication_status":"published","issue":"2","volume":131,"ec_funded":1,"_id":"913","status":"public","pubrep_id":"988","type":"journal_article","ddc":["581"],"date_updated":"2023-09-26T15:47:50Z","file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"JiFr"}],"publisher":"Company of Biologists","quality_controlled":"1","oa":1,"day":"29","publication":"Journal of Cell Science","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-01-29T00:00:00Z","doi":"10.1242/jcs.204198","date_created":"2018-12-11T11:49:10Z","article_number":"jcs.204198","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. 2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.","chicago":"Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer, Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.204198.","ama":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 2018;131(2). doi:10.1242/jcs.204198","apa":"Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L., & Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.204198","ieee":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana,” Journal of Cell Science, vol. 131, no. 2. Company of Biologists, 2018.","short":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J. Friml, Journal of Cell Science 131 (2018).","mla":"Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science, vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:10.1242/jcs.204198."},"title":"PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana","publist_id":"6530","author":[{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"first_name":"Cecilia","last_name":"Rodríguez Furlán","full_name":"Rodríguez Furlán, Cecilia"},{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"first_name":"Lorena","last_name":"Norambuena","full_name":"Norambuena, Lorena"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"article_processing_charge":"No","external_id":{"isi":["000424842400019"]}}]