[{"publisher":"Zenodo","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7858567"}],"month":"04","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"oa_version":"Published Version","doi":"10.5281/ZENODO.7858567","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"13117"}]},"date_published":"2023-04-28T00:00:00Z","date_created":"2023-06-06T07:36:50Z","year":"2023","day":"28","type":"research_data_reference","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":"13124","author":[{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander","first_name":"Alexander"},{"full_name":"Sett, Riya","last_name":"Sett","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Zemlicka, Martin","last_name":"Zemlicka"},{"first_name":"Alexander","full_name":"Poddubny, Alexander","last_name":"Poddubny"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"article_processing_charge":"No","title":"Tunable directional photon scattering from a pair of superconducting qubits","department":[{"_id":"JoFi"}],"citation":{"ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, 10.5281/ZENODO.7858567.","chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567.","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023.","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567","ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567","mla":"Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567."},"date_updated":"2023-08-02T06:10:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"]},{"year":"2023","day":"31","related_material":{"record":[{"id":"13106","status":"public","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.7789417","date_published":"2023-03-31T00:00:00Z","date_created":"2023-06-06T06:46:16Z","abstract":[{"text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1","lang":"eng"}],"oa_version":"Published Version","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7789418"}],"oa":1,"month":"03","date_updated":"2023-08-02T06:08:56Z","citation":{"ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, 10.5281/ZENODO.7789417.","chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7789417.","short":"R. Sahu, (2023).","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. https://doi.org/10.5281/ZENODO.7789417","ama":"Sahu R. Entangling microwaves with light. 2023. doi:10.5281/ZENODO.7789417","mla":"Sahu, Rishabh. Entangling Microwaves with Light. Zenodo, 2023, doi:10.5281/ZENODO.7789417."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","last_name":"Sahu"}],"article_processing_charge":"No","department":[{"_id":"JoFi"}],"title":"Entangling microwaves with light","_id":"13122","type":"research_data_reference","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"},{"abstract":[{"lang":"eng","text":"Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 13","publication_identifier":{"eissn":["2045-2322"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2023-06-26T09:58:53Z","file_size":4844149,"date_created":"2023-06-26T09:58:53Z","file_name":"2023_ScientificReports_Vetrova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"13170","checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","success":1}],"language":[{"iso":"eng"}],"volume":13,"_id":"13166","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","date_updated":"2023-08-02T06:17:18Z","ddc":["570"],"department":[{"_id":"GradSch"}],"file_date_updated":"2023-06-26T09:58:53Z","acknowledgement":"We thank N.A. Pertsov White Sea Biological Station of Moscow State University for the help and support in obtaining samples and providing access to all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy (CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009 of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to S.K.).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"09","publication":"Scientific Reports","doi":"10.1038/s41598-023-35979-8","date_published":"2023-06-09T00:00:00Z","date_created":"2023-06-25T22:00:46Z","article_number":"9382","citation":{"ista":"Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 13, 9382.","chicago":"Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35979-8.","short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023).","ieee":"A. A. Vetrova et al., “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” Scientific Reports, vol. 13. Springer Nature, 2023.","apa":"Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., & Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35979-8","ama":"Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 2023;13. doi:10.1038/s41598-023-35979-8","mla":"Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports, vol. 13, 9382, Springer Nature, 2023, doi:10.1038/s41598-023-35979-8."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Vetrova, Alexandra A.","last_name":"Vetrova","first_name":"Alexandra A."},{"first_name":"Daria M.","full_name":"Kupaeva, Daria M.","last_name":"Kupaeva"},{"id":"a521c60b-0815-11ed-9b02-b8bd522477c8","first_name":"Alena","last_name":"Kizenko","full_name":"Kizenko, Alena"},{"full_name":"Lebedeva, Tatiana S.","last_name":"Lebedeva","first_name":"Tatiana S."},{"full_name":"Walentek, Peter","last_name":"Walentek","first_name":"Peter"},{"first_name":"Nikoloz","full_name":"Tsikolia, Nikoloz","last_name":"Tsikolia"},{"first_name":"Stanislav V.","last_name":"Kremnyov","full_name":"Kremnyov, Stanislav V."}],"external_id":{"isi":["001006690200045"],"pmid":["37296138"]},"article_processing_charge":"No","title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. ","date_created":"2023-06-18T22:00:46Z","date_published":"2023-05-01T00:00:00Z","doi":"10.1103/PhysRevB.107.184312","year":"2023","isi":1,"publication":"Physical Review B","day":"01","article_number":"184312","article_processing_charge":"No","external_id":{"arxiv":["2303.00729"],"isi":["001003686900004"]},"author":[{"first_name":"Pavel","full_name":"Orlov, Pavel","last_name":"Orlov"},{"first_name":"Anastasiia","full_name":"Tiutiakina, Anastasiia","last_name":"Tiutiakina"},{"first_name":"Rustem","full_name":"Sharipov, Rustem","last_name":"Sharipov"},{"last_name":"Petrova","full_name":"Petrova, Elena","first_name":"Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede"},{"first_name":"Vladimir","last_name":"Gritsev","full_name":"Gritsev, Vladimir"},{"first_name":"Denis V.","full_name":"Kurlov, Denis V.","last_name":"Kurlov"}],"title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain","citation":{"apa":"Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., & Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.184312","ama":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 2023;107(18). doi:10.1103/PhysRevB.107.184312","short":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023).","ieee":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” Physical Review B, vol. 107, no. 18. American Physical Society, 2023.","mla":"Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:10.1103/PhysRevB.107.184312.","ista":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312.","chicago":"Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.184312."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.00729"}],"scopus_import":"1","intvolume":" 107","month":"05","abstract":[{"text":"We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain.","lang":"eng"}],"oa_version":"Preprint","issue":"18","volume":107,"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"13138","department":[{"_id":"GradSch"}],"date_updated":"2023-08-02T06:16:02Z"},{"file":[{"date_created":"2023-07-13T13:26:33Z","file_name":"2023_PlantPhys_Chen.pdf","creator":"cchlebak","date_updated":"2023-07-13T13:26:33Z","file_size":2076977,"file_id":"13220","checksum":"5492e1d18ac3eaf202633d210fa0fb75","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"publication_status":"published","volume":192,"issue":"3","pmid":1,"oa_version":"Published Version","abstract":[{"text":"The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth.","lang":"eng"}],"month":"07","intvolume":" 192","ddc":["575"],"date_updated":"2023-08-02T06:27:55Z","file_date_updated":"2023-07-13T13:26:33Z","department":[{"_id":"JiFr"}],"_id":"13213","status":"public","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)"},"day":"01","publication":"Plant Physiology","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.1093/plphys/kiad207","date_published":"2023-07-01T00:00:00Z","date_created":"2023-07-12T07:32:58Z","page":"2243-2260","acknowledgement":"We thank Dong liu for offering iron staining technique; ZhiChang Chen and Zhenbiao Yang for discussion; Dandan Zheng for earlier attempt; Liwen Jiang and Dingquan Huang for initial tests of the TEM experiment; John C. Sedbrook for a donation of sku5 and pSKU5::SKU5-GFP seeds; Catherine Perrot-Rechenmann and Ke Zhou for the donation of sks1, sks2, and sku5 sks1 seeds; Zengyu Liu and Zhongquan Lin for live-imaging microscopy assistance. We are grateful to Can Peng, and Xixia Li for helping with sample preparation, and taking TEM images, at the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science.","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Chen, C., Zhang, Y., Cai, J., Qiu, Y., Li, L., Gao, C., … Gao, Z. (2023). Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiad207","ama":"Chen C, Zhang Y, Cai J, et al. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 2023;192(3):2243-2260. doi:10.1093/plphys/kiad207","short":"C. Chen, Y. Zhang, J. Cai, Y. Qiu, L. Li, C. Gao, Y. Gao, M. Ke, S. Wu, C. Wei, J. Chen, T. Xu, J. Friml, J. Wang, R. Li, D. Chao, B. Zhang, X. Chen, Z. Gao, Plant Physiology 192 (2023) 2243–2260.","ieee":"C. Chen et al., “Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots,” Plant Physiology, vol. 192, no. 3. American Society of Plant Biologists, pp. 2243–2260, 2023.","mla":"Chen, C., et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology, vol. 192, no. 3, American Society of Plant Biologists, 2023, pp. 2243–60, doi:10.1093/plphys/kiad207.","ista":"Chen C, Zhang Y, Cai J, Qiu Y, Li L, Gao C, Gao Y, Ke M, Wu S, Wei C, Chen J, Xu T, Friml J, Wang J, Li R, Chao D, Zhang B, Chen X, Gao Z. 2023. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 192(3), 2243–2260.","chicago":"Chen, C, Y Zhang, J Cai, Y Qiu, L Li, C Gao, Y Gao, et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology. American Society of Plant Biologists, 2023. https://doi.org/10.1093/plphys/kiad207."},"title":"Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots","author":[{"full_name":"Chen, C","last_name":"Chen","first_name":"C"},{"first_name":"Y","last_name":"Zhang","full_name":"Zhang, Y"},{"full_name":"Cai, J","last_name":"Cai","first_name":"J"},{"full_name":"Qiu, Y","last_name":"Qiu","first_name":"Y"},{"first_name":"L","full_name":"Li, L","last_name":"Li"},{"first_name":"C","full_name":"Gao, C","last_name":"Gao"},{"first_name":"Y","full_name":"Gao, Y","last_name":"Gao"},{"first_name":"M","full_name":"Ke, M","last_name":"Ke"},{"full_name":"Wu, S","last_name":"Wu","first_name":"S"},{"first_name":"C","last_name":"Wei","full_name":"Wei, C"},{"full_name":"Chen, J","last_name":"Chen","first_name":"J"},{"first_name":"T","last_name":"Xu","full_name":"Xu, T"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"J","full_name":"Wang, J","last_name":"Wang"},{"full_name":"Li, R","last_name":"Li","first_name":"R"},{"full_name":"Chao, D","last_name":"Chao","first_name":"D"},{"last_name":"Zhang","full_name":"Zhang, B","first_name":"B"},{"first_name":"X","full_name":"Chen, X","last_name":"Chen"},{"full_name":"Gao, Z","last_name":"Gao","first_name":"Z"}],"article_processing_charge":"No","external_id":{"pmid":["37010107"],"isi":["000971795800001"]}},{"file_date_updated":"2023-07-31T07:16:34Z","department":[{"_id":"CaGu"}],"date_updated":"2023-08-02T06:25:04Z","ddc":["570"],"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":"12478","volume":14,"publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published","file":[{"success":1,"file_id":"13322","checksum":"7dd322347512afaa5daf72a0154f2f07","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_FrontiersMicrobiology_Guet.pdf","date_created":"2023-07-31T07:16:34Z","creator":"dernst","file_size":6452841,"date_updated":"2023-07-31T07:16:34Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 14","abstract":[{"text":"In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"author":[{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"last_name":"Bruneaux","full_name":"Bruneaux, L","first_name":"L"},{"full_name":"Oikonomou, P","last_name":"Oikonomou","first_name":"P"},{"first_name":"M","last_name":"Aldana","full_name":"Aldana, M"},{"first_name":"P","full_name":"Cluzel, P","last_name":"Cluzel"}],"article_processing_charge":"Yes","external_id":{"isi":["001030002600001"],"pmid":["37485524"]},"title":"Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression","citation":{"chicago":"Guet, Calin C, L Bruneaux, P Oikonomou, M Aldana, and P Cluzel. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1049255.","ista":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. 2023. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 14, 1049255.","mla":"Guet, Calin C., et al. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology, vol. 14, 1049255, Frontiers, 2023, doi:10.3389/fmicb.2023.1049255.","short":"C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in Microbiology 14 (2023).","ieee":"C. C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, and P. Cluzel, “Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","ama":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1049255","apa":"Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., & Cluzel, P. (2023). Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1049255"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"1049255","doi":"10.3389/fmicb.2023.1049255","date_published":"2023-06-20T00:00:00Z","date_created":"2023-02-02T08:13:28Z","isi":1,"has_accepted_license":"1","year":"2023","day":"20","publication":"Frontiers in Microbiology","publisher":"Frontiers","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by NIH P50 award P50GM081892-02 to the University of Chicago, a catalyst grant from the Chicago Biomedical Consortium with support from The Searle Funds at The Chicago Community Trust to PC, and a Yen Fellowship to CCG. MA was partially supported by PAPIIT-UNAM grant IN-11322."},{"author":[{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"first_name":"Daoyuan","last_name":"Qian","full_name":"Qian, Daoyuan"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Michele","full_name":"Vendruscolo, Michele","last_name":"Vendruscolo"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"full_name":"Knowles, Tuomas P.J.","last_name":"Knowles","first_name":"Tuomas P.J."}],"external_id":{"isi":["001017539800001"]},"article_processing_charge":"No","title":"Amyloid formation as a protein phase transition","citation":{"ista":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023. Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.","chicago":"Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo, Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-023-00598-9.","short":"T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397.","ieee":"T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P. J. Knowles, “Amyloid formation as a protein phase transition,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 379–397, 2023.","apa":"Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., & Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-023-00598-9","ama":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. Nature Reviews Physics. 2023;5:379–397. doi:10.1038/s42254-023-00598-9","mla":"Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 379–397, doi:10.1038/s42254-023-00598-9."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"The authors acknowledge support from the Institute for the Physics of Living Systems, University College London (T.C.T.M.), the Swedish Research Council (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C. Flandoli for help with illustrations.","page":"379–397","date_published":"2023-07-01T00:00:00Z","doi":"10.1038/s42254-023-00598-9","date_created":"2023-07-16T22:01:12Z","isi":1,"year":"2023","day":"01","publication":"Nature Reviews Physics","article_type":"original","type":"journal_article","status":"public","_id":"13237","department":[{"_id":"AnSa"}],"date_updated":"2023-08-02T06:28:38Z","scopus_import":"1","month":"07","intvolume":" 5","abstract":[{"lang":"eng","text":"The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases."}],"oa_version":"None","volume":5,"publication_identifier":{"eissn":["2522-5820"]},"publication_status":"published","language":[{"iso":"eng"}]},{"file_date_updated":"2023-07-18T07:59:58Z","department":[{"_id":"CaHe"}],"date_updated":"2023-08-02T06:33:14Z","ddc":["570"],"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":"13229","issue":"6","volume":21,"ec_funded":1,"publication_identifier":{"eissn":["1545-7885"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"13246","checksum":"8e88cb0e5a6433a2f1939a9030bed384","success":1,"creator":"dernst","date_updated":"2023-07-18T07:59:58Z","file_size":4431723,"date_created":"2023-07-18T07:59:58Z","file_name":"2023_PloSBiology_Shamipour.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 21","abstract":[{"lang":"eng","text":"Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation."}],"pmid":1,"oa_version":"Published Version","author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"last_name":"Hofmann","full_name":"Hofmann, Laura","first_name":"Laura","id":"b88d43f2-dc74-11ea-a0a7-e41b7912e031"},{"last_name":"Steccari","full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland","full_name":"Kardos, Roland","last_name":"Kardos"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"article_processing_charge":"No","external_id":{"pmid":["37289834"],"isi":["001003199100005"]},"title":"Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes","citation":{"ieee":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” PLoS Biology, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023.","short":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146.","ama":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 2023;21(6):e3002146. doi:10.1371/journal.pbio.3002146","apa":"Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., & Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002146","mla":"Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:10.1371/journal.pbio.3002146.","ista":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146.","chicago":"Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002146."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"page":"e3002146","date_published":"2023-06-08T00:00:00Z","doi":"10.1371/journal.pbio.3002146","date_created":"2023-07-16T22:01:09Z","has_accepted_license":"1","isi":1,"year":"2023","day":"08","publication":"PLoS Biology","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"acknowledgement":"This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."},{"_id":"13197","article_type":"original","type":"journal_article","status":"public","keyword":["Physics and Astronomy (miscellaneous)","General Materials Science"],"date_updated":"2023-08-02T06:34:47Z","ddc":["537"],"department":[{"_id":"ScWa"}],"file_date_updated":"2023-07-07T12:49:51Z","abstract":[{"lang":"eng","text":"Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop\r\nan analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally."}],"oa_version":"Submitted Version","month":"06","intvolume":" 7","publication_identifier":{"issn":["2475-9953"]},"publication_status":"published","file":[{"creator":"ggrosjea","date_updated":"2023-07-07T12:49:51Z","file_size":1127040,"date_created":"2023-07-07T12:49:51Z","file_name":"Mosaic_asymmetries.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"13198","checksum":"75584730d9cdd50eeccb4c52c509776d","success":1}],"language":[{"iso":"eng"}],"volume":7,"issue":"6","ec_funded":1,"article_number":"065601","project":[{"call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ieee":"G. M. Grosjean and S. R. Waitukaitis, “Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts,” Physical Review Materials, vol. 7, no. 6. American Physical Society, 2023.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Materials 7 (2023).","apa":"Grosjean, G. M., & Waitukaitis, S. R. (2023). Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. American Physical Society. https://doi.org/10.1103/physrevmaterials.7.065601","ama":"Grosjean GM, Waitukaitis SR. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 2023;7(6). doi:10.1103/physrevmaterials.7.065601","mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials, vol. 7, no. 6, 065601, American Physical Society, 2023, doi:10.1103/physrevmaterials.7.065601.","ista":"Grosjean GM, Waitukaitis SR. 2023. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 7(6), 065601.","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials. American Physical Society, 2023. https://doi.org/10.1103/physrevmaterials.7.065601."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","last_name":"Grosjean","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M"},{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis"}],"external_id":{"isi":["001019565900002"],"arxiv":["2304.12861"]},"article_processing_charge":"No","title":"Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts","acknowledgement":"This project has received funding from the European Research Council Grant Agreement No. 949120 and from\r\nthe European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant\r\nAgreement No. 754411. ","quality_controlled":"1","publisher":"American Physical Society","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"13","publication":"Physical Review Materials","doi":"10.1103/physrevmaterials.7.065601","date_published":"2023-06-13T00:00:00Z","date_created":"2023-07-07T12:48:01Z"},{"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals."}],"intvolume":" 19","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"13247","checksum":"800761fa2c647fabd6ad034589bc526e","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-07-18T08:07:59Z","file_name":"2023_PloSCompBio_Charlton.pdf","date_updated":"2023-07-18T08:07:59Z","file_size":2281868,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1553-7358"]},"issue":"6","volume":19,"_id":"13230","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-08-02T06:33:50Z","file_date_updated":"2023-07-18T08:07:59Z","department":[{"_id":"MaJö"}],"acknowledgement":"The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback.","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","publication":"PLoS Computational Biology","day":"08","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-07-16T22:01:09Z","doi":"10.1371/journal.pcbi.1011104","date_published":"2023-06-08T00:00:00Z","article_number":"e1011104","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023).","ieee":"J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” PLoS Computational Biology, vol. 19, no. 6. Public Library of Science, 2023.","ama":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 2023;19(6). doi:10.1371/journal.pcbi.1011104","apa":"Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., & Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011104","mla":"Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1011104.","ista":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104.","chicago":"Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1011104."},"title":"Environmental dynamics shape perceptual decision bias","article_processing_charge":"No","external_id":{"pmid":["37289753"],"isi":["001003410200003"]},"author":[{"last_name":"Charlton","full_name":"Charlton, Julie A.","first_name":"Julie A."},{"last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yoon H.","full_name":"Bai, Yoon H.","last_name":"Bai"},{"last_name":"Hermundstad","full_name":"Hermundstad, Ann M.","first_name":"Ann M."},{"full_name":"Goris, Robbe L.T.","last_name":"Goris","first_name":"Robbe L.T."}]},{"acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","quality_controlled":"1","publisher":"MDPI","oa":1,"day":"01","publication":"Vaccines","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-06-01T00:00:00Z","doi":"10.3390/vaccines11061014","date_created":"2023-07-16T22:01:10Z","article_number":"1014","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014.","ieee":"D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI, 2023.","short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6). doi:10.3390/vaccines11061014","apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014","mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI, 2023, doi:10.3390/vaccines11061014."},"title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"last_name":"Katsin","full_name":"Katsin, Mikalai","first_name":"Mikalai"},{"first_name":"Maria","full_name":"Stegantseva, Maria","last_name":"Stegantseva"},{"first_name":"Sergey","full_name":"Golenchenko, Sergey","last_name":"Golenchenko"},{"last_name":"Shapira","full_name":"Shapira, Michail","first_name":"Michail"},{"first_name":"Simon","full_name":"Dubovik, Simon","last_name":"Dubovik"},{"last_name":"Lutskovich","full_name":"Lutskovich, Dzmitry","first_name":"Dzmitry"},{"last_name":"Kavaleuski","orcid":"0000-0003-2091-526X","full_name":"Kavaleuski, Anton","first_name":"Anton","id":"62304f89-eb97-11eb-a6c2-8903dd183976"},{"last_name":"Meleshko","full_name":"Meleshko, Alexander","first_name":"Alexander"}],"article_processing_charge":"No","external_id":{"isi":["001017740000001"]},"oa_version":"Published Version","abstract":[{"text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study.","lang":"eng"}],"month":"06","intvolume":" 11","scopus_import":"1","file":[{"date_updated":"2023-07-18T07:25:43Z","file_size":2339746,"creator":"dernst","date_created":"2023-07-18T07:25:43Z","file_name":"2023_Vaccines_Dormeshkin.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"13244","checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2076-393X"]},"publication_status":"published","issue":"6","volume":11,"_id":"13232","status":"public","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)"},"ddc":["570"],"date_updated":"2023-08-02T06:31:19Z","department":[{"_id":"LeSa"}],"file_date_updated":"2023-07-18T07:25:43Z"},{"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"article_processing_charge":"No","external_id":{"pmid":["37310395"],"isi":["001008564800001"]},"author":[{"last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Li","full_name":"Li, Mingquan","first_name":"Mingquan"},{"full_name":"Wan, Shanhong","last_name":"Wan","first_name":"Shanhong"},{"last_name":"Lim","full_name":"Lim, Khak Ho","first_name":"Khak Ho"},{"last_name":"Zhang","full_name":"Zhang, Yu","first_name":"Yu"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"last_name":"Li","full_name":"Li, Junshan","first_name":"Junshan"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Min","full_name":"Hong, Min","last_name":"Hong"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"title":"Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance","citation":{"short":"Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong, A. Cabot, ACS Nano 17 (2023) 11923–11934.","ieee":"Y. Liu et al., “Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance,” ACS Nano, vol. 17, no. 12. American Chemical Society, pp. 11923–11934, 2023.","apa":"Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023). Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c03541","ama":"Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 2023;17(12):11923–11934. doi:10.1021/acsnano.3c03541","mla":"Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano, vol. 17, no. 12, American Chemical Society, 2023, pp. 11923–11934, doi:10.1021/acsnano.3c03541.","ista":"Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 17(12), 11923–11934.","chicago":"Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li, Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.3c03541."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Chemical Society","quality_controlled":"1","acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (Grant No. 22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.","page":"11923–11934","date_created":"2023-07-16T22:01:11Z","date_published":"2023-06-13T00:00:00Z","doi":"10.1021/acsnano.3c03541","year":"2023","isi":1,"publication":"ACS Nano","day":"13","article_type":"original","type":"journal_article","status":"public","_id":"13235","department":[{"_id":"MaIb"}],"date_updated":"2023-08-02T06:29:55Z","scopus_import":"1","intvolume":" 17","month":"06","abstract":[{"text":"AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications.","lang":"eng"}],"oa_version":"None","pmid":1,"issue":"12","volume":17,"publication_status":"published","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"language":[{"iso":"eng"}]},{"date_updated":"2023-08-02T06:30:46Z","department":[{"_id":"BiCh"}],"_id":"13231","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"6","volume":107,"abstract":[{"lang":"eng","text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01545","open_access":"1"}],"month":"06","intvolume":" 107","citation":{"short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023).","ieee":"M. Schörner et al., “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” Physical Review E, vol. 107, no. 6. American Physical Society, 2023.","ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 2023;107(6). doi:10.1103/PhysRevE.107.065207","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., & Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.065207","mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:10.1103/PhysRevE.107.065207.","ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207.","chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.065207."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Maximilian","last_name":"Schörner","full_name":"Schörner, Maximilian"},{"first_name":"Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","full_name":"Bethkenhagen, Mandy","last_name":"Bethkenhagen"},{"full_name":"Döppner, Tilo","last_name":"Döppner","first_name":"Tilo"},{"full_name":"Kraus, Dominik","last_name":"Kraus","first_name":"Dominik"},{"first_name":"Luke B.","last_name":"Fletcher","full_name":"Fletcher, Luke B."},{"first_name":"Siegfried H.","last_name":"Glenzer","full_name":"Glenzer, Siegfried H."},{"first_name":"Ronald","full_name":"Redmer, Ronald","last_name":"Redmer"}],"external_id":{"arxiv":["2301.01545"],"isi":["001020265000002"]},"article_processing_charge":"No","title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","article_number":"065207","isi":1,"year":"2023","day":"14","publication":"Physical Review E","date_published":"2023-06-14T00:00:00Z","doi":"10.1103/PhysRevE.107.065207","date_created":"2023-07-16T22:01:10Z","acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"oa_version":"Preprint","abstract":[{"text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters.","lang":"eng"}],"intvolume":" 107","month":"06","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.01022","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"ec_funded":1,"issue":"6","volume":107,"_id":"13233","status":"public","type":"journal_article","article_type":"letter_note","date_updated":"2023-08-02T06:31:52Z","department":[{"_id":"MiLe"},{"_id":"OnHo"}],"acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review A","day":"20","year":"2023","isi":1,"date_created":"2023-07-16T22:01:10Z","date_published":"2023-06-20T00:00:00Z","doi":"10.1103/PhysRevA.107.L061304","article_number":"L061304","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 2023;107(6). doi:10.1103/PhysRevA.107.L061304","apa":"Agafonova, S., Lemeshko, M., & Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L061304","short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","mla":"Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L061304.","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","chicago":"Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L061304."},"title":"Finite-range bias in fitting three-body loss to the zero-range model","article_processing_charge":"No","external_id":{"arxiv":["2302.01022"],"isi":["001019748000005"]},"author":[{"first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","full_name":"Agafonova, Sofya","last_name":"Agafonova"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}]},{"file_date_updated":"2023-07-31T08:00:01Z","department":[{"_id":"CaMu"}],"ddc":["550"],"date_updated":"2023-08-02T06:38:07Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"13256","volume":6,"file":[{"creator":"dernst","date_updated":"2023-07-31T08:00:01Z","file_size":1750712,"date_created":"2023-07-31T08:00:01Z","file_name":"2023_npjclimate_Goswami.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"e9967d436a83b8ffcc6f58782e1f7500","file_id":"13326","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2397-3722"]},"publication_status":"published","month":"07","intvolume":" 6","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate."}],"title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","author":[{"full_name":"Goswami, Bidyut B","last_name":"Goswami","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"Bidyut B"},{"first_name":"Soon Il","last_name":"An","full_name":"An, Soon Il"}],"external_id":{"isi":["001024920300002"]},"article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science. Springer Nature, 2023. https://doi.org/10.1038/s41612-023-00411-5.","ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” npj Climate and Atmospheric Science, vol. 6. Springer Nature, 2023.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","apa":"GOSWAMI, B. B., & An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. Npj Climate and Atmospheric Science. Springer Nature. https://doi.org/10.1038/s41612-023-00411-5","ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 2023;6. doi:10.1038/s41612-023-00411-5","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science, vol. 6, 82, Springer Nature, 2023, doi:10.1038/s41612-023-00411-5."},"article_number":"82","doi":"10.1038/s41612-023-00411-5","date_published":"2023-07-08T00:00:00Z","date_created":"2023-07-23T22:01:10Z","day":"08","publication":"npj Climate and Atmospheric Science","has_accepted_license":"1","isi":1,"year":"2023","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations."},{"_id":"13260","status":"public","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)"},"ddc":["570"],"date_updated":"2023-08-02T06:42:35Z","file_date_updated":"2023-08-01T06:58:34Z","department":[{"_id":"BeVi"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines.","lang":"eng"}],"month":"07","intvolume":" 15","scopus_import":"1","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"13339","checksum":"70de3c4878de6efe00dc56de2df8812f","file_size":2382587,"date_updated":"2023-08-01T06:58:34Z","creator":"dernst","file_name":"2023_GBE_Barata.pdf","date_created":"2023-08-01T06:58:34Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1759-6653"]},"publication_status":"published","volume":15,"issue":"7","related_material":{"link":[{"relation":"software","url":"https://github.com/carolbarata/dpseudo-n-beyond"}]},"article_number":"evad113","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution. Oxford Academic, 2023. https://doi.org/10.1093/gbe/evad113.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., & Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome Biology and Evolution. Oxford Academic. https://doi.org/10.1093/gbe/evad113","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 2023;15(7). doi:10.1093/gbe/evad113","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” Genome biology and evolution, vol. 15, no. 7. Oxford Academic, 2023.","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:10.1093/gbe/evad113."},"title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","author":[{"id":"20565186-803f-11ed-ab7e-96a4ff7694ef","first_name":"Carolina","last_name":"De Castro Barbosa Rodrigues Barata","full_name":"De Castro Barbosa Rodrigues Barata, Carolina"},{"last_name":"Snook","full_name":"Snook, Rhonda R.","first_name":"Rhonda R."},{"first_name":"Michael G.","full_name":"Ritchie, Michael G.","last_name":"Ritchie"},{"last_name":"Kosiol","full_name":"Kosiol, Carolin","first_name":"Carolin"}],"external_id":{"pmid":["37341535"],"isi":["001023444700003"]},"article_processing_charge":"Yes","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","quality_controlled":"1","publisher":"Oxford Academic","oa":1,"day":"01","publication":"Genome biology and evolution","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-07-01T00:00:00Z","doi":"10.1093/gbe/evad113","date_created":"2023-07-23T22:01:11Z"},{"status":"public","type":"preprint","article_number":"2307.03237","_id":"13447","title":"Asteroseismology with the Roman galactic bulge time-domain survey","department":[{"_id":"LiBu"}],"external_id":{"arxiv":["2307.03237"]},"article_processing_charge":"No","author":[{"first_name":"Daniel","last_name":"Huber","full_name":"Huber, Daniel"},{"first_name":"Marc","full_name":"Pinsonneault, Marc","last_name":"Pinsonneault"},{"last_name":"Beck","full_name":"Beck, Paul","first_name":"Paul"},{"full_name":"Bedding, Timothy R.","last_name":"Bedding","first_name":"Timothy R."},{"last_name":"Joss Bland-Hawthorn","full_name":"Joss Bland-Hawthorn, Joss Bland-Hawthorn","first_name":"Joss Bland-Hawthorn"},{"first_name":"Sylvain N.","full_name":"Breton, Sylvain N.","last_name":"Breton"},{"last_name":"Bugnet","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle"},{"last_name":"Chaplin","full_name":"Chaplin, William J.","first_name":"William J."},{"first_name":"Rafael A.","full_name":"Garcia, Rafael A.","last_name":"Garcia"},{"first_name":"Samuel K.","full_name":"Grunblatt, Samuel K.","last_name":"Grunblatt"},{"first_name":"Joyce A.","last_name":"Guzik","full_name":"Guzik, Joyce A."},{"first_name":"Saskia","last_name":"Hekker","full_name":"Hekker, Saskia"},{"first_name":"Steven D.","full_name":"Kawaler, Steven D.","last_name":"Kawaler"},{"last_name":"Mathis","full_name":"Mathis, Stephane","first_name":"Stephane"},{"first_name":"Savita","full_name":"Mathur, Savita","last_name":"Mathur"},{"full_name":"Metcalfe, Travis","last_name":"Metcalfe","first_name":"Travis"},{"first_name":"Benoit","last_name":"Mosser","full_name":"Mosser, Benoit"},{"first_name":"Melissa K.","last_name":"Ness","full_name":"Ness, Melissa K."},{"first_name":"Anthony L.","full_name":"Piro, Anthony L.","last_name":"Piro"},{"first_name":"Aldo","last_name":"Serenelli","full_name":"Serenelli, Aldo"},{"last_name":"Sharma","full_name":"Sharma, Sanjib","first_name":"Sanjib"},{"first_name":"David R.","full_name":"Soderblom, David R.","last_name":"Soderblom"},{"first_name":"Keivan G.","full_name":"Stassun, Keivan G.","last_name":"Stassun"},{"full_name":"Stello, Dennis","last_name":"Stello","first_name":"Dennis"},{"full_name":"Tayar, Jamie","last_name":"Tayar","first_name":"Jamie"},{"first_name":"Gerard T. van","full_name":"Belle, Gerard T. van","last_name":"Belle"},{"first_name":"Joel C.","last_name":"Zinn","full_name":"Zinn, Joel C."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-02T07:36:00Z","citation":{"ieee":"D. Huber et al., “Asteroseismology with the Roman galactic bulge time-domain survey,” arXiv. .","short":"D. Huber, M. Pinsonneault, P. Beck, T.R. Bedding, J.B.-H. Joss Bland-Hawthorn, S.N. Breton, L.A. Bugnet, W.J. Chaplin, R.A. Garcia, S.K. Grunblatt, J.A. Guzik, S. Hekker, S.D. Kawaler, S. Mathis, S. Mathur, T. Metcalfe, B. Mosser, M.K. Ness, A.L. Piro, A. Serenelli, S. Sharma, D.R. Soderblom, K.G. Stassun, D. Stello, J. Tayar, G.T. van Belle, J.C. Zinn, ArXiv (n.d.).","apa":"Huber, D., Pinsonneault, M., Beck, P., Bedding, T. R., Joss Bland-Hawthorn, J. B.-H., Breton, S. N., … Zinn, J. C. (n.d.). Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. https://doi.org/10.48550/arXiv.2307.03237","ama":"Huber D, Pinsonneault M, Beck P, et al. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. doi:10.48550/arXiv.2307.03237","mla":"Huber, Daniel, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, 2307.03237, doi:10.48550/arXiv.2307.03237.","ista":"Huber D, Pinsonneault M, Beck P, Bedding TR, Joss Bland-Hawthorn JB-H, Breton SN, Bugnet LA, Chaplin WJ, Garcia RA, Grunblatt SK, Guzik JA, Hekker S, Kawaler SD, Mathis S, Mathur S, Metcalfe T, Mosser B, Ness MK, Piro AL, Serenelli A, Sharma S, Soderblom DR, Stassun KG, Stello D, Tayar J, Belle GT van, Zinn JC. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv, 2307.03237.","chicago":"Huber, Daniel, Marc Pinsonneault, Paul Beck, Timothy R. Bedding, Joss Bland-Hawthorn Joss Bland-Hawthorn, Sylvain N. Breton, Lisa Annabelle Bugnet, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.03237."},"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.03237"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology is a prime example, with oscillation periods and amplitudes that are readily detectable with time-domain space-based telescopes. These oscillations can be used to infer masses, ages and radii for large numbers of stars, providing unique constraints on stellar populations in our galaxy. The cadence, duration, and spatial resolution of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology and will probe an important population not studied by prior missions. We identify photometric precision as a key requirement for realizing the potential of asteroseismology with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars will enable detections of the populous red clump star population in the Galactic bulge. If the survey efficiency is better than expected, we argue for repeat observations of the same fields to improve photometric precision, or covering additional fields to expand the stellar population reach if the photometric precision for saturated stars is better than 1 mmag. Asteroseismology is relatively insensitive to the timing of the observations during the mission, and the prime red clump targets can be observed in a single 70 day campaign in any given field. Complementary stellar characterization, particularly astrometry tied to the Gaia system, will also dramatically expand the diagnostic power of asteroseismology. We also highlight synergies to Roman GBTDS exoplanet science using transits and microlensing."}],"date_created":"2023-08-02T07:30:43Z","doi":"10.48550/arXiv.2307.03237","date_published":"2023-07-06T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","day":"06","publication_status":"submitted","year":"2023"},{"file_date_updated":"2023-04-20T07:02:59Z","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"supervisor":[{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"date_updated":"2023-08-04T08:54:51Z","ddc":["570","572"],"type":"dissertation","status":"public","_id":"12781","related_material":{"record":[{"status":"public","id":"12138","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"checksum":"5ebb6345cb4119f93460c81310265a6d","file_id":"12852","embargo":"2024-04-20","content_type":"application/pdf","embargo_to":"local","access_level":"closed","relation":"main_file","date_created":"2023-04-19T14:33:41Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","date_updated":"2023-04-19T14:33:41Z","file_size":6071553,"creator":"vkravchu"},{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"local","file_id":"12853","checksum":"c12055c48411d030d2afa51de2166221","embargo":"2024-04-20","creator":"vkravchu","date_updated":"2023-04-20T07:02:59Z","file_size":19468766,"date_created":"2023-04-19T14:33:52Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"03","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"oa_version":"Published Version","author":[{"full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk","first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","citation":{"ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"name":"Structure and mechanism of respiratory chain molecular machines","grant_number":"101020697","call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}],"page":"127","doi":"10.15479/at:ista:12781","date_published":"2023-03-23T00:00:00Z","date_created":"2023-03-31T12:24:42Z","has_accepted_license":"1","year":"2023","day":"23","publisher":"Institute of Science and Technology Austria"},{"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2023-05-23T00:00:00Z","doi":"10.15479/at:ista:13074","date_created":"2023-05-23T17:07:53Z","page":"147","day":"23","has_accepted_license":"1","year":"2023","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"title":"Efficiency and generalization of sparse neural networks","author":[{"full_name":"Peste, Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria."},"month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11458"},{"relation":"part_of_dissertation","id":"13053","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"12299"}]},"ec_funded":1,"file":[{"creator":"epeste","file_size":2152072,"date_updated":"2023-05-24T16:11:16Z","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","date_created":"2023-05-24T16:11:16Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"6b3354968403cb9d48cc5a83611fb571","file_id":"13087"},{"file_id":"13088","checksum":"8d0df94bbcf4db72c991f22503b3fd60","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2023-05-24T16:12:59Z","file_name":"PhD_Thesis_APeste.zip","creator":"epeste","date_updated":"2023-05-24T16:12:59Z","file_size":1658293}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","status":"public","type":"dissertation","_id":"13074","file_date_updated":"2023-05-24T16:12:59Z","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"ddc":["000"],"supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"date_updated":"2023-08-04T10:33:27Z"},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","year":"2023","day":"17","page":"146","date_published":"2023-05-17T00:00:00Z","doi":"10.15479/at:ista:12964","date_created":"2023-05-15T14:52:36Z","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964.","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","last_name":"Boocock","first_name":"Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Mechanochemical pattern formation across biological scales","abstract":[{"lang":"eng","text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","publication_identifier":{"isbn":["978-3-99078-032-9"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"dboocock","date_updated":"2023-05-19T07:04:25Z","file_size":40414730,"date_created":"2023-05-17T13:39:54Z","file_name":"thesis_boocock.pdf","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","file_id":"12988","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","embargo":"2024-05-17"},{"date_created":"2023-05-17T13:39:53Z","file_name":"thesis_boocock.zip","date_updated":"2023-05-17T14:35:13Z","file_size":34338567,"creator":"dboocock","checksum":"581a2313ffeb40fe77e8a122a25a7795","file_id":"12989","content_type":"application/zip","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8602"}]},"ec_funded":1,"_id":"12964","type":"dissertation","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","supervisor":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"}],"date_updated":"2023-08-04T11:02:40Z","ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"EdHa"}],"file_date_updated":"2023-05-19T07:04:25Z"},{"language":[{"iso":"eng"}],"file":[{"date_created":"2023-08-07T09:48:08Z","file_name":"2023_PhysRevB_Brighi.pdf","date_updated":"2023-08-07T09:48:08Z","file_size":3051398,"creator":"dernst","file_id":"13981","checksum":"f763000339b5fd543c14377109920690","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"ec_funded":1,"volume":108,"issue":"5","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The many-body localization (MBL) proximity effect is an intriguing phenomenon where a thermal bath localizes due to the interaction with a disordered system. The interplay of thermal and nonergodic behavior in these systems gives rise to a rich phase diagram, whose exploration is an active field of research. In this paper, we study a bosonic Hubbard model featuring two particle species representing the bath and the disordered system. Using state-of-the-art numerical techniques, we investigate the dynamics of the model in different regimes, based on which we obtain a tentative phase diagram as a function of coupling strength and bath size. When the bath is composed of a single particle, we observe clear signatures of a transition from an MBL proximity effect to a delocalized phase. Increasing the bath size, however, its thermalizing effect becomes stronger and eventually the whole system delocalizes in the range of moderate interaction strengths studied. In this regime, we characterize particle transport, revealing diffusive behavior of the originally localized bosons."}],"intvolume":" 108","month":"08","scopus_import":"1","ddc":["530"],"date_updated":"2023-08-07T09:51:39Z","file_date_updated":"2023-08-07T09:48:08Z","department":[{"_id":"MaSe"}],"_id":"13963","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"Physical Review B","day":"01","year":"2023","has_accepted_license":"1","date_created":"2023-08-05T18:25:22Z","doi":"10.1103/physrevb.108.054201","date_published":"2023-08-01T00:00:00Z","acknowledgement":"We thank A. A. Michailidis and A. Mirlin for insightful discussions. P.B., M.L., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was\r\nsupported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597) and by the Swiss National Science Foundation. P.B., M.L., and M.S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD simulations were performed using the ITensor library [60].","oa":1,"quality_controlled":"1","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Brighi, Pietro, et al. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B, vol. 108, no. 5, 054201, American Physical Society, 2023, doi:10.1103/physrevb.108.054201.","apa":"Brighi, P., Ljubotina, M., Abanin, D. A., & Serbyn, M. (2023). Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.054201","ama":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 2023;108(5). doi:10.1103/physrevb.108.054201","short":"P. Brighi, M. Ljubotina, D.A. Abanin, M. Serbyn, Physical Review B 108 (2023).","ieee":"P. Brighi, M. Ljubotina, D. A. Abanin, and M. Serbyn, “Many-body localization proximity effect in a two-species bosonic Hubbard model,” Physical Review B, vol. 108, no. 5. American Physical Society, 2023.","chicago":"Brighi, Pietro, Marko Ljubotina, Dmitry A. Abanin, and Maksym Serbyn. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.054201.","ista":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. 2023. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 108(5), 054201."},"title":"Many-body localization proximity effect in a two-species bosonic Hubbard model","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2303.16876"]},"author":[{"last_name":"Brighi","orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko","last_name":"Ljubotina"},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"article_number":"054201","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}]},{"_id":"13966","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-07T08:41:29Z","department":[{"_id":"MiLe"},{"_id":"TaHa"}],"abstract":[{"lang":"eng","text":"We present a low-scaling diagrammatic Monte Carlo approach to molecular correlation energies. Using combinatorial graph theory to encode many-body Hugenholtz diagrams, we sample the Møller-Plesset (MPn) perturbation series, obtaining accurate correlation energies up to n=5, with quadratic scaling in the number of basis functions. Our technique reduces the computational complexity of the molecular many-fermion correlation problem, opening up the possibility of low-scaling, accurate stochastic computations for a wide class of many-body systems described by Hugenholtz diagrams."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.12666","open_access":"1"}],"month":"07","intvolume":" 108","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":108,"ec_funded":1,"article_number":"045115","project":[{"name":"A path-integral approach to composite impurities","grant_number":"M02641","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26B96266-B435-11E9-9278-68D0E5697425","grant_number":"M02751","name":"Algebro-Geometric Applications of Factorization Homology"},{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B, vol. 108, no. 4, 045115, American Physical Society, 2023, doi:10.1103/PhysRevB.108.045115.","short":"G. Bighin, Q.P. Ho, M. Lemeshko, T.V. Tscherbul, Physical Review B 108 (2023).","ieee":"G. Bighin, Q. P. Ho, M. Lemeshko, and T. V. Tscherbul, “Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling,” Physical Review B, vol. 108, no. 4. American Physical Society, 2023.","ama":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 2023;108(4). doi:10.1103/PhysRevB.108.045115","apa":"Bighin, G., Ho, Q. P., Lemeshko, M., & Tscherbul, T. V. (2023). Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.045115","chicago":"Bighin, Giacomo, Quoc P Ho, Mikhail Lemeshko, and T. V. Tscherbul. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.045115.","ista":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. 2023. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 108(4), 045115."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"first_name":"Quoc P","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","full_name":"Ho, Quoc P","last_name":"Ho"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"first_name":"T. V.","last_name":"Tscherbul","full_name":"Tscherbul, T. V."}],"external_id":{"arxiv":["2203.12666"]},"article_processing_charge":"No","title":"Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling","acknowledgement":"We acknowledge stimulating discussions with Sergey Varganov, Artur Izmaylov, Jacek Kłos, Piotr Żuchowski, Dominika Zgid, Nikolay Prokof'ev, Boris Svistunov, Robert Parrish, and Andreas Heßelmann. G.B. and Q.P.H. acknowledge support from the Austrian Science Fund (FWF) under Projects No. M2641-N27 and No. M2751. M.L. acknowledges support by the FWF under Project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.V.T. was supported by the NSF CAREER award No. PHY-2045681. This work is supported by the German Research Foundation (DFG) under Germany's Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster). The authors acknowledge support by the state of Baden-Württemberg through bwHPC.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"year":"2023","day":"15","publication":"Physical Review B","date_published":"2023-07-15T00:00:00Z","doi":"10.1103/PhysRevB.108.045115","date_created":"2023-08-06T22:01:10Z"},{"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15227/orgsyn.100.0271"}],"scopus_import":"1","intvolume":" 100","month":"07","publication_status":"published","publication_identifier":{"issn":["0078-6209"],"eissn":["2333-3553"]},"language":[{"iso":"eng"}],"volume":100,"_id":"13970","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-07T08:21:45Z","department":[{"_id":"BaPi"}],"oa":1,"quality_controlled":"1","publisher":"Organic Syntheses","year":"2023","publication":"Organic Syntheses","day":"01","page":"271-286","date_created":"2023-08-06T22:01:11Z","doi":"10.15227/orgsyn.100.0271","date_published":"2023-07-01T00:00:00Z","citation":{"ista":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 100, 271–286.","chicago":"Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger, and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses. Organic Syntheses, 2023. https://doi.org/10.15227/orgsyn.100.0271.","short":"A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses 100 (2023) 271–286.","ieee":"A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,” Organic Syntheses, vol. 100. Organic Syntheses, pp. 271–286, 2023.","apa":"Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., & Pieber, B. (2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. Organic Syntheses. https://doi.org/10.15227/orgsyn.100.0271","ama":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 2023;100:271-286. doi:10.15227/orgsyn.100.0271","mla":"Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:10.15227/orgsyn.100.0271."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Amiera","full_name":"Madani, Amiera","last_name":"Madani"},{"full_name":"Sletten, Eric T.","last_name":"Sletten","first_name":"Eric T."},{"last_name":"Cavedon","full_name":"Cavedon, Cristian","first_name":"Cristian"},{"first_name":"Peter H.","full_name":"Seeberger, Peter H.","last_name":"Seeberger"},{"first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"}],"title":"Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose"},{"_id":"13127","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-07T13:09:09Z","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"file_date_updated":"2023-06-13T08:05:46Z","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense."}],"month":"06","intvolume":" 14","scopus_import":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"4af0393e3ed47b3fc46e68b81c3c1007","file_id":"13132","success":1,"date_updated":"2023-06-13T08:05:46Z","file_size":2358167,"creator":"dernst","date_created":"2023-06-13T08:05:46Z","file_name":"2023_NatureComm_CasillasPerez.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","volume":14,"related_material":{"record":[{"relation":"research_data","status":"public","id":"12945"}]},"ec_funded":1,"article_number":"3232","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y.","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 2023;14. doi:10.1038/s41467-023-38947-y","apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y."},"title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","author":[{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","orcid":"0000-0002-7214-0171","full_name":"Bod'Ová, Katarína","last_name":"Bod'Ová"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"external_id":{"pmid":["37270641"],"isi":["001002562700005"]},"article_processing_charge":"Yes","acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"03","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.1038/s41467-023-38947-y","date_published":"2023-06-03T00:00:00Z","date_created":"2023-06-11T22:00:40Z"},{"title":"Data from: \"Dynamic pathogen detection and social feedback shape collective hygiene in ants\" ","department":[{"_id":"SyCr"}],"file_date_updated":"2023-05-12T08:04:08Z","author":[{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2023-08-07T13:09:09Z","citation":{"ista":"Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12945.","chicago":"Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12945.","short":"S. Cremer, (2023).","ieee":"S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.","apa":"Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12945","ama":"Cremer S. Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945","mla":"Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12945."},"status":"public","keyword":["collective behavior","host-pathogen interactions","social immunity","epidemiology","social insects","probabilistic modeling"],"type":"research_data","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":"12945","date_published":"2023-05-12T00:00:00Z","related_material":{"record":[{"status":"public","id":"13127","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:12945","date_created":"2023-05-11T21:35:17Z","contributor":[{"last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","contributor_type":"data_collector","first_name":"Barbara E"},{"last_name":"Grasse","contributor_type":"data_collector","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"last_name":"Bodova","first_name":"Katarina","contributor_type":"researcher"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor"}],"file":[{"date_created":"2023-05-12T08:04:04Z","file_name":"Experimental_data.zip","creator":"scremer","date_updated":"2023-05-12T08:04:04Z","file_size":3414674,"file_id":"12947","checksum":"3eadf17fd59ad8c98bf10bf63061863c","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip"},{"file_name":"README_Experimental_Data.md","date_created":"2023-05-12T08:04:08Z","file_size":2113,"date_updated":"2023-05-12T08:04:08Z","creator":"scremer","success":1,"file_id":"12948","checksum":"1b5e8e01a0989154a76b44e6d8d68f89","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access"}],"day":"12","has_accepted_license":"1","year":"2023","month":"05","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"None","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","abstract":[{"text":"basic data for use in code for experimental data analysis for manuscript under revision: \r\nDynamic pathogen detection and social feedback shape collective hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}]},{"page":"82","date_published":"2023-04-28T00:00:00Z","doi":"10.15479/at:ista:12885","date_created":"2023-05-02T07:58:57Z","has_accepted_license":"1","year":"2023","day":"28","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","last_name":"Calcabrini"}],"article_processing_charge":"No","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","citation":{"chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","mla":"Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.","apa":"Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10806","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10042"},{"relation":"part_of_dissertation","status":"public","id":"12237"},{"id":"9118","status":"public","relation":"part_of_dissertation"},{"id":"10123","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_created":"2023-05-02T07:43:18Z","file_name":"Thesis_Calcabrini.docx","date_updated":"2023-05-02T07:43:18Z","file_size":99627036,"creator":"mcalcabr","checksum":"9347b0e09425f56fdcede5d3528404dc","file_id":"12887","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"},{"file_name":"Thesis_Calcabrini_pdfa.pdf","date_created":"2023-05-02T07:42:45Z","file_size":8742220,"date_updated":"2023-05-02T07:42:45Z","creator":"mcalcabr","success":1,"checksum":"2d188b76621086cd384f0b9264b0a576","file_id":"12888","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"04","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. "}],"oa_version":"Published Version","file_date_updated":"2023-05-02T07:43:18Z","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"supervisor":[{"last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"date_updated":"2023-08-14T07:25:26Z","ddc":["546","541"],"type":"dissertation","status":"public","_id":"12885"},{"page":"717-750","date_published":"2023-03-01T00:00:00Z","doi":"10.1007/s00023-022-01220-x","date_created":"2022-09-11T22:01:57Z","isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Annales Henri Poincare","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","author":[{"first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","full_name":"Wirth, Melchior","orcid":"0000-0002-0519-4241","last_name":"Wirth"},{"last_name":"Zhang","full_name":"Zhang, Haonan","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"external_id":{"isi":["000837499800002"],"arxiv":["2105.08303"]},"article_processing_charge":"Yes (via OA deal)","title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","citation":{"chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01220-x.","ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 717–50, doi:10.1007/s00023-022-01220-x.","ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 717–750, 2023.","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750.","ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 2023;24:717-750. doi:10.1007/s00023-022-01220-x","apa":"Wirth, M., & Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01220-x"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","name":"Curvature-dimension in noncommutative analysis","grant_number":"M03337"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"volume":24,"ec_funded":1,"publication_identifier":{"issn":["1424-0637"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8c7b185eba5ccd92ef55c120f654222c","file_id":"14051","success":1,"date_updated":"2023-08-14T11:38:28Z","file_size":554871,"creator":"dernst","date_created":"2023-08-14T11:38:28Z","file_name":"2023_AnnalesHenriPoincare_Wirth.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 24","abstract":[{"lang":"eng","text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups."}],"oa_version":"Published Version","department":[{"_id":"JaMa"}],"file_date_updated":"2023-08-14T11:38:28Z","date_updated":"2023-08-14T11:39:28Z","ddc":["510"],"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":"12087"},{"date_published":"2023-03-01T00:00:00Z","doi":"10.1007/s11856-022-2448-6","date_created":"2021-07-14T07:01:28Z","page":"501-554","day":"01","publication":"Israel Journal of Mathematics","isi":1,"has_accepted_license":"1","year":"2023","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This work was done while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.","title":"Highly irregular separated nets","author":[{"full_name":"Dymond, Michael","last_name":"Dymond","first_name":"Michael"},{"id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","first_name":"Vojtech","last_name":"Kaluza","full_name":"Kaluza, Vojtech","orcid":"0000-0002-2512-8698"}],"external_id":{"arxiv":["1903.05923"],"isi":["000904950300003"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal of Mathematics. 253, 501–554.","chicago":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6.","ama":"Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics. 2023;253:501-554. doi:10.1007/s11856-022-2448-6","apa":"Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6","ieee":"M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.","short":"M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.","mla":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6."},"volume":253,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9653","checksum":"6fa0a3207dd1d6467c309fd1bcc867d1","creator":"vkaluza","date_updated":"2021-07-14T07:41:50Z","file_size":900422,"date_created":"2021-07-14T07:41:50Z","file_name":"separated_nets.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1565-8511"]},"publication_status":"published","month":"03","intvolume":" 253","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice. We study weaker notions of equivalence of separated nets and demonstrate that such notions also give rise to distinct equivalence classes. Put differently, we find occurrences of particularly strong divergence of separated nets from the integer lattice. Our approach generalises that of Burago and Kleiner and McMullen which takes place largely in a continuous setting. Existence of irregular separated nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞). In the present work we obtain stronger types of non-realisable densities.","lang":"eng"}],"department":[{"_id":"UlWa"}],"file_date_updated":"2021-07-14T07:41:50Z","ddc":["515","516"],"date_updated":"2023-08-14T11:26:34Z","status":"public","keyword":["Lipschitz","bilipschitz","bounded displacement","modulus of continuity","separated net","non-realisable density","Burago--Kleiner construction"],"type":"journal_article","article_type":"original","_id":"9652"},{"acknowledgement":"Scientific Research Program Funded by Shaanxi Provincial Education Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi (Grant No.2022JZ-31), Young Talent fund of University Association for Science and Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation (Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology (Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry and Technology for Chemical Industry, Ministry of Education, Shaanxi University of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology, Shaanxi University of Science and Technology (Grant No. KFKT2022-15).","quality_controlled":"1","publisher":"Elsevier","publication":"Applied Surface Science","day":"15","year":"2023","isi":1,"date_created":"2023-01-12T11:55:02Z","date_published":"2023-03-15T00:00:00Z","doi":"10.1016/j.apsusc.2022.156101","article_number":"156101","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. Elsevier. https://doi.org/10.1016/j.apsusc.2022.156101","ama":"Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 2023;613. doi:10.1016/j.apsusc.2022.156101","short":"L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H. Wang, Applied Surface Science 613 (2023).","ieee":"L. Zhang et al., “Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient,” Applied Surface Science, vol. 613. Elsevier, 2023.","mla":"Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science, vol. 613, 156101, Elsevier, 2023, doi:10.1016/j.apsusc.2022.156101.","ista":"Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 613, 156101.","chicago":"Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science. Elsevier, 2023. https://doi.org/10.1016/j.apsusc.2022.156101."},"title":"Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient","article_processing_charge":"No","external_id":{"isi":["000911497000001"]},"author":[{"full_name":"Zhang, Li","last_name":"Zhang","first_name":"Li"},{"full_name":"Liu, Xingyu","last_name":"Liu","first_name":"Xingyu"},{"first_name":"Ting","full_name":"Wu, Ting","last_name":"Wu"},{"id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f","first_name":"Shengduo","last_name":"Xu","full_name":"Xu, Shengduo"},{"first_name":"Guoquan","last_name":"Suo","full_name":"Suo, Guoquan"},{"first_name":"Xiaohui","full_name":"Ye, Xiaohui","last_name":"Ye"},{"first_name":"Xiaojiang","last_name":"Hou","full_name":"Hou, Xiaojiang"},{"first_name":"Yanling","full_name":"Yang, Yanling","last_name":"Yang"},{"full_name":"Liu, Qingfeng","last_name":"Liu","first_name":"Qingfeng"},{"last_name":"Wang","full_name":"Wang, Hongqiang","first_name":"Hongqiang"}],"oa_version":"None","abstract":[{"lang":"eng","text":"The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices."}],"intvolume":" 613","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0169-4332"]},"volume":613,"_id":"12113","keyword":["Surfaces","Coatings and Films","Condensed Matter Physics","Surfaces and Interfaces","General Physics and Astronomy","General Chemistry"],"status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-14T11:47:06Z","department":[{"_id":"MaIb"}]},{"scopus_import":"1","intvolume":" 11","month":"09","abstract":[{"lang":"eng","text":"We study the large scale behavior of elliptic systems with stationary random coefficient that have only slowly decaying correlations. To this aim we analyze the so-called corrector equation, a degenerate elliptic equation posed in the probability space. In this contribution, we use a parabolic approach and optimally quantify the time decay of the semigroup. For the theoretical point of view, we prove an optimal decay estimate of the gradient and flux of the corrector when spatially averaged over a scale R larger than 1. For the numerical point of view, our results provide convenient tools for the analysis of various numerical methods."}],"oa_version":"Published Version","volume":11,"publication_status":"published","publication_identifier":{"issn":["2194-0401"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"f83dcaecdbd3ace862c4ed97a20e8501","file_id":"14052","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_StochPartialDiffEquations_Clozeau.pdf","date_created":"2023-08-14T11:51:04Z","creator":"dernst","file_size":1635193,"date_updated":"2023-08-14T11:51:04Z"}],"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":"10173","department":[{"_id":"JuFi"}],"file_date_updated":"2023-08-14T11:51:04Z","date_updated":"2023-08-14T11:51:47Z","ddc":["510"],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"I would like to thank my advisor Antoine Gloria for suggesting this problem to me, as well for many interesting discussions and suggestions.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","page":"1254–1378","date_created":"2021-10-23T10:50:22Z","doi":"10.1007/s40072-022-00254-w","date_published":"2023-09-01T00:00:00Z","year":"2023","has_accepted_license":"1","isi":1,"publication":"Stochastics and Partial Differential Equations: Analysis and Computations","day":"01","external_id":{"isi":["000799715600001"],"arxiv":["2102.07452"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Clozeau, Nicolas","last_name":"Clozeau","first_name":"Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b"}],"title":"Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields","citation":{"ista":"Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 11, 1254–1378.","chicago":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-022-00254-w.","ama":"Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 2023;11:1254–1378. doi:10.1007/s40072-022-00254-w","apa":"Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-022-00254-w","ieee":"N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields,” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11. Springer Nature, pp. 1254–1378, 2023.","short":"N. Clozeau, Stochastics and Partial Differential Equations: Analysis and Computations 11 (2023) 1254–1378.","mla":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11, Springer Nature, 2023, pp. 1254–1378, doi:10.1007/s40072-022-00254-w."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"text":"Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 185","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"publication_status":"published","file":[{"date_updated":"2023-08-14T12:47:32Z","file_size":782278,"creator":"dernst","date_created":"2023-08-14T12:47:32Z","file_name":"2023_ProbabilityTheory_Cipolloni.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"b9247827dae5544d1d19c37abe547abc","file_id":"14054","success":1}],"language":[{"iso":"eng"}],"volume":185,"_id":"11741","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","date_updated":"2023-08-14T12:48:09Z","ddc":["510"],"file_date_updated":"2023-08-14T12:47:32Z","department":[{"_id":"LaEr"}],"acknowledgement":"The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Probability Theory and Related Fields","page":"1183–1218","date_published":"2023-04-01T00:00:00Z","doi":"10.1007/s00440-022-01156-7","date_created":"2022-08-07T22:02:00Z","citation":{"ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-022-01156-7.","ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 2023;185:1183–1218. doi:10.1007/s00440-022-01156-7","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-022-01156-7","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” Probability Theory and Related Fields, vol. 185. Springer Nature, pp. 1183–1218, 2023.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218.","mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:10.1007/s00440-022-01156-7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000830344500001"],"arxiv":["2106.10200"]},"title":"Quenched universality for deformed Wigner matrices"},{"acknowledgement":"The National Key Research and Development Program of China (2018YFA0702100), the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Natural Science Foundation of China (51571007 and 51772012), the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian Science Fund (FWF).","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"day":"24","publication":"Chemistry of Materials","has_accepted_license":"1","isi":1,"year":"2023","date_published":"2023-01-24T00:00:00Z","doi":"10.1021/acs.chemmater.2c03542","date_created":"2023-01-22T23:00:55Z","page":"755-763","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D. Zhao, Chemistry of Materials 35 (2023) 755–763.","ieee":"S. Wang et al., “Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials, vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.","apa":"Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023). Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.2c03542","ama":"Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542","mla":"Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials, vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542.","ista":"Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763.","chicago":"Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542."},"title":"Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe","author":[{"first_name":"Siqi","last_name":"Wang","full_name":"Wang, Siqi"},{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"first_name":"Shulin","last_name":"Bai","full_name":"Bai, Shulin"},{"last_name":"Qin","full_name":"Qin, Bingchao","first_name":"Bingchao"},{"full_name":"Zhu, Yingcai","last_name":"Zhu","first_name":"Yingcai"},{"full_name":"Zhan, Shaoping","last_name":"Zhan","first_name":"Shaoping"},{"first_name":"Junqing","last_name":"Zheng","full_name":"Zheng, Junqing"},{"full_name":"Tang, Shuwei","last_name":"Tang","first_name":"Shuwei"},{"last_name":"Zhao","full_name":"Zhao, Li Dong","first_name":"Li Dong"}],"article_processing_charge":"No","external_id":{"isi":["000914749700001"]},"oa_version":"Published Version","abstract":[{"text":"High carrier mobility is critical to improving thermoelectric performance over a broad temperature range. However, traditional doping inevitably deteriorates carrier mobility. Herein, we develop a strategy for fine tuning of defects to improve carrier mobility. To begin, n-type PbTe is created by compensating for the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering, resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is introduced to compensate for the remaining intrinsic Pb vacancies. We find that excess Ag exhibits a dynamic doping process with increasing temperatures, increasing both the carrier concentration and carrier mobility throughout a wide temperature range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier concentration suppresses the bipolar thermal conductivity at high temperatures. The final step is using iodine to optimize the carrier concentration to ∼1019 cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of ∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance carrier mobility and improve thermoelectric performance.","lang":"eng"}],"month":"01","intvolume":" 35","scopus_import":"1","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14055","checksum":"b21dca2aa7a80c068bc256bdd1fea9df","file_size":2961043,"date_updated":"2023-08-14T12:57:25Z","creator":"dernst","file_name":"2023_ChemistryMaterials_Wang.pdf","date_created":"2023-08-14T12:57:25Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0897-4756"],"eissn":["1520-5002"]},"publication_status":"published","issue":"2","volume":35,"_id":"12331","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["540"],"date_updated":"2023-08-14T12:57:44Z","department":[{"_id":"MaIb"}],"file_date_updated":"2023-08-14T12:57:25Z"},{"date_created":"2022-08-28T22:02:01Z","date_published":"2023-04-01T00:00:00Z","doi":"10.1007/s00454-022-00394-9","page":"745–770","publication":"Discrete and Computational Geometry","day":"01","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","title":"Inserting one edge into a simple drawing is hard","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M","full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara"},{"last_name":"Klute","full_name":"Klute, Fabian","first_name":"Fabian"},{"last_name":"Parada","full_name":"Parada, Irene","first_name":"Irene"},{"last_name":"Vogtenhuber","full_name":"Vogtenhuber, Birgit","first_name":"Birgit"},{"first_name":"Raimund","full_name":"Seidel, Raimund","last_name":"Seidel"},{"first_name":"Tilo","full_name":"Wiedera, Tilo","last_name":"Wiedera"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 2023;69:745–770. doi:10.1007/s00454-022-00394-9","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., & Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023, pp. 745–770, doi:10.1007/s00454-022-00394-9."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"volume":69,"language":[{"iso":"eng"}],"file":[{"creator":"alisjak","date_updated":"2022-08-29T11:23:15Z","file_size":1002218,"date_created":"2022-08-29T11:23:15Z","file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"def7ae3b28d9fd6aec16450e40090302","file_id":"12006","success":1}],"publication_status":"published","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"intvolume":" 69","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles."}],"file_date_updated":"2022-08-29T11:23:15Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2023-08-14T12:51:25Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"11999"},{"abstract":[{"text":"The design and implementation of efficient concurrent data structures has seen significant attention. However, most of this work has focused on concurrent data structures providing good worst-case guarantees, although, in real workloads, objects are often accessed at different rates. Efficient distribution-adaptive data structures, such as splay-trees, are known in the sequential case; however, they often are hard to translate efficiently to the concurrent case. We investigate distribution-adaptive concurrent data structures, and propose a new design called the splay-list. At a high level, the splay-list is similar to a standard skip-list, with the key distinction that the height of each element adapts dynamically to its access rate: popular elements “move up,” whereas rarely-accessed elements decrease in height. We show that the splay-list provides order-optimal amortized complexity bounds for a subset of operations, while being amenable to efficient concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity for performance, and can outperform the only previously-known distribution-adaptive concurrent design in certain workloads.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2008.01009","open_access":"1"}],"month":"09","intvolume":" 36","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":36,"_id":"12330","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-14T12:54:32Z","department":[{"_id":"DaAl"}],"quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"year":"2023","day":"01","publication":"Distributed Computing","page":"395-418","doi":"10.1007/s00446-022-00441-x","date_published":"2023-09-01T00:00:00Z","date_created":"2023-01-22T23:00:55Z","citation":{"chicago":"Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.","ista":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.","mla":"Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 395–418, doi:10.1007/s00446-022-00441-x.","short":"V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing 36 (2023) 395–418.","ieee":"V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list: A distribution-adaptive concurrent skip-list,” Distributed Computing, vol. 36. Springer Nature, pp. 395–418, 2023.","apa":"Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00441-x","ama":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii","last_name":"Aksenov","full_name":"Aksenov, Vitalii"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexandra","full_name":"Drozdova, Alexandra","last_name":"Drozdova"},{"last_name":"Mohtashami","full_name":"Mohtashami, Amirkeivan","first_name":"Amirkeivan"}],"article_processing_charge":"No","external_id":{"isi":["000913424000001"],"arxiv":["2008.01009"]},"title":"The splay-list: A distribution-adaptive concurrent skip-list"},{"acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"01","publication":"Molecular Ecology","has_accepted_license":"1","isi":1,"year":"2023","doi":"10.1111/mec.16793","date_published":"2023-03-01T00:00:00Z","date_created":"2023-01-12T12:09:17Z","page":"1441-1457","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457."},"title":"On the origin and structure of haplotype blocks","author":[{"full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226","last_name":"Shipilina","first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4530-8469","full_name":"Pal, Arka","last_name":"Pal","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"oa_version":"Published Version","pmid":1,"abstract":[{"text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.","lang":"eng"}],"month":"03","intvolume":" 32","scopus_import":"1","file":[{"file_name":"2023_MolecularEcology_Shipilina.pdf","date_created":"2023-08-16T08:15:41Z","creator":"dernst","file_size":7144607,"date_updated":"2023-08-16T08:15:41Z","success":1,"checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_id":"14062","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"publication_status":"published","volume":32,"issue":"6","_id":"12159","status":"public","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"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)"},"ddc":["570"],"date_updated":"2023-08-16T08:18:47Z","file_date_updated":"2023-08-16T08:15:41Z","department":[{"_id":"NiBa"}]},{"department":[{"_id":"PaSc"}],"file_date_updated":"2023-08-16T09:36:28Z","date_updated":"2023-08-16T09:37:25Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","keyword":["Structural Biology"],"_id":"12114","volume":7,"publication_identifier":{"issn":["2590-1524"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14064","checksum":"b4b1c10a31018aafe053b7d55a470e54","success":1,"date_updated":"2023-08-16T09:36:28Z","file_size":5132322,"creator":"dernst","date_created":"2023-08-16T09:36:28Z","file_name":"2023_JourStrucBiologyX_Gauto.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 7","abstract":[{"text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"last_name":"Lebedenko","full_name":"Lebedenko, Olga O.","first_name":"Olga O."},{"id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","last_name":"Becker","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R."},{"last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"article_processing_charge":"No","external_id":{"pmid":["36578472"]},"title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","citation":{"short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).","ieee":"D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” Journal of Structural Biology: X, vol. 7. Elsevier, 2023.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X, vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"100079","doi":"10.1016/j.yjsbx.2022.100079","date_published":"2023-01-01T00:00:00Z","date_created":"2023-01-12T11:55:38Z","has_accepted_license":"1","year":"2023","day":"01","publication":"Journal of Structural Biology: X","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”."},{"scopus_import":"1","month":"03","intvolume":" 597","abstract":[{"lang":"eng","text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time."}],"oa_version":"Published Version","pmid":1,"volume":597,"issue":"6","publication_identifier":{"eissn":["1873-3468"],"issn":["0014-5793"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14063","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","file_size":3148143,"date_updated":"2023-08-16T08:31:04Z","creator":"dernst","file_name":"2023_FEBSLetters_Loose.pdf","date_created":"2023-08-16T08:31:04Z"}],"language":[{"iso":"eng"}],"article_type":"review","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"_id":"12163","department":[{"_id":"MaLo"}],"file_date_updated":"2023-08-16T08:31:04Z","date_updated":"2023-08-16T08:32:29Z","ddc":["570"],"quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","page":"762-777","doi":"10.1002/1873-3468.14540","date_published":"2023-03-01T00:00:00Z","date_created":"2023-01-12T12:09:58Z","isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"FEBS Letters","author":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"},{"last_name":"Auer","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","first_name":"Albert"},{"last_name":"Brognara","full_name":"Brognara, Gabriel","first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"id":"55380f95-15b2-11ec-abd3-aff8e230696b","first_name":"Hanifatul R","full_name":"Budiman, Hanifatul R","last_name":"Budiman"},{"full_name":"Kowalski, Lukasz M","last_name":"Kowalski","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","first_name":"Lukasz M"},{"first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","last_name":"Matijevic","full_name":"Matijevic, Ivana"}],"external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"article_processing_charge":"Yes (via OA deal)","title":"In vitro reconstitution of small GTPase regulation","citation":{"mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters. Wiley. https://doi.org/10.1002/1873-3468.14540","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777. doi:10.1002/1873-3468.14540","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2023-03-01T00:00:00Z","doi":"10.1007/s00446-022-00439-5","date_created":"2023-01-12T12:10:08Z","page":"29-43","day":"01","publication":"Distributed Computing","isi":1,"year":"2023","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","title":"Long-lived counters with polylogarithmic amortized step complexity","author":[{"full_name":"Baig, Mirza Ahad","last_name":"Baig","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad"},{"first_name":"Danny","full_name":"Hendler, Danny","last_name":"Hendler"},{"last_name":"Milani","full_name":"Milani, Alessia","first_name":"Alessia"},{"first_name":"Corentin","last_name":"Travers","full_name":"Travers, Corentin"}],"external_id":{"isi":["000890138700001"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” Distributed Computing, vol. 36. Springer Nature, pp. 29–43, 2023.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00439-5","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5","mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 29–43, doi:10.1007/s00446-022-00439-5.","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5."},"volume":36,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"publication_status":"published","month":"03","intvolume":" 36","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity."}],"department":[{"_id":"KrPi"}],"date_updated":"2023-08-16T08:39:36Z","status":"public","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"type":"journal_article","article_type":"original","_id":"12164"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier, 2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.","ama":"Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part 1):40-47. doi:10.1016/j.matpr.2022.11.037","apa":"Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037","ieee":"B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings, vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.","short":"B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings 78 (2023) 40–47.","chicago":"Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings. Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037.","ista":"Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part 1), 40–47."},"title":"Experimental analysis of Cascade CSTRs with step and pulse inputs","article_processing_charge":"No","author":[{"first_name":"Bushra","last_name":"Khatoon","full_name":"Khatoon, Bushra"},{"full_name":"Kamil, Shoaib","last_name":"Kamil","id":"185a19af-dc7d-11ea-9b2f-8eb2201959e9","first_name":"Shoaib"},{"first_name":"Hitesh","full_name":"Babu, Hitesh","last_name":"Babu"},{"full_name":"Siraj Alam, M.","last_name":"Siraj Alam","first_name":"M."}],"quality_controlled":"1","publisher":"Elsevier","publication":"Materials Today: Proceedings","day":"20","year":"2023","date_created":"2023-01-12T12:11:26Z","date_published":"2023-03-20T00:00:00Z","doi":"10.1016/j.matpr.2022.11.037","page":"40-47","_id":"12172","keyword":["General Medicine"],"status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-16T09:08:11Z","department":[{"_id":"BjHo"}],"oa_version":"None","abstract":[{"lang":"eng","text":"In industrial reactors and equipment, non-ideality is quite a common phenomenon rather than an exception. These deviations from ideality impact the process's overall efficiency and the effectiveness of the equipment. To recognize the associated non-ideality, one needs to have enough understanding of the formulation of the equations and in-depth knowledge of the residence time distribution (RTD) data of real reactors. In the current work, step input and pulse input were used to create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the aforementioned configuration, experiments were run at various flow rates to validate the developed characteristic equations. To produce RTD data, distilled water was utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior of tracer concentration exits age distribution, and cumulative fraction for each setup and each input was plotted and experimental results were compared with perfect behavior. Deviation of concentration exit age distribution and cumulative fractional distribution from ideal behavior is more in pulse input as compared to a step input. For ideal cases, the exit age distribution curve and cumulative fraction curves are independent of the type of input. But a significant difference was observed for the two cases, which may be due to non-measurable fluctuations in volumetric flow rate, non-achievement of instant injection of tracer in case of pulse input, and slight variations in the sampling period. Further, with increasing flow rate, concentration, exit age, and cumulative fractional curves shifted upward, and this behavior matches with the actual case."}],"intvolume":" 78","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2214-7853"]},"issue":"Part 1","volume":78},{"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.","lang":"eng"}],"month":"01","intvolume":" 16","scopus_import":"1","file":[{"success":1,"file_id":"12518","checksum":"49cd40f3bda6f267079427042e7d15e3","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf","date_created":"2023-02-06T07:56:14Z","creator":"dernst","file_size":21943473,"date_updated":"2023-02-06T07:56:14Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1662-5129"]},"publication_status":"published","volume":16,"_id":"12515","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-16T11:37:52Z","department":[{"_id":"PeJo"}],"file_date_updated":"2023-02-06T07:56:14Z","acknowledgement":"This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study.","quality_controlled":"1","publisher":"Frontiers","oa":1,"day":"10","publication":"Frontiers in Neuroanatomy","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-01-10T00:00:00Z","doi":"10.3389/fnana.2022.1097467","date_created":"2023-02-05T23:01:00Z","article_number":"1097467","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467","apa":"Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467","ieee":"I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers in Neuroanatomy, vol. 16. Frontiers, 2023.","short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467.","ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers, 2023. https://doi.org/10.3389/fnana.2022.1097467."},"title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","author":[{"last_name":"Ortiz-Leal","full_name":"Ortiz-Leal, Irene","first_name":"Irene"},{"first_name":"Mateo V.","last_name":"Torres","full_name":"Torres, Mateo V."},{"last_name":"Vargas Barroso","full_name":"Vargas Barroso, Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M"},{"first_name":"Luis Eusebio","last_name":"Fidalgo","full_name":"Fidalgo, Luis Eusebio"},{"first_name":"Ana María","full_name":"López-Beceiro, Ana María","last_name":"López-Beceiro"},{"first_name":"Jorge A.","full_name":"Larriva-Sahd, Jorge A.","last_name":"Larriva-Sahd"},{"first_name":"Pablo","last_name":"Sánchez-Quinteiro","full_name":"Sánchez-Quinteiro, Pablo"}],"article_processing_charge":"No","external_id":{"isi":["000919786900001"],"pmid":["36704406"]}},{"publication_status":"published","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2023_NatureBioTech_Yeung.pdf","date_created":"2023-08-16T11:30:45Z","creator":"dernst","file_size":12040976,"date_updated":"2023-08-16T11:30:45Z","success":1,"checksum":"668447a1c8d360b68f8aaf9e08ed644f","file_id":"14066","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"volume":41,"abstract":[{"lang":"eng","text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 41","month":"06","date_updated":"2023-08-16T11:32:33Z","ddc":["570"],"department":[{"_id":"ScienComp"}],"file_date_updated":"2023-08-16T11:30:45Z","_id":"12106","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","year":"2023","has_accepted_license":"1","isi":1,"publication":"Nature Biotechnology","day":"01","page":"813–823","date_created":"2023-01-08T23:00:53Z","doi":"10.1038/s41587-022-01560-3","date_published":"2023-06-01T00:00:00Z","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., & Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-022-01560-3","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823, 2023.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000909067600003"]},"article_processing_charge":"No","author":[{"last_name":"Yeung","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b","first_name":"Jake"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"full_name":"Zeller, Peter","last_name":"Zeller","first_name":"Peter"},{"last_name":"De Barbanson","full_name":"De Barbanson, Buys Anton","first_name":"Buys Anton"},{"full_name":"Wellenstein, Max D.","last_name":"Wellenstein","first_name":"Max D."},{"last_name":"Van Oudenaarden","full_name":"Van Oudenaarden, Alexander","first_name":"Alexander"}],"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells"},{"author":[{"last_name":"Boccato","full_name":"Boccato, Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","first_name":"Chiara"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"external_id":{"arxiv":["2205.15284"],"isi":["000910751800002"]},"article_processing_charge":"No","title":"The Bose Gas in a box with Neumann boundary conditions","citation":{"mla":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.","ieee":"C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560, 2023.","short":"C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.","ama":"Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3","apa":"Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3","chicago":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.","ista":"Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 1505–1560."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"page":"1505-1560","doi":"10.1007/s00023-022-01252-3","date_published":"2023-05-01T00:00:00Z","date_created":"2023-01-15T23:00:52Z","isi":1,"year":"2023","day":"01","publication":"Annales Henri Poincare","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged.","department":[{"_id":"RoSe"}],"date_updated":"2023-08-16T11:34:03Z","type":"journal_article","article_type":"original","status":"public","_id":"12183","volume":24,"ec_funded":1,"publication_identifier":{"issn":["1424-0637"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2205.15284","open_access":"1"}],"month":"05","intvolume":" 24","abstract":[{"lang":"eng","text":"We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii regime, with an optimal bound on the condensate depletion. Moreover, our lower bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann bracketing) a lower bound for the ground state energy of N bosons in a large box [−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit."}],"oa_version":"Preprint"},{"citation":{"mla":"Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85, doi:10.1021/acs.jcim.2c01346.","apa":"Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. American Chemical Society. https://doi.org/10.1021/acs.jcim.2c01346","ama":"Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","ieee":"P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society, pp. 973–985, 2023.","chicago":"Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling. American Chemical Society, 2023. https://doi.org/10.1021/acs.jcim.2c01346.","ista":"Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 63(3), 973–985."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["36638318"],"isi":["000920370700001"]},"article_processing_charge":"No","author":[{"last_name":"Koehl","full_name":"Koehl, Patrice","first_name":"Patrice"},{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"grant_number":"Z00342","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"year":"2023","has_accepted_license":"1","isi":1,"publication":"Journal of Chemical Information and Modeling","day":"13","page":"973-985","date_created":"2023-02-12T23:00:59Z","date_published":"2023-02-13T00:00:00Z","doi":"10.1021/acs.jcim.2c01346","acknowledgement":"P.K. acknowledges support from the University of California Multicampus Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant No.1760485). H.E. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access is funded by the Austrian Science Fund (FWF).","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","date_updated":"2023-08-16T12:22:07Z","ddc":["510","540"],"file_date_updated":"2023-08-16T12:21:13Z","department":[{"_id":"HeEd"}],"_id":"12544","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["1549-960X"],"issn":["1549-9596"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14070","checksum":"7d20562269edff1e31b9d6019d4983b0","creator":"dernst","file_size":8069223,"date_updated":"2023-08-16T12:21:13Z","file_name":"2023_JCIM_Koehl.pdf","date_created":"2023-08-16T12:21:13Z"}],"ec_funded":1,"volume":63,"issue":"3","abstract":[{"lang":"eng","text":"Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 63","month":"02"},{"file_date_updated":"2023-08-16T11:54:59Z","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"date_updated":"2023-08-16T11:55:48Z","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","article_type":"original","status":"public","_id":"12543","ec_funded":1,"related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/"}]},"volume":7,"publication_status":"published","publication_identifier":{"eissn":["2397-334X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-08-16T11:54:59Z","file_size":1600499,"creator":"dernst","date_created":"2023-08-16T11:54:59Z","file_name":"2023_NatureEcoEvo_Stock.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14069","checksum":"8244f4650a0e7aeea488d1bcd4a31702","success":1}],"scopus_import":"1","intvolume":" 7","month":"03","abstract":[{"lang":"eng","text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts."}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","pmid":1,"external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"article_processing_charge":"No","author":[{"id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock","full_name":"Stock, Miriam"},{"first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","last_name":"Milutinovic","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara"},{"last_name":"Hönigsberger","full_name":"Hönigsberger, Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60","first_name":"Michaela"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse"},{"full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer","id":"39523C54-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87","first_name":"Niklas","last_name":"Kampleitner","full_name":"Kampleitner, Niklas"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671"},{"last_name":"Schmitt","full_name":"Schmitt, Thomas","first_name":"Thomas"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"title":"Pathogen evasion of social immunity","citation":{"ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460.","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6.","apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6","ieee":"M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.","short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"page":"450-460","date_created":"2023-02-12T23:00:59Z","date_published":"2023-03-01T00:00:00Z","doi":"10.1038/s41559-023-01981-6","year":"2023","has_accepted_license":"1","isi":1,"publication":"Nature Ecology and Evolution","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C."},{"title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","author":[{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac"},{"first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001021692200001"],"pmid":["37065438"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004."},"project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"article_number":"qrac004","date_published":"2023-02-01T00:00:00Z","doi":"10.1093/evlett/qrac004","date_created":"2023-02-06T13:59:12Z","day":"01","publication":"Evolution Letters","isi":1,"has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file_date_updated":"2023-08-16T11:43:33Z","ddc":["570"],"date_updated":"2023-08-16T11:44:32Z","status":"public","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"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)"},"_id":"12521","volume":7,"issue":"1","ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14068","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_size":2592189,"date_updated":"2023-08-16T11:43:33Z","creator":"dernst","file_name":"2023_EvLetters_Mrnjavac.pdf","date_created":"2023-08-16T11:43:33Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2056-3744"]},"publication_status":"published","month":"02","intvolume":" 7","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.","lang":"eng"}]},{"keyword":["General Neuroscience"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"review","_id":"12679","department":[{"_id":"SiHi"}],"file_date_updated":"2023-08-16T12:29:06Z","ddc":["570"],"date_updated":"2023-08-16T12:30:25Z","intvolume":" 79","month":"04","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression.","lang":"eng"}],"ec_funded":1,"issue":"4","volume":79,"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-08-16T12:29:06Z","file_size":1787894,"creator":"dernst","date_created":"2023-08-16T12:29:06Z","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14071","checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","success":1}],"publication_status":"published","publication_identifier":{"issn":["0959-4388"]},"project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"article_number":"102695","title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["36842274"],"isi":["000953497700001"]},"author":[{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2023.102695","ama":"Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4). doi:10.1016/j.conb.2023.102695","short":"S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).","ieee":"S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights from developing cerebral cortex,” Current Opinion in Neurobiology, vol. 79, no. 4. Elsevier, 2023.","mla":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol. 79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","chicago":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology. Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695."},"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"I wish to thank all current and past members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. I apologize to colleagues whose work I could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agree-ment no. 725780 LinPro) to SH.","date_created":"2023-02-26T12:24:21Z","doi":"10.1016/j.conb.2023.102695","date_published":"2023-04-01T00:00:00Z","publication":"Current Opinion in Neurobiology","day":"01","year":"2023","isi":1,"has_accepted_license":"1"},{"author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","last_name":"Agresti","full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962"},{"last_name":"Lindemulder","full_name":"Lindemulder, Nick","first_name":"Nick"},{"last_name":"Veraar","full_name":"Veraar, Mark","first_name":"Mark"}],"external_id":{"isi":["000914134900001"],"arxiv":["2104.05063"]},"article_processing_charge":"No","title":"On the trace embedding and its applications to evolution equations","citation":{"chicago":"Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding and Its Applications to Evolution Equations.” Mathematische Nachrichten. Wiley, 2023. https://doi.org/10.1002/mana.202100192.","ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.","mla":"Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution Equations.” Mathematische Nachrichten, vol. 296, no. 4, Wiley, 2023, pp. 1319–50, doi:10.1002/mana.202100192.","apa":"Agresti, A., Lindemulder, N., & Veraar, M. (2023). On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. Wiley. https://doi.org/10.1002/mana.202100192","ama":"Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 2023;296(4):1319-1350. doi:10.1002/mana.202100192","ieee":"A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its applications to evolution equations,” Mathematische Nachrichten, vol. 296, no. 4. Wiley, pp. 1319–1350, 2023.","short":"A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023) 1319–1350."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"The first author has been partially supported by the Nachwuchsring—Network for the promotion of young scientists—at TU Kaiserslautern. The second and third authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","page":"1319-1350","date_published":"2023-04-01T00:00:00Z","doi":"10.1002/mana.202100192","date_created":"2023-01-29T23:00:59Z","has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"Mathematische Nachrichten","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","_id":"12429","department":[{"_id":"JuFi"}],"file_date_updated":"2023-08-16T11:40:02Z","date_updated":"2023-08-16T11:41:42Z","ddc":["510"],"scopus_import":"1","month":"04","intvolume":" 296","abstract":[{"lang":"eng","text":"In this paper, we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement is that we can allow general interpolation couples. The abstract results are applied to regularity problems for fractional evolution equations and stochastic evolution equations, where uniform trace estimates on the half-line are shown."}],"oa_version":"Published Version","volume":296,"issue":"4","publication_identifier":{"issn":["0025-584X"],"eissn":["1522-2616"]},"publication_status":"published","file":[{"date_created":"2023-08-16T11:40:02Z","file_name":"2023_MathNachrichten_Agresti.pdf","creator":"dernst","date_updated":"2023-08-16T11:40:02Z","file_size":449280,"file_id":"14067","checksum":"6f099f1d064173784d1a27716a2cc795","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}]},{"article_number":"2350006","citation":{"apa":"Falconi, M., Leopold, N. K., Mitrouskas, D. J., & Petrat, S. P. (2023). Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X2350006X","ama":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 2023;35(4). doi:10.1142/S0129055X2350006X","ieee":"M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov dynamics and higher-order corrections for the regularized Nelson model,” Reviews in Mathematical Physics, vol. 35, no. 4. World Scientific Publishing, 2023.","short":"M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical Physics 35 (2023).","mla":"Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” Reviews in Mathematical Physics, vol. 35, no. 4, 2350006, World Scientific Publishing, 2023, doi:10.1142/S0129055X2350006X.","ista":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 35(4), 2350006.","chicago":"Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” Reviews in Mathematical Physics. World Scientific Publishing, 2023. https://doi.org/10.1142/S0129055X2350006X."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Falconi, Marco","last_name":"Falconi","first_name":"Marco"},{"full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","last_name":"Leopold","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889","last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P"}],"external_id":{"isi":["000909760300001"],"arxiv":["2110.00458"]},"article_processing_charge":"No","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","quality_controlled":"1","publisher":"World Scientific Publishing","oa":1,"isi":1,"year":"2023","day":"09","publication":"Reviews in Mathematical Physics","date_published":"2023-01-09T00:00:00Z","doi":"10.1142/S0129055X2350006X","date_created":"2023-01-29T23:00:59Z","_id":"12430","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-16T11:47:27Z","department":[{"_id":"RoSe"}],"abstract":[{"text":"We study the time evolution of the Nelson model in a mean-field limit in which N nonrelativistic bosons weakly couple (with respect to the particle number) to a positive or zero mass quantized scalar field. Our main result is the derivation of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove the convergence of the approximate wave function to the many-body wave function in norm, with a convergence rate proportional to the number of corrections taken into account in the approximation. We prove an analogous result for the unitary propagator. As an application, we derive a simple system of partial differential equations describing the time evolution of the first- and second-order approximations to the one-particle reduced density matrices of the particles and the quantum field, respectively.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2110.00458"}],"month":"01","intvolume":" 35","publication_identifier":{"issn":["0129-055X"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":35,"issue":"4"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"12762","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"file_date_updated":"2023-08-16T12:39:57Z","date_updated":"2023-08-16T12:41:53Z","ddc":["570"],"scopus_import":"1","intvolume":" 3","month":"03","abstract":[{"text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":3,"publication_status":"published","publication_identifier":{"eissn":["2662-8457"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","file_id":"14073","success":1,"date_updated":"2023-08-16T12:39:57Z","file_size":4474284,"creator":"dernst","date_created":"2023-08-16T12:39:57Z","file_name":"2023_NatureCompScience_Lombardi.pdf"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"external_id":{"arxiv":["2108.06686"]},"article_processing_charge":"No","author":[{"first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","first_name":"Selver","last_name":"Pepic","full_name":"Pepic, Selver"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"}],"title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","citation":{"mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9.","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-023-00410-9","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.).","page":"254-263","date_created":"2023-03-26T22:01:08Z","date_published":"2023-03-20T00:00:00Z","doi":"10.1038/s43588-023-00410-9","year":"2023","has_accepted_license":"1","publication":"Nature Computational Science","day":"20"},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","year":"2023","day":"05","page":"190","date_published":"2023-05-05T00:00:00Z","doi":"10.15479/at:ista:12891","date_created":"2023-05-05T08:48:20Z","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"citation":{"ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891","apa":"Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891","mla":"Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142"}],"article_processing_charge":"No","title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"date_created":"2023-05-05T13:01:14Z","file_name":"Thesis_Schauer_final.pdf","date_updated":"2023-05-05T13:01:14Z","file_size":31434230,"creator":"aschauer","file_id":"12907","checksum":"59b0303dc483f40a96a610a90aab7ee9","embargo":"2024-05-05","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","relation":"main_file"},{"checksum":"25f54e12479b6adaabd129a20568e6c1","file_id":"12908","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-05-05T13:04:15Z","file_name":"Thesis_Schauer_final.docx","creator":"aschauer","date_updated":"2023-05-05T13:04:15Z","file_size":43809109}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8966"},{"relation":"part_of_dissertation","status":"public","id":"7888"}]},"ec_funded":1,"_id":"12891","type":"dissertation","status":"public","supervisor":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"date_updated":"2023-08-21T06:25:48Z","ddc":["570"],"file_date_updated":"2023-05-05T13:04:15Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}]},{"date_published":"2023-07-01T00:00:00Z","doi":"10.4230/LIPIcs.ICALP.2023.69","date_created":"2023-08-20T22:01:14Z","has_accepted_license":"1","year":"2023","day":"01","publication":"50th International Colloquium on Automata, Languages, and Programming","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There, he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their insightful comments.","author":[{"first_name":"Gramoz","last_name":"Goranci","full_name":"Goranci, Gramoz"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"}],"article_processing_charge":"Yes","external_id":{"unknown":["2211.09606"]},"title":"Efficient data structures for incremental exact and approximate maximum flow","citation":{"ieee":"G. Goranci and M. H. Henzinger, “Efficient data structures for incremental exact and approximate maximum flow,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","short":"G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","apa":"Goranci, G., & Henzinger, M. H. (2023). Efficient data structures for incremental exact and approximate maximum flow. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69","ama":"Goranci G, Henzinger MH. Efficient data structures for incremental exact and approximate maximum flow. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.69","mla":"Goranci, Gramoz, and Monika H. Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.69.","ista":"Goranci G, Henzinger MH. 2023. Efficient data structures for incremental exact and approximate maximum flow. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 69.","chicago":"Goranci, Gramoz, and Monika H Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.69."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"article_number":"69","volume":261,"ec_funded":1,"publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"publication_status":"published","file":[{"success":1,"checksum":"074177e815a1656de5d4071c7a3dffa6","file_id":"14089","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_LIPIcsICALP_Goranci.pdf","date_created":"2023-08-21T06:59:05Z","file_size":875910,"date_updated":"2023-08-21T06:59:05Z","creator":"dernst"}],"language":[{"iso":"eng"}],"alternative_title":["LIPIcs"],"scopus_import":"1","month":"07","intvolume":" 261","abstract":[{"text":"We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed, unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm in general sparse graphs with arbitrarily good approximation guarantee.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"MoHe"}],"file_date_updated":"2023-08-21T06:59:05Z","date_updated":"2023-08-21T07:00:49Z","ddc":["000"],"type":"conference","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany","end_date":"2023-07-14","start_date":"2023-07-10"},"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":"14085"},{"author":[{"first_name":"David G.","full_name":"Harris, David G.","last_name":"Harris"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2007.10824"]},"title":"Parameter estimation for Gibbs distributions","citation":{"ista":"Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 72.","chicago":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.72.","ama":"Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72","apa":"Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs distributions. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72","ieee":"D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","short":"D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.72."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"72","date_published":"2023-07-01T00:00:00Z","doi":"10.4230/LIPIcs.ICALP.2023.72","date_created":"2023-08-20T22:01:14Z","has_accepted_license":"1","year":"2023","day":"01","publication":"50th International Colloquium on Automata, Languages, and Programming","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"We thank Heng Guo for helpful explanations of algorithms for sampling connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the Wang-Landau algorithm and its use in physics.","department":[{"_id":"VlKo"}],"file_date_updated":"2023-08-21T06:45:16Z","date_updated":"2023-08-21T06:49:11Z","ddc":["000","510"],"type":"conference","conference":{"start_date":"2023-07-10","location":"Paderborn, Germany","end_date":"2023-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"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":"14084","volume":261,"publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"publication_status":"published","file":[{"date_created":"2023-08-21T06:45:16Z","file_name":"2023_LIPIcsICALP_Harris.pdf","creator":"dernst","date_updated":"2023-08-21T06:45:16Z","file_size":917791,"checksum":"6dee0684245bb1c524b9c955db1e933d","file_id":"14088","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["LIPIcs"],"month":"07","intvolume":" 261","abstract":[{"text":"A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We will consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²) samples for integer-valued distributions (ignoring some second-order terms and parameters), We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs and perfect matchings in a graph.","lang":"eng"}],"oa_version":"Published Version"},{"ec_funded":1,"volume":261,"language":[{"iso":"eng"}],"file":[{"date_created":"2023-08-21T07:04:36Z","file_name":"2023_LIPIcsICALP_HenzingerM.pdf","date_updated":"2023-08-21T07:04:36Z","file_size":930943,"creator":"dernst","checksum":"a5eef225014e003efbfbe4830fdd23cb","file_id":"14090","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"isbn":["9783959772785"],"issn":["18688969"]},"intvolume":" 261","month":"07","scopus_import":"1","alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The maximization of submodular functions have found widespread application in areas such as machine learning, combinatorial optimization, and economics, where practitioners often wish to enforce various constraints; the matroid constraint has been investigated extensively due to its algorithmic properties and expressive power. Though tight approximation algorithms for general matroid constraints exist in theory, the running times of such algorithms typically scale quadratically, and are not practical for truly large scale settings. Recent progress has focused on fast algorithms for important classes of matroids given in explicit form. Currently, nearly-linear time algorithms only exist for graphic and partition matroids [Alina Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone submodular maximization constrained by graphic, transversal matroids, or laminar matroids in time near-linear in the size of their representation. Our algorithms achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the running time of our algorithm cannot be improved within the fast continuous greedy framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák, 2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures that maintain bases with approximate maximum cardinality and weight under certain element updates. These data structures need to support a weight decrease operation and a novel Freeze operation that allows the algorithm to freeze elements (i.e. force to be contained) in its basis regardless of future data structure operations. For the laminar matroid, we present a new dynamic data structure using the top tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et al., 2005] that maintains the maximum weight basis under insertions and deletions of elements in O(log n) time. This data structure needs to support certain subtree query and path update operations that are performed every insertion and deletion that are non-trivial to handle in conjunction. For the transversal matroid the Freeze operation corresponds to requiring the data structure to keep a certain set S of vertices matched, a property that we call S-stability. While there is a large body of work on dynamic matching algorithms, none are S-stable and maintain an approximate maximum weight matching under vertex updates. We give the first such algorithm for bipartite graphs with total running time linear (up to log factors) in the number of edges."}],"department":[{"_id":"MoHe"}],"file_date_updated":"2023-08-21T07:04:36Z","ddc":["000"],"date_updated":"2023-08-21T07:05:47Z","status":"public","conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"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":"conference","_id":"14086","date_created":"2023-08-20T22:01:14Z","doi":"10.4230/LIPIcs.ICALP.2023.74","date_published":"2023-07-01T00:00:00Z","publication":"50th International Colloquium on Automata, Languages, and Programming","day":"01","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","acknowledgement":" Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by NSF Award 2127781.","title":"Faster submodular maximization for several classes of matroids","article_processing_charge":"Yes","external_id":{"arxiv":["2305.00122"]},"author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Paul","full_name":"Liu, Paul","last_name":"Liu"},{"full_name":"Vondrák, Jan","last_name":"Vondrák","first_name":"Jan"},{"first_name":"Da Wei","full_name":"Zheng, Da Wei","last_name":"Zheng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Henzinger, Monika H., et al. “Faster Submodular Maximization for Several Classes of Matroids.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.74.","ieee":"M. H. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization for several classes of matroids,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","short":"M.H. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ama":"Henzinger MH, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for several classes of matroids. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.74","apa":"Henzinger, M. H., Liu, P., Vondrák, J., & Zheng, D. W. (2023). Faster submodular maximization for several classes of matroids. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.74","chicago":"Henzinger, Monika H, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular Maximization for Several Classes of Matroids.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.74.","ista":"Henzinger MH, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization for several classes of matroids. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 74."},"project":[{"call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"article_number":"74"},{"citation":{"ista":"Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 99.","chicago":"Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.99.","short":"N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","ama":"Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.99","apa":"Resch, N., Yuan, C., & Zhang, Y. (2023). Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.99","mla":"Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.99."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"arxiv":["2210.07754"]},"author":[{"last_name":"Resch","full_name":"Resch, Nicolas","first_name":"Nicolas"},{"first_name":"Chen","last_name":"Yuan","full_name":"Yuan, Chen"},{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","last_name":"Zhang","full_name":"Zhang, Yihan","orcid":"0000-0002-6465-6258"}],"title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","article_number":"99","year":"2023","has_accepted_license":"1","publication":"50th International Colloquium on Automata, Languages, and Programming","day":"01","date_created":"2023-08-20T22:01:13Z","date_published":"2023-07-01T00:00:00Z","doi":"10.4230/LIPIcs.ICALP.2023.99","acknowledgement":"Nicolas Resch: Research supported in part by ERC H2020 grant No.74079 (ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions.","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","date_updated":"2023-08-21T07:26:01Z","ddc":["000"],"file_date_updated":"2023-08-21T07:23:18Z","department":[{"_id":"MaMo"}],"_id":"14083","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany","end_date":"2023-07-14","start_date":"2023-07-10"},"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":"conference","status":"public","publication_status":"published","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"language":[{"iso":"eng"}],"file":[{"file_size":1141497,"date_updated":"2023-08-21T07:23:18Z","creator":"dernst","file_name":"2023_LIPIcsICALP_Resch.pdf","date_created":"2023-08-21T07:23:18Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14091","checksum":"a449143fec3fbebb092cb8ef3b53c226"}],"volume":261,"abstract":[{"text":"In this work we consider the list-decodability and list-recoverability of arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable if every radius pn Hamming ball contains less than L codewords; (p,𝓁,L)_q-list-recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length 𝓁 and again stipulate that there be less than L codewords.\r\nOur main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate (p,𝓁,L)_q-list-recoverable codes, the quantity we call the zero-rate threshold. Denoting this value by p_*, we in fact show that codes correcting a p_*+ε fraction of errors must have size O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin bound.\" To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p_*-ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin bound boils down to demonstrating the Schur convexity of a certain function defined on the q-simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q-ary list-decoding; however, we point out that this earlier proof is flawed.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"intvolume":" 261","month":"07"},{"status":"public","keyword":["General Physics","Electrostatics","Triboelectricity","Soft Matter","Acoustic Levitation","Granular Materials"],"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)"},"_id":"12697","department":[{"_id":"ScWa"}],"file_date_updated":"2023-02-28T12:37:54Z","ddc":["530","537"],"date_updated":"2023-08-22T08:41:32Z","month":"03","intvolume":" 130","main_file_link":[{"url":"https://arxiv.org/abs/2211.02488","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"Models for same-material contact electrification in granular media often rely on a local charge-driving parameter whose spatial variations lead to a stochastic origin for charge exchange. Measuring the charge transfer from individual granular spheres after contacts with substrates of the same material, we find instead a “global” charging behavior, coherent over the sample’s whole surface. Cleaning and baking samples fully resets charging magnitude and direction, which indicates the underlying global parameter is not intrinsic to the material, but acquired from its history. Charging behavior is randomly and irreversibly affected by changes in relative humidity, hinting at a mechanism where adsorbates, in particular, water, are fundamental to the charge-transfer process.","lang":"eng"}],"related_material":{"record":[{"id":"8101","status":"public","relation":"research_paper"}]},"volume":130,"issue":"9","ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"c4f2f6eea0408811f8f4898e15890355","file_id":"12698","file_size":2301864,"date_updated":"2023-02-28T12:20:27Z","creator":"ggrosjea","file_name":"Main_Preprint.pdf","date_created":"2023-02-28T12:20:27Z"},{"success":1,"checksum":"6af6ed6c97a977f923de4162294b43c4","file_id":"12699","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Suppl_info.pdf","date_created":"2023-02-28T12:20:55Z","file_size":1138625,"date_updated":"2023-02-28T12:20:55Z","creator":"ggrosjea"},{"content_type":"video/mp4","access_level":"open_access","relation":"main_file","file_id":"12700","checksum":"3f20365fb9515bdba3a111d912c8d8b4","success":1,"date_updated":"2023-02-28T12:37:54Z","file_size":793449,"creator":"ggrosjea","date_created":"2023-02-28T12:37:54Z","file_name":"Suppl_vid1.mp4"},{"access_level":"open_access","relation":"main_file","content_type":"video/mp4","checksum":"90cecacbe0e2f9dea11f91a4ba20c32e","file_id":"12701","success":1,"creator":"ggrosjea","date_updated":"2023-02-28T12:37:54Z","file_size":455925,"date_created":"2023-02-28T12:37:54Z","file_name":"Suppl_vid2.mp4"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","project":[{"grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"098202","title":"Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media","author":[{"id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M","orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M","last_name":"Grosjean"},{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"}],"article_processing_charge":"No","external_id":{"isi":["000946178200008"],"arxiv":["2211.02488"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” Physical Review Letters, vol. 130, no. 9, 098202, American Physical Society, 2023, doi:10.1103/physrevlett.130.098202.","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media,” Physical Review Letters, vol. 130, no. 9. American Physical Society, 2023.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).","apa":"Grosjean, G. M., & Waitukaitis, S. R. (2023). Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.098202","ama":"Grosjean GM, Waitukaitis SR. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 2023;130(9). doi:10.1103/physrevlett.130.098202","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.098202.","ista":"Grosjean GM, Waitukaitis SR. 2023. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 130(9), 098202."},"quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"We would like to thank Troy Shinbrot, Victor Lee and Daniele Foresti for helpful discussions. This project has received funding from the European Research Council Grant Agreement No. 949120 and from the the Marie Sk lodowska-Curie Grant Agreement No. 754411 under\r\nthe European Union’s Horizon 2020 research and innovation program.","doi":"10.1103/physrevlett.130.098202","date_published":"2023-03-03T00:00:00Z","date_created":"2023-02-28T12:14:46Z","day":"03","publication":"Physical Review Letters","has_accepted_license":"1","isi":1,"year":"2023"},{"_id":"13175","type":"dissertation","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","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-24T11:16:35Z","ddc":["537","535","539"],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"file_date_updated":"2023-07-06T11:35:15Z","abstract":[{"text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"success":1,"checksum":"7d03f1a5a5258ee43dfc3323dea4e08f","file_id":"13176","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"thesis_pdfa.pdf","date_created":"2023-06-30T08:17:25Z","file_size":18688376,"date_updated":"2023-06-30T08:17:25Z","creator":"cchlebak"},{"file_size":37847025,"date_updated":"2023-07-06T11:35:15Z","creator":"cchlebak","file_name":"thesis.zip","date_created":"2023-07-06T11:35:15Z","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"c3b45317ae58e0527533f98c202d81b7","file_id":"13196"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"old_edition","status":"public","id":"12900"},{"status":"public","id":"10924","relation":"part_of_dissertation"},{"id":"9114","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"citation":{"ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13175","mla":"Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13175."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Sahu","full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh"}],"article_processing_charge":"No","title":"Cavity quantum electrooptics","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2023","day":"05","page":"202","date_published":"2023-05-05T00:00:00Z","doi":"10.15479/at:ista:13175","date_created":"2023-06-30T08:07:43Z"},{"file_date_updated":"2023-07-06T11:37:40Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"supervisor":[{"last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-24T11:16:35Z","ddc":["537","535","539"],"type":"dissertation","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","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"_id":"12900","related_material":{"record":[{"id":"13175","status":"public","relation":"new_edition"},{"status":"public","id":"10924","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9114"}]},"ec_funded":1,"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-030-5"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"thesis.zip","date_created":"2023-05-09T08:45:14Z","creator":"rsahu","file_size":36767177,"date_updated":"2023-06-06T22:30:03Z","checksum":"8cbdab9c37ee55e591092a6f66b272c4","file_id":"12928","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed"},{"file_name":"thesis_pdfa_final.pdf","date_created":"2023-05-09T08:51:17Z","creator":"rsahu","file_size":17501990,"date_updated":"2023-07-06T11:37:40Z","checksum":"439659ead46618147309be39d9dd5a8c","file_id":"12929","relation":"main_file","access_level":"closed","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"lang":"eng","text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. "}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"oa_version":"Published Version","author":[{"last_name":"Sahu","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Cavity quantum electrooptics","citation":{"ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900.","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12900","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12900."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"page":"190","date_published":"2023-05-05T00:00:00Z","doi":"10.15479/at:ista:12900","date_created":"2023-05-05T11:08:50Z","has_accepted_license":"1","year":"2023","day":"05","publisher":"Institute of Science and Technology Austria"},{"project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"},{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"title":"Quantization-aware interval bound propagation for training certifiably robust quantized neural networks","article_processing_charge":"No","external_id":{"arxiv":["2211.16187"]},"author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"last_name":"Zikelic","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lechner, Mathias, et al. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol. 37, no. 12, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–73, doi:10.1609/aaai.v37i12.26747.","short":"M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, D. Rus, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–14973.","ieee":"M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware interval bound propagation for training certifiably robust quantized neural networks,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.","ama":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence. Vol 37. Association for the Advancement of Artificial Intelligence; 2023:14964-14973. doi:10.1609/aaai.v37i12.26747","apa":"Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., & Rus, D. (2023). Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 14964–14973). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i12.26747","chicago":"Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, Thomas A Henzinger, and Daniela Rus. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” In Proceedings of the 37th AAAI Conference on Artificial Intelligence, 37:14964–73. Association for the Advancement of Artificial Intelligence, 2023. https://doi.org/10.1609/aaai.v37i12.26747.","ista":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. 2023. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 14964–14973."},"oa":1,"quality_controlled":"1","publisher":"Association for the Advancement of Artificial Intelligence","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Research was sponsored by the United\r\nStates Air Force Research Laboratory and the United States Air Force Artificial Intelligence Accelerator and was accomplished under Cooperative Agreement Number FA8750-19-2-\r\n1000. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied,\r\nof the United States Air Force or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright\r\nnotation herein. The research was also funded in part by the AI2050 program at Schmidt Futures (Grant G-22-63172) and Capgemini SE.","date_created":"2023-08-27T22:01:17Z","doi":"10.1609/aaai.v37i12.26747","date_published":"2023-06-26T00:00:00Z","page":"14964-14973","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","day":"26","year":"2023","status":"public","conference":{"start_date":"2023-02-07","end_date":"2023-02-14","location":"Washington, DC, United States","name":"AAAI: Conference on Artificial Intelligence"},"type":"conference","_id":"14242","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2023-09-05T07:06:14Z","intvolume":" 37","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.16187"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We study the problem of training and certifying adversarially robust quantized neural networks (QNNs). Quantization is a technique for making neural networks more efficient by running them using low-bit integer arithmetic and is therefore commonly adopted in industry. Recent work has shown that floating-point neural networks that have been verified to be robust can become vulnerable to adversarial attacks after quantization, and certification of the quantized representation is necessary to guarantee robustness. In this work, we present quantization-aware interval bound propagation (QA-IBP), a novel method for training robust QNNs. Inspired by advances in robust learning of non-quantized networks, our training algorithm computes the gradient of an abstract representation of the actual network. Unlike existing approaches, our method can handle the discrete semantics of QNNs. Based on QA-IBP, we also develop a complete verification procedure for verifying the adversarial robustness of QNNs, which is guaranteed to terminate and produce a correct answer. Compared to existing approaches, the key advantage of our verification procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate experimentally that our approach significantly outperforms existing methods and establish the new state-of-the-art for training and certifying the robustness of QNNs.","lang":"eng"}],"ec_funded":1,"volume":37,"issue":"12","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781577358800"]}},{"year":"2023","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","day":"27","page":"5464-5471","date_created":"2023-08-27T22:01:18Z","date_published":"2023-06-27T00:00:00Z","doi":"10.1609/aaai.v37i5.25679","acknowledgement":"This research was supported in part by ISF grant no.1679/21, by the ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","oa":1,"quality_controlled":"1","citation":{"short":"G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, 2023, pp. 5464–5471.","ieee":"G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable budgets,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.","ama":"Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable budgets. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence. Vol 37. ; 2023:5464-5471. doi:10.1609/aaai.v37i5.25679","apa":"Avni, G., Jecker, I. R., & Zikelic, D. (2023). Bidding graph games with partially-observable budgets. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 5464–5471). Washington, DC, United States. https://doi.org/10.1609/aaai.v37i5.25679","mla":"Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.” Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol. 37, no. 5, 2023, pp. 5464–71, doi:10.1609/aaai.v37i5.25679.","ista":"Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 5464–5471.","chicago":"Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with Partially-Observable Budgets.” In Proceedings of the 37th AAAI Conference on Artificial Intelligence, 37:5464–71, 2023. https://doi.org/10.1609/aaai.v37i5.25679."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2211.13626"]},"article_processing_charge":"No","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287"},{"full_name":"Jecker, Ismael R","last_name":"Jecker","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","first_name":"Ismael R"},{"last_name":"Zikelic","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"title":"Bidding graph games with partially-observable budgets","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"publication_status":"published","publication_identifier":{"isbn":["9781577358800"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":37,"issue":"5","abstract":[{"lang":"eng","text":"Two-player zero-sum \"graph games\" are central in logic, verification, and multi-agent systems. The game proceeds by placing a token on a vertex of a graph, and allowing the players to move it to produce an infinite path, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In \"bidding games\", however, the players have budgets and in each turn, an auction (bidding) determines which player moves the token. So far, bidding games have only been studied as full-information games. In this work we initiate the study of partial-information bidding games: we study bidding games in which a player's initial budget is drawn from a known probability distribution. We show that while for some bidding mechanisms and objectives, it is straightforward to adapt the results from the full-information setting to the partial-information setting, for others, the analysis is significantly more challenging, requires new techniques, and gives rise to interesting results. Specifically, we study games with \"mean-payoff\" objectives in combination with \"poorman\" bidding. We construct optimal strategies for a partially-informed player who plays against a fully-informed adversary. We show that, somewhat surprisingly, the \"value\" under pure strategies does not necessarily exist in such games."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1609/aaai.v37i5.25679"}],"scopus_import":"1","intvolume":" 37","month":"06","date_updated":"2023-09-05T08:37:00Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"_id":"14243","conference":{"location":"Washington, DC, United States","end_date":"2023-02-14","start_date":"2023-02-07","name":"AAAI: Conference on Artificial Intelligence"},"type":"conference","status":"public"},{"department":[{"_id":"BeBi"}],"date_updated":"2023-09-05T07:22:03Z","type":"conference","conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2023-08-06","end_date":"2023-08-10","location":"Los Angeles, CA, United States"},"status":"public","_id":"14241","publication_identifier":{"isbn":["9798400701597"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.05944"}],"month":"07","abstract":[{"text":"We present a technique to optimize the reflectivity of a surface while preserving its overall shape. The naïve optimization of the mesh vertices using the gradients of reflectivity simulations results in undesirable distortion. In contrast, our robust formulation optimizes the surface normal as an independent variable that bridges the reflectivity term with differential rendering, and the regularization term with as-rigid-as-possible elastic energy. We further adaptively subdivide the input mesh to improve the convergence. Consequently, our method can minimize the retroreflectivity of a wide range of input shapes, resulting in sharply creased shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by changing the reward for the direction of the outgoing light directions, our method can be applied to other reflectivity design tasks, such as the optimization of architectural walls to concentrate light in a specific region. We have tested the proposed method using light-transport simulations and real-world 3D-printed objects.","lang":"eng"}],"oa_version":"Preprint","author":[{"full_name":"Tojo, Kenji","last_name":"Tojo","first_name":"Kenji"},{"full_name":"Shamir, Ariel","last_name":"Shamir","first_name":"Ariel"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"last_name":"Umetani","full_name":"Umetani, Nobuyuki","first_name":"Nobuyuki"}],"external_id":{"arxiv":["2305.05944"]},"article_processing_charge":"No","title":"Stealth shaper: Reflectivity optimization as surface stylization","citation":{"mla":"Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for Computing Machinery, 2023, doi:10.1145/3588432.3591542.","ieee":"K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity optimization as surface stylization,” in SIGGRAPH 2023 Conference Proceedings, Los Angeles, CA, United States, 2023.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference Proceedings, Association for Computing Machinery, 2023.","ama":"Tojo K, Shamir A, Bickel B, Umetani N. Stealth shaper: Reflectivity optimization as surface stylization. In: SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery; 2023. doi:10.1145/3588432.3591542","apa":"Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2023). Stealth shaper: Reflectivity optimization as surface stylization. In SIGGRAPH 2023 Conference Proceedings. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3588432.3591542","chicago":"Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” In SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591542.","ista":"Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 20."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"20","doi":"10.1145/3588432.3591542","date_published":"2023-07-23T00:00:00Z","date_created":"2023-08-27T22:01:17Z","year":"2023","day":"23","publication":"SIGGRAPH 2023 Conference Proceedings","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"acknowledgement":"The authors would like to thank Yuki Koyama and Takeo Igarashi for early discussions, and Yuta Yaguchi for support in 3D printing. This research is partially supported by the Israel Science Foundation grant number 1390/19.\r\n"},{"issue":"3","volume":129,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1522-1598"],"issn":["0022-3077"]},"intvolume":" 129","month":"03","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons."}],"department":[{"_id":"SiHi"}],"date_updated":"2023-09-05T12:13:34Z","keyword":["Physiology","General Neuroscience"],"status":"public","type":"journal_article","article_type":"original","_id":"12562","date_created":"2023-02-15T14:46:14Z","doi":"10.1152/jn.00172.2022","date_published":"2023-03-01T00:00:00Z","page":"501-512","publication":"Journal of Neurophysiology","day":"01","year":"2023","isi":1,"quality_controlled":"1","publisher":"American Physiological Society","acknowledgement":"The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University.","title":"Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons","article_processing_charge":"No","external_id":{"pmid":["36695533"],"isi":["000957721600001"]},"author":[{"first_name":"David R.","full_name":"Ladle, David R.","last_name":"Ladle"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512.","chicago":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology. American Physiological Society, 2023. https://doi.org/10.1152/jn.00172.2022.","short":"D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.","ieee":"D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” Journal of Neurophysiology, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023.","apa":"Ladle, D. R., & Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00172.2022","ama":"Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 2023;129(3):501-512. doi:10.1152/jn.00172.2022","mla":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:10.1152/jn.00172.2022."}},{"ddc":["000"],"date_updated":"2023-09-05T15:14:00Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2023-07-31T08:11:20Z","_id":"13310","status":"public","conference":{"start_date":"2023-07-17","end_date":"2023-07-22","location":"Paris, France","name":"CAV: Computer Aided Verification"},"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":"conference","language":[{"iso":"eng"}],"file":[{"file_size":647760,"date_updated":"2023-07-31T08:11:20Z","creator":"dernst","file_name":"2023_LNCS_CAV_HenzingerT.pdf","date_created":"2023-07-31T08:11:20Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"ccaf94bf7d658ba012c016e11869b54c","file_id":"13327"}],"publication_status":"published","publication_identifier":{"eisbn":["9783031377037"],"issn":["0302-9743"],"isbn":["9783031377020"],"eissn":["1611-3349"]},"ec_funded":1,"volume":13965,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation."}],"intvolume":" 13965","month":"07","alternative_title":["LNCS"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness. In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382. doi:10.1007/978-3-031-37703-7_17","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965, pp. 358–382.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382.","mla":"Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17.","ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13965, 358–382.","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17."},"title":"Monitoring algorithmic fairness","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2305.15979"]},"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Mahyar","id":"f1dedef5-2f78-11ee-989a-c4c97bccf506","orcid":"0009-0005-0820-1696","full_name":"Karimi, Mahyar","last_name":"Karimi"},{"last_name":"Kueffner","full_name":"Kueffner, Konstantin","orcid":"0000-0001-8974-2542","first_name":"Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515"},{"first_name":"Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","last_name":"Mallik"}],"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"publication":"Computer Aided Verification","day":"18","year":"2023","has_accepted_license":"1","date_created":"2023-07-25T18:32:40Z","date_published":"2023-07-18T00:00:00Z","doi":"10.1007/978-3-031-37703-7_17","page":"358–382","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"volume":30,"related_material":{"record":[{"status":"public","id":"12115","relation":"other"}]},"publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"publication_status":"published","file":[{"success":1,"checksum":"36a1200e1011f4b2155a8041d0308f34","file_id":"12490","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_AnnalsSurgicalOncology_Glajzer.pdf","date_created":"2023-02-02T13:01:20Z","creator":"dernst","file_size":365865,"date_updated":"2023-02-02T13:01:20Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 30","abstract":[{"lang":"eng","text":"Background: This study seeks to evaluate the impact of breast cancer (BRCA) gene status on tumor dissemination pattern, surgical outcome and survival in a multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data from 190 patients were gathered retrospectively. All patients had surgery at pOC and at least one further rOC surgery at four European high-volume centers. Patients were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut) and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor presentation, surgical outcome and survival data were analyzed between the two groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years younger and had significantly more tumor involvement upon diagnosis. Patients with BRCAmut disease showed higher debulking rates at all stages. Multivariate analysis showed that only patient age had significant predictive value for complete tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated with optimal debulking. Patients with BRCAmut disease showed significantly prolonged overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged in the BRCAmut group at all stages as well, reaching statistical significance during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a more aggressive course of disease with earlier onset and more extensive tumor dissemination at pOC. However, surgical outcome and OS were significantly better in patients with BRCAmut disease compared with patients with BRCAwt disease. We therefore propose to consider BRCAmut status in regard to patient selection for cytoreductive surgery, especially in rOC."}],"oa_version":"Published Version","file_date_updated":"2023-02-02T13:01:20Z","department":[{"_id":"JoDa"}],"date_updated":"2023-09-05T15:18:37Z","ddc":["610"],"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","keyword":["Oncology","Surgery"],"_id":"12205","page":"35-45","doi":"10.1245/s10434-022-12459-3","date_published":"2023-01-01T00:00:00Z","date_created":"2023-01-16T09:44:36Z","isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Annals of Surgical Oncology","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin Berlin and the Berlin Institute of Health. This work was supported by European Commission’s Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen Access funding enabled and organized by Projekt DEAL.","author":[{"last_name":"Glajzer","full_name":"Glajzer, Jacek","first_name":"Jacek"},{"first_name":"Dan Cacsire","full_name":"Castillo-Tong, Dan Cacsire","last_name":"Castillo-Tong"},{"first_name":"Rolf","last_name":"Richter","full_name":"Richter, Rolf"},{"first_name":"Ignace","full_name":"Vergote, Ignace","last_name":"Vergote"},{"first_name":"Hagen","last_name":"Kulbe","full_name":"Kulbe, Hagen"},{"last_name":"Vanderstichele","full_name":"Vanderstichele, Adriaan","first_name":"Adriaan"},{"full_name":"Ruscito, Ilary","last_name":"Ruscito","first_name":"Ilary"},{"full_name":"Trillsch, Fabian","last_name":"Trillsch","first_name":"Fabian"},{"first_name":"Alexander","last_name":"Mustea","full_name":"Mustea, Alexander"},{"last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Charlie","full_name":"Gourley, Charlie","last_name":"Gourley"},{"first_name":"Hani","full_name":"Gabra, Hani","last_name":"Gabra"},{"first_name":"Eliane T.","full_name":"Taube, Eliane T.","last_name":"Taube"},{"full_name":"Dorigo, Oliver","last_name":"Dorigo","first_name":"Oliver"},{"first_name":"David","last_name":"Horst","full_name":"Horst, David"},{"first_name":"Carlotta","full_name":"Keunecke, Carlotta","last_name":"Keunecke"},{"first_name":"Joanna","full_name":"Baum, Joanna","last_name":"Baum"},{"full_name":"Angelotti, Timothy","last_name":"Angelotti","first_name":"Timothy"},{"last_name":"Sehouli","full_name":"Sehouli, Jalid","first_name":"Jalid"},{"full_name":"Braicu, Elena Ioana","last_name":"Braicu","first_name":"Elena Ioana"}],"external_id":{"isi":["000852125500006"]},"article_processing_charge":"No","title":"Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium","citation":{"chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3.","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.","mla":"Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3","ieee":"J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 35–45."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"external_id":{"isi":["000879151800001"]},"article_processing_charge":"No","author":[{"last_name":"Glajzer","full_name":"Glajzer, Jacek","first_name":"Jacek"},{"first_name":"Dan Cacsire","full_name":"Castillo-Tong, Dan Cacsire","last_name":"Castillo-Tong"},{"first_name":"Rolf","full_name":"Richter, Rolf","last_name":"Richter"},{"last_name":"Vergote","full_name":"Vergote, Ignace","first_name":"Ignace"},{"last_name":"Kulbe","full_name":"Kulbe, Hagen","first_name":"Hagen"},{"full_name":"Vanderstichele, Adriaan","last_name":"Vanderstichele","first_name":"Adriaan"},{"first_name":"Ilary","last_name":"Ruscito","full_name":"Ruscito, Ilary"},{"first_name":"Fabian","full_name":"Trillsch, Fabian","last_name":"Trillsch"},{"first_name":"Alexander","last_name":"Mustea","full_name":"Mustea, Alexander"},{"full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"last_name":"Gourley","full_name":"Gourley, Charlie","first_name":"Charlie"},{"last_name":"Gabra","full_name":"Gabra, Hani","first_name":"Hani"},{"full_name":"Taube, Eliane T.","last_name":"Taube","first_name":"Eliane T."},{"first_name":"Oliver","last_name":"Dorigo","full_name":"Dorigo, Oliver"},{"last_name":"Horst","full_name":"Horst, David","first_name":"David"},{"full_name":"Keunecke, Carlotta","last_name":"Keunecke","first_name":"Carlotta"},{"first_name":"Joanna","full_name":"Baum, Joanna","last_name":"Baum"},{"full_name":"Angelotti, Timothy","last_name":"Angelotti","first_name":"Timothy"},{"last_name":"Sehouli","full_name":"Sehouli, Jalid","first_name":"Jalid"},{"full_name":"Braicu, Elena Ioana","last_name":"Braicu","first_name":"Elena Ioana"}],"title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","citation":{"ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47. doi:10.1245/s10434-022-12681-z","ieee":"J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 46–47, 2023.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","mla":"Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 46–47, doi:10.1245/s10434-022-12681-z."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","page":"46-47","date_created":"2023-01-12T11:56:22Z","date_published":"2023-01-01T00:00:00Z","doi":"10.1245/s10434-022-12681-z","year":"2023","isi":1,"publication":"Annals of Surgical Oncology","day":"01","article_type":"original","type":"journal_article","keyword":["Oncology","Surgery"],"status":"public","_id":"12115","department":[{"_id":"JoDa"}],"date_updated":"2023-09-05T15:18:36Z","main_file_link":[{"url":"https://doi.org/10.1245/s10434-022-12681-z","open_access":"1"}],"scopus_import":"1","intvolume":" 30","month":"01","oa_version":"Published Version","related_material":{"record":[{"id":"12205","status":"public","relation":"other"}]},"volume":30,"publication_status":"published","publication_identifier":{"eissn":["1534-4681"],"issn":["1068-9265"]},"language":[{"iso":"eng"}]},{"date_published":"2023-08-26T00:00:00Z","doi":"10.1038/s41467-023-40930-6","date_created":"2023-09-03T22:01:14Z","has_accepted_license":"1","year":"2023","day":"26","publication":"Nature Communications","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank Kayla Templeton and Peter Turcanu for technical assistance, Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648 (J.S.T.), and F32NS108519 (N.C.V.).","author":[{"first_name":"Nicholas C.","last_name":"Vierra","full_name":"Vierra, Nicholas C."},{"first_name":"Luisa","full_name":"Ribeiro-Silva, Luisa","last_name":"Ribeiro-Silva"},{"first_name":"Michael","last_name":"Kirmiz","full_name":"Kirmiz, Michael"},{"full_name":"Van Der List, Deborah","last_name":"Van Der List","first_name":"Deborah"},{"first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481"},{"first_name":"Olivia A.","last_name":"Mack","full_name":"Mack, Olivia A."},{"last_name":"Carroll","full_name":"Carroll, James","first_name":"James"},{"first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","last_name":"Le Monnier","full_name":"Le Monnier, Elodie"},{"full_name":"Aicher, Sue A.","last_name":"Aicher","first_name":"Sue A."},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"full_name":"Trimmer, James S.","last_name":"Trimmer","first_name":"James S."}],"external_id":{"pmid":["37633939"]},"article_processing_charge":"Yes","title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","citation":{"ista":"Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA, Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 14, 5231.","chicago":"Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40930-6.","short":"N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A. Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature Communications 14 (2023).","ieee":"N. C. Vierra et al., “Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling,” Nature Communications, vol. 14. Springer Nature, 2023.","ama":"Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 2023;14. doi:10.1038/s41467-023-40930-6","apa":"Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P., Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40930-6","mla":"Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications, vol. 14, 5231, Springer Nature, 2023, doi:10.1038/s41467-023-40930-6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"5231","volume":14,"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"file_name":"2023_NatureComm_Vierra.pdf","date_created":"2023-09-06T06:50:07Z","file_size":9412549,"date_updated":"2023-09-06T06:50:07Z","creator":"dernst","success":1,"checksum":"6ab8aab4e957f626a09a1c73db3388fb","file_id":"14270","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 14","abstract":[{"lang":"eng","text":"Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell."}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"RySh"}],"file_date_updated":"2023-09-06T06:50:07Z","date_updated":"2023-09-06T06:53:32Z","ddc":["570"],"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":"14253"},{"_id":"14259","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","location":"Paris, France","start_date":"2023-07-17"},"ddc":["000"],"date_updated":"2023-09-06T08:27:33Z","file_date_updated":"2023-09-06T08:25:50Z","department":[{"_id":"KrCh"}],"oa_version":"Published Version","abstract":[{"text":"We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning.","lang":"eng"}],"month":"07","intvolume":" 13964","scopus_import":"1","alternative_title":["LNCS"],"file":[{"file_name":"2023_LNCS_CAV_Kretinsky.pdf","date_created":"2023-09-06T08:25:50Z","creator":"dernst","file_size":428354,"date_updated":"2023-09-06T08:25:50Z","success":1,"checksum":"ed66278b61bb869e1baba3d9b9081271","file_id":"14276","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377051"]},"publication_status":"published","volume":13964,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In 35th International Conference on Computer Aided Verification , 13964:390–414. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_20.","apa":"Kretinsky, J., Meggendorfer, T., Prokop, M., & Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In 35th International Conference on Computer Aided Verification (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_20","ama":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: 35th International Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:390-414. doi:10.1007/978-3-031-37706-8_20","ieee":"J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in 35th International Conference on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 390–414.","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.","mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” 35th International Conference on Computer Aided Verification , vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20."},"title":"Guessing winning policies in LTL synthesis by semantic learning","author":[{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165"},{"first_name":"Maximilian","last_name":"Prokop","full_name":"Prokop, Maximilian"},{"last_name":"Rieder","full_name":"Rieder, Sabine","first_name":"Sabine"}],"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"17","publication":"35th International Conference on Computer Aided Verification ","has_accepted_license":"1","year":"2023","doi":"10.1007/978-3-031-37706-8_20","date_published":"2023-07-17T00:00:00Z","date_created":"2023-09-03T22:01:16Z","page":"390-414"},{"department":[{"_id":"LiBu"}],"file_date_updated":"2023-09-06T07:13:19Z","date_updated":"2023-09-06T11:05:58Z","ddc":["520"],"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","_id":"14256","volume":676,"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14271","checksum":"7b30d26fb2b7bcb5b5be1414950615f9","success":1,"date_updated":"2023-09-06T07:13:19Z","file_size":458120,"creator":"dernst","date_created":"2023-09-06T07:13:19Z","file_name":"2023_AstronomyAstrophysics_Mathis.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 676","abstract":[{"lang":"eng","text":"Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies.\r\nResults. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries."}],"oa_version":"Published Version","author":[{"full_name":"Mathis, S.","last_name":"Mathis","first_name":"S."},{"first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000"}],"external_id":{"arxiv":["2306.11587"],"isi":["001046037700007"]},"article_processing_charge":"Yes (in subscription journal)","title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","citation":{"ista":"Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 676, L9.","chicago":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy and Astrophysics. EDP Sciences, 2023. https://doi.org/10.1051/0004-6361/202346832.","ieee":"S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields,” Astronomy and Astrophysics, vol. 676. EDP Sciences, 2023.","short":"S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).","ama":"Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 2023;676. doi:10.1051/0004-6361/202346832","apa":"Mathis, S., & Bugnet, L. A. (2023). Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202346832","mla":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy and Astrophysics, vol. 676, L9, EDP Sciences, 2023, doi:10.1051/0004-6361/202346832."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"L9","doi":"10.1051/0004-6361/202346832","date_published":"2023-08-01T00:00:00Z","date_created":"2023-09-03T22:01:15Z","isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Astronomy and Astrophysics","publisher":"EDP Sciences","quality_controlled":"1","oa":1,"acknowledgement":"The authors are grateful to the referee for her/his detailed and constructive report, which has allowed us to improve our article. S. M. acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU). We thank R. A. Garcia for fruitful discussions and suggestions."},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403.","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707.","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01707","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","mla":"Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:10.1021/acs.jpclett.3c01707."},"title":"Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems","author":[{"first_name":"Jakob","full_name":"Gamper, Jakob","last_name":"Gamper"},{"last_name":"Kluibenschedl","full_name":"Kluibenschedl, Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian"},{"first_name":"Alexander K.H.","full_name":"Weiss, Alexander K.H.","last_name":"Weiss"},{"full_name":"Hofer, Thomas S.","last_name":"Hofer","first_name":"Thomas S."}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["37566743"],"isi":["001048165800001"]},"acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"day":"11","publication":"Journal of Physical Chemistry Letters","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-08-11T00:00:00Z","doi":"10.1021/acs.jpclett.3c01707","date_created":"2023-09-03T22:01:16Z","page":"7395-7403","_id":"14261","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530","540"],"date_updated":"2023-09-06T11:04:31Z","file_date_updated":"2023-09-06T07:32:39Z","department":[{"_id":"GradSch"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing."}],"month":"08","intvolume":" 14","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14272","checksum":"637454e2b3a357498d8d622d241c4bf6","creator":"dernst","file_size":4986859,"date_updated":"2023-09-06T07:32:39Z","file_name":"2023_JourPhysChemistry_Gamper.pdf","date_created":"2023-09-06T07:32:39Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1948-7185"]},"publication_status":"published","issue":"33","volume":14},{"file_date_updated":"2023-09-15T06:30:50Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-09-15T06:39:17Z","status":"public","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)"},"_id":"14277","volume":1,"issue":"1","ec_funded":1,"file":[{"checksum":"f881d98c89eb9f1aa136d7b781511553","file_id":"14335","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-09-15T06:30:50Z","file_name":"2023_PRXLife_Boocock.pdf","creator":"dernst","date_updated":"2023-09-15T06:30:50Z","file_size":2559520}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2835-8279"]},"publication_status":"published","month":"07","intvolume":" 1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels."}],"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","author":[{"full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631","last_name":"Boocock","first_name":"Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001.","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:10.1103/prxlife.1.013001.","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” PRX Life, vol. 1, no. 1. American Physical Society, 2023.","ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001","apa":"Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001"},"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}],"article_number":"013001","date_published":"2023-07-20T00:00:00Z","doi":"10.1103/prxlife.1.013001","date_created":"2023-09-06T08:30:59Z","day":"20","publication":"PRX Life","has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS."},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"14314","department":[{"_id":"JoCs"}],"file_date_updated":"2023-09-15T07:12:46Z","ddc":["570"],"date_updated":"2023-09-15T07:14:12Z","intvolume":" 42","month":"09","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations."}],"ec_funded":1,"issue":"9","volume":42,"language":[{"iso":"eng"}],"file":[{"file_size":4879455,"date_updated":"2023-09-15T07:12:46Z","creator":"dernst","file_name":"2023_CellPress_Nardin.pdf","date_created":"2023-09-15T07:12:46Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14337","checksum":"ca77a304fb813c292550b8604b0fb41d"}],"publication_status":"published","publication_identifier":{"eissn":["2211-1247"]},"project":[{"name":"Inter-and intracellular signalling in schizophrenia","grant_number":"607616","call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"article_number":"113015","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","article_processing_charge":"Yes","external_id":{"pmid":["37632747"]},"author":[{"first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","last_name":"Nardin"},{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","last_name":"Käfer","full_name":"Käfer, Karola"},{"full_name":"Stella, Federico","orcid":"0000-0001-9439-3148","last_name":"Stella","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” Cell Reports, vol. 42, no. 9, 113015, Elsevier, 2023, doi:10.1016/j.celrep.2023.113015.","ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” Cell Reports, vol. 42, no. 9. Elsevier, 2023.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","apa":"Nardin, M., Käfer, K., Stella, F., & Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113015","ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 2023;42(9). doi:10.1016/j.celrep.2023.113015","chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113015.","ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015."},"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","date_created":"2023-09-10T22:01:11Z","doi":"10.1016/j.celrep.2023.113015","date_published":"2023-09-26T00:00:00Z","publication":"Cell Reports","day":"26","year":"2023","has_accepted_license":"1"},{"status":"public","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)"},"_id":"14315","file_date_updated":"2023-09-15T06:59:10Z","department":[{"_id":"MaHe"}],"ddc":["570"],"date_updated":"2023-09-15T07:07:10Z","month":"09","intvolume":" 12","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.","lang":"eng"}],"volume":12,"file":[{"creator":"dernst","date_updated":"2023-09-15T06:59:10Z","file_size":3703097,"date_created":"2023-09-15T06:59:10Z","file_name":"2023_eLife_Cho.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14336","checksum":"db24bf3d595507387b48d3799c33e289","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","article_number":"RP89066","title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","author":[{"full_name":"Cho, Ukrae H.","last_name":"Cho","first_name":"Ukrae H."},{"last_name":"Hetzer","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"article_processing_charge":"Yes","external_id":{"pmid":["37665327"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Cho, U. H., & Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.89066","ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 2023;12. doi:10.7554/eLife.89066","short":"U.H. Cho, M. Hetzer, ELife 12 (2023).","ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” eLife, vol. 12. eLife Sciences Publications, 2023.","mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:10.7554/eLife.89066.","ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.89066."},"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","doi":"10.7554/eLife.89066","date_published":"2023-09-04T00:00:00Z","date_created":"2023-09-10T22:01:11Z","day":"04","publication":"eLife","has_accepted_license":"1","year":"2023"},{"doi":"10.37236/11714","date_published":"2023-07-28T00:00:00Z","date_created":"2023-09-10T22:01:12Z","day":"28","publication":"Electronic Journal of Combinatorics","has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"Electronic Journal of Combinatorics","oa":1,"acknowledgement":"Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).","title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","author":[{"last_name":"Anastos","full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael"},{"last_name":"Fabian","full_name":"Fabian, David","first_name":"David"},{"first_name":"Alp","full_name":"Müyesser, Alp","last_name":"Müyesser"},{"first_name":"Tibor","last_name":"Szabó","full_name":"Szabó, Tibor"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2212.03100"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic Journal of Combinatorics, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:10.37236/11714.","apa":"Anastos, M., Fabian, D., Müyesser, A., & Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11714","ama":"Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 2023;30(3). doi:10.37236/11714","ieee":"M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” Electronic Journal of Combinatorics, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.","short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023).","chicago":"Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11714.","ista":"Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10."},"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"article_number":"P3.10","volume":30,"issue":"3","license":"https://creativecommons.org/licenses/by-nd/4.0/","ec_funded":1,"file":[{"success":1,"checksum":"52c46c8cb329f9aaee9ade01525f317b","file_id":"14338","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_elecJournCombinatorics_Anastos.pdf","date_created":"2023-09-15T08:02:09Z","creator":"dernst","file_size":247917,"date_updated":"2023-09-15T08:02:09Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1077-8926"]},"publication_status":"published","month":"07","intvolume":" 30","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."}],"file_date_updated":"2023-09-15T08:02:09Z","department":[{"_id":"MaKw"}],"ddc":["510"],"date_updated":"2023-09-15T08:12:30Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"_id":"14319"},{"ec_funded":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/boyvolcano/PRR"}]},"volume":13966,"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377082"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-09-20T08:24:47Z","file_size":624647,"creator":"dernst","date_created":"2023-09-20T08:24:47Z","file_name":"2023_LNCS_Sun.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14348","checksum":"42917e086f8c7699f3bccf84f74fe000","success":1}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 13966","month":"07","abstract":[{"lang":"eng","text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice."}],"oa_version":"Published Version","department":[{"_id":"KrCh"}],"file_date_updated":"2023-09-20T08:24:47Z","date_updated":"2023-09-20T08:25:57Z","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer Aided Verification","start_date":"2023-07-17","location":"Paris, France","end_date":"2023-07-22"},"type":"conference","status":"public","_id":"14318","page":"16-39","date_created":"2023-09-10T22:01:12Z","doi":"10.1007/978-3-031-37709-9_2","date_published":"2023-07-17T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"Computer Aided Verification","day":"17","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Sun","full_name":"Sun, Yican","first_name":"Yican"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady"}],"title":"Automated tail bound analysis for probabilistic recurrence relations","citation":{"short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in Computer Aided Verification, Paris, France, 2023, vol. 13966, pp. 16–39.","apa":"Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In Computer Aided Verification (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_2","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: Computer Aided Verification. Vol 13966. Springer Nature; 2023:16-39. doi:10.1007/978-3-031-37709-9_2","mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” Computer Aided Verification, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:10.1007/978-3-031-37709-9_2.","ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In Computer Aided Verification, 13966:16–39. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_2."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}]},{"title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Akshay, S.","last_name":"Akshay","first_name":"S."},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: International Conference on Computer Aided Verification. Vol 13966. Springer Nature; 2023:86-112. doi:10.1007/978-3-031-37709-9_5","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., & Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In International Conference on Computer Aided Verification (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_5","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in International Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966, pp. 86–112.","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” International Conference on Computer Aided Verification, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:10.1007/978-3-031-37709-9_5.","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.","chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In International Conference on Computer Aided Verification, 13966:86–112. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_5."},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"date_created":"2023-09-10T22:01:12Z","doi":"10.1007/978-3-031-37709-9_5","date_published":"2023-07-17T00:00:00Z","page":"86-112","publication":"International Conference on Computer Aided Verification","day":"17","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","department":[{"_id":"KrCh"}],"file_date_updated":"2023-09-20T08:46:43Z","ddc":["000"],"date_updated":"2023-09-20T09:04:40Z","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)"},"conference":{"name":"CAV: Computer Aided Verification","start_date":"2023-07-17","location":"Paris, France","end_date":"2023-07-22"},"type":"conference","_id":"14317","ec_funded":1,"volume":13966,"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-09-20T08:46:43Z","file_size":531745,"creator":"dernst","date_created":"2023-09-20T08:46:43Z","file_name":"2023_LNCS_Akshay.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f143c8eedf609f20f2aad2eeb496d53f","file_id":"14349","success":1}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031377082"],"eissn":["1611-3349"]},"intvolume":" 13966","month":"07","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Published Version","abstract":[{"text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples.","lang":"eng"}]},{"status":"public","type":"journal_article","article_type":"original","_id":"14316","department":[{"_id":"DaSi"}],"date_updated":"2023-09-20T09:14:15Z","intvolume":" 136","month":"09","main_file_link":[{"url":"https://doi.org/10.1101/2023.03.27.534325","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Preprint","abstract":[{"text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway.","lang":"eng"}],"issue":"17","volume":136,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"article_number":"jcs261448","title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","article_processing_charge":"No","external_id":{"pmid":["37539494"]},"author":[{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"first_name":"Kaito","full_name":"Aoshima, Kaito","last_name":"Aoshima"},{"first_name":"Hiroki","full_name":"Shimamura, Hiroki","last_name":"Shimamura"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus"},{"full_name":"Toshima, Junko Y.","last_name":"Toshima","first_name":"Junko Y."},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 2023;136(17). doi:10.1242/jcs.261448","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., & Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.261448","short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” Journal of Cell Science, vol. 136, no. 17. The Company of Biologists, 2023.","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell Science, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:10.1242/jcs.261448.","ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448.","chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261448."},"oa":1,"quality_controlled":"1","publisher":"The Company of Biologists","date_created":"2023-09-10T22:01:12Z","date_published":"2023-09-01T00:00:00Z","doi":"10.1242/jcs.261448","publication":"Journal of Cell Science","day":"01","year":"2023"},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.06310","open_access":"1"}],"month":"09","intvolume":" 108","abstract":[{"lang":"eng","text":"The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance."}],"oa_version":"Preprint","issue":"12","volume":108,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"14320","department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"date_updated":"2023-09-20T09:38:24Z","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations.","date_published":"2023-09-15T00:00:00Z","doi":"10.1103/physrevb.108.125411","date_created":"2023-09-12T07:12:12Z","year":"2023","day":"15","publication":"Physical Review B","article_number":"125411","author":[{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M","last_name":"Henderson","orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"first_name":"Alexander A.","full_name":"Zibrov, Alexander A.","last_name":"Zibrov"},{"last_name":"Young","full_name":"Young, Andrea F.","first_name":"Andrea F."},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"article_processing_charge":"No","external_id":{"arxiv":["2210.06310"]},"title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","citation":{"chicago":"Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.125411.","ista":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.","mla":"Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” Physical Review B, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:10.1103/physrevb.108.125411.","ieee":"P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” Physical Review B, vol. 108, no. 12. American Physical Society, 2023.","short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023).","apa":"Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., & Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.125411","ama":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 2023;108(12). doi:10.1103/physrevb.108.125411"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"12732","type":"dissertation","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","supervisor":[{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"date_updated":"2023-09-20T10:44:12Z","ddc":["530"],"file_date_updated":"2023-03-23T16:43:14Z","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"abstract":[{"lang":"eng","text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"None","alternative_title":["ISTA Thesis"],"month":"03","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"content_type":"application/zip","relation":"source_file","access_level":"closed","file_id":"12753","checksum":"5d2de651ef9449c1b8dc27148ca74777","file_size":42167561,"date_updated":"2023-03-23T16:42:56Z","creator":"pbrighi","file_name":"Thesis_sub_PBrighi.zip","date_created":"2023-03-23T16:42:56Z"},{"success":1,"checksum":"7caa153d4a5b0873a79358787d2dfe1e","file_id":"12754","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_PBrighi.pdf","date_created":"2023-03-23T16:43:14Z","creator":"pbrighi","file_size":13977000,"date_updated":"2023-03-23T16:43:14Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"11470","relation":"part_of_dissertation"},{"id":"8308","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11469"},{"id":"12750","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"citation":{"ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732","apa":"Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","mla":"Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","last_name":"Brighi"}],"article_processing_charge":"No","title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2023","day":"21","page":"158","doi":"10.15479/at:ista:12732","date_published":"2023-03-21T00:00:00Z","date_created":"2023-03-17T13:30:48Z"},{"doi":"10.21468/scipostphys.15.3.093","date_published":"2023-09-13T00:00:00Z","date_created":"2023-09-14T13:08:23Z","has_accepted_license":"1","year":"2023","day":"13","publication":"SciPost Physics","quality_controlled":"1","publisher":"SciPost Foundation","oa":1,"acknowledgement":"We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry Abanin for useful\r\ndiscussions.The authors acknowledge support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger International\r\nInstitute for Mathematics and Physics (ESI).","author":[{"orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro"},{"orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"article_processing_charge":"No","external_id":{"arxiv":["2210.15607"]},"title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","citation":{"mla":"Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics, vol. 15, no. 3, 093, SciPost Foundation, 2023, doi:10.21468/scipostphys.15.3.093.","ieee":"P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models,” SciPost Physics, vol. 15, no. 3. SciPost Foundation, 2023.","short":"P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).","ama":"Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 2023;15(3). doi:10.21468/scipostphys.15.3.093","apa":"Brighi, P., Ljubotina, M., & Serbyn, M. (2023). Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.15.3.093","chicago":"Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.3.093.","ista":"Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"article_number":"093","related_material":{"record":[{"relation":"earlier_version","id":"12750","status":"public"}]},"volume":15,"issue":"3","ec_funded":1,"publication_identifier":{"issn":["2542-4653"]},"publication_status":"published","file":[{"file_name":"2023_SciPostPhysics_Brighi.pdf","date_created":"2023-09-20T10:46:10Z","file_size":4866506,"date_updated":"2023-09-20T10:46:10Z","creator":"dernst","success":1,"file_id":"14350","checksum":"4cef6a8021f6b6c47ab2f2f2b1387ac2","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"month":"09","intvolume":" 15","abstract":[{"text":"Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2023-09-20T10:46:10Z","department":[{"_id":"MaSe"}],"date_updated":"2023-09-20T10:46:29Z","ddc":["530"],"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","keyword":["General Physics and Astronomy"],"_id":"14334"},{"oa":1,"quality_controlled":"1","publisher":"AIP Publishing","acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","date_created":"2023-09-13T09:25:09Z","doi":"10.1063/5.0165806","date_published":"2023-09-11T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"The Journal of Chemical Physics","day":"11","project":[{"name":"Non-equilibrium Field Theory of Molecular Rotations","grant_number":"101062862","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"article_number":"104103","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2306.17592"],"pmid":["37694742"]},"author":[{"last_name":"Al Hyder","full_name":"Al Hyder, Ragheed","first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}],"title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","citation":{"ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806.","ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 2023;159(10). doi:10.1063/5.0165806","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806","ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” The Journal of Chemical Physics, vol. 159, no. 10. AIP Publishing, 2023.","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 159","month":"09","abstract":[{"lang":"eng","text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers."}],"oa_version":"Published Version","pmid":1,"ec_funded":1,"volume":159,"issue":"10","publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14322","checksum":"507ab65ab29e2c987c94cabad7c5370b","success":1,"creator":"acappell","date_updated":"2023-09-13T09:34:20Z","file_size":5749653,"date_created":"2023-09-13T09:34:20Z","file_name":"104103_1_5.0165806.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)"},"article_type":"original","type":"journal_article","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"status":"public","_id":"14321","department":[{"_id":"MiLe"}],"file_date_updated":"2023-09-13T09:34:20Z","date_updated":"2023-09-20T09:48:12Z","ddc":["530"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics Letters, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:10.1063/5.0161713.","ama":"Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 2023;123(9). doi:10.1063/5.0161713","apa":"Lorenc, D., & Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0161713","ieee":"D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam,” Applied Physics Letters, vol. 123, no. 9. AIP Publishing, 2023.","short":"D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics Letters. AIP Publishing, 2023. https://doi.org/10.1063/5.0161713.","ista":"Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104."},"title":"Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam","author":[{"full_name":"Lorenc, Dusan","last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2306.09043"]},"article_processing_charge":"Yes (in subscription journal)","article_number":"091104","day":"28","publication":"Applied Physics Letters","has_accepted_license":"1","year":"2023","doi":"10.1063/5.0161713","date_published":"2023-08-28T00:00:00Z","date_created":"2023-09-17T22:01:09Z","acknowledgement":"The work was supported by IST Austria. The authors would like to gratefully acknowledge the help and assistance of Professor John M. Dudley.","publisher":"AIP Publishing","quality_controlled":"1","oa":1,"ddc":["530"],"date_updated":"2023-09-20T11:50:06Z","file_date_updated":"2023-09-20T11:36:16Z","department":[{"_id":"ZhAl"}],"_id":"14342","status":"public","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_name":"2023_ApplPhysLetter_Lorenc.pdf","date_created":"2023-09-20T11:36:16Z","file_size":1486715,"date_updated":"2023-09-20T11:36:16Z","creator":"dernst","success":1,"file_id":"14353","checksum":"89a1b604d58b209fec66c6b6f919ac98","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0003-6951"]},"publication_status":"published","volume":123,"issue":"9","oa_version":"Published Version","abstract":[{"text":"We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared frequency range that avoids using sophisticated infrared detectors. Our approach is based on using a near-infrared probe beam which interacts with a mid-IR beam via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring XPM-induced spectral modifications in the probe beam and comparing the experimental data with simulation results, we extract the value for the non-degenerate Kerr index. Finally, in order to obtain the value of degenerate mid-IR Kerr index, we use the well-established two-band formalism of Sheik-Bahae et al., which is shown to become particularly simple in the limit of low frequencies. The proposed technique is complementary to the conventional techniques, such as z-scan, and has the advantage of not requiring any mid-infrared detectors.","lang":"eng"}],"month":"08","intvolume":" 123","scopus_import":"1"},{"year":"2023","day":"07","publication":"Nature","page":"71-74","date_published":"2023-09-07T00:00:00Z","doi":"10.1038/s41586-023-06399-5","date_created":"2023-09-17T22:01:09Z","acknowledgement":"We acknowledge the assistance of the Miba machine shop and the team of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.","quality_controlled":"1","publisher":"Springer Nature","citation":{"mla":"Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature, vol. 621, no. 7977, Springer Nature, 2023, pp. 71–74, doi:10.1038/s41586-023-06399-5.","apa":"Scarselli, D., Lopez Alonso, J. M., Varshney, A., & Hof, B. (2023). Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06399-5","ama":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 2023;621(7977):71-74. doi:10.1038/s41586-023-06399-5","short":"D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.","ieee":"D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression by cardiac-cycle-inspired driving of pipe flow,” Nature, vol. 621, no. 7977. Springer Nature, pp. 71–74, 2023.","chicago":"Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06399-5.","ista":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide","last_name":"Scarselli","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide"},{"last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","first_name":"Jose M"},{"last_name":"Varshney","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"article_processing_charge":"No","external_id":{"pmid":["37673988"]},"title":"Turbulence suppression by cardiac-cycle-inspired driving of pipe flow","project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"I04188","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":621,"issue":"7977","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://www.ista.ac.at/en/news/pumping-like-the-heart/"}]},"abstract":[{"text":"Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"09","intvolume":" 621","date_updated":"2023-09-20T12:10:22Z","department":[{"_id":"BjHo"}],"_id":"14341","article_type":"original","type":"journal_article","status":"public"},{"article_number":"15","title":"Closure properties of general grammars - formally verified","author":[{"last_name":"Dvorak","full_name":"Dvorak, Martin","orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","first_name":"Martin"},{"first_name":"Jasmin","full_name":"Blanchette, Jasmin","last_name":"Blanchette"}],"article_processing_charge":"No","external_id":{"arxiv":["2302.06420"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” 14th International Conference on Interactive Theorem Proving, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ITP.2023.15.","ama":"Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: 14th International Conference on Interactive Theorem Proving. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ITP.2023.15","apa":"Dvorak, M., & Blanchette, J. (2023). Closure properties of general grammars - formally verified. In 14th International Conference on Interactive Theorem Proving (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITP.2023.15","ieee":"M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in 14th International Conference on Interactive Theorem Proving, Bialystok, Poland, 2023, vol. 268.","short":"M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In 14th International Conference on Interactive Theorem Proving, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ITP.2023.15.","ista":"Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally verified. 14th International Conference on Interactive Theorem Proving. ITP: International Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15."},"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"Jasmin Blanchette: This research has received funding from the Netherlands Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No. 016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making this collaboration possible. We\r\nthank Václav Končický for discussing ideas about the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano Testa for their small yet very valuable contributions to our code. We thank Eric Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting textual improvements. We thank the anonymous reviewers for very helpful comments. Finally, we thank the Lean community for helping us with various technical issues and answering many questions. ","date_published":"2023-07-27T00:00:00Z","doi":"10.4230/LIPIcs.ITP.2023.15","date_created":"2023-06-05T07:29:05Z","day":"27","publication":"14th International Conference on Interactive Theorem Proving","has_accepted_license":"1","year":"2023","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"end_date":"2023-08-04","location":"Bialystok, Poland","start_date":"2023-07-31","name":"ITP: International Conference on Interactive Theorem Proving"},"_id":"13120","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"file_date_updated":"2023-08-07T11:55:43Z","ddc":["000"],"date_updated":"2023-09-25T11:04:29Z","month":"07","intvolume":" 268","scopus_import":"1","alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"text":"We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction.","lang":"eng"}],"volume":268,"related_material":{"link":[{"url":"https://github.com/madvorak/grammars/tree/publish","relation":"software"}]},"file":[{"date_created":"2023-08-07T11:55:43Z","file_name":"2023_LIPIcS_Dvorak.pdf","creator":"dernst","date_updated":"2023-08-07T11:55:43Z","file_size":715976,"file_id":"13982","checksum":"773a0197f05b67feaa6cb1e17ec3642d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783959772846"],"eissn":["1868-8969"]},"publication_status":"published"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"13969","file_date_updated":"2023-08-07T08:00:48Z","department":[{"_id":"UlWa"}],"date_updated":"2023-09-25T10:56:10Z","ddc":["510"],"scopus_import":"1","intvolume":" 27","month":"07","abstract":[{"text":"Bundling crossings is a strategy which can enhance the readability\r\nof graph drawings. In this paper we consider good drawings, i.e., we require that\r\nany two edges have at most one common point which can be a common vertex or a\r\ncrossing. Our main result is that there is a polynomial-time algorithm to compute an\r\n8-approximation of the bundled crossing number of a good drawing with no toothed\r\nhole. In general the number of toothed holes has to be added to the 8-approximation.\r\nIn the special case of circular drawings the approximation factor is 8, this improves\r\nupon the 10-approximation of Fink et al. [14]. Our approach also works with the same\r\napproximation factor for families of pseudosegments, i.e., curves intersecting at most\r\nonce. We also show how to compute a 9/2-approximation when the intersection graph of\r\nthe pseudosegments is bipartite and has no toothed hole.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"6","related_material":{"record":[{"relation":"earlier_version","id":"11185","status":"public"}]},"volume":27,"publication_status":"published","publication_identifier":{"issn":["1526-1719"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":865774,"date_updated":"2023-08-07T08:00:48Z","file_name":"2023_JourGraphAlgorithms_Arroyo.pdf","date_created":"2023-08-07T08:00:48Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"9c30d2b8e324cc1c904f2aeec92013a3","file_id":"13979"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2109.14892"]},"author":[{"last_name":"Arroyo Guevara","orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M"},{"first_name":"Stefan","full_name":"Felsner, Stefan","last_name":"Felsner"}],"title":"Approximating the bundled crossing number","citation":{"ista":"Arroyo Guevara AM, Felsner S. 2023. Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. 27(6), 433–457.","chicago":"Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled Crossing Number.” Journal of Graph Algorithms and Applications. Brown University, 2023. https://doi.org/10.7155/jgaa.00629.","apa":"Arroyo Guevara, A. M., & Felsner, S. (2023). Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00629","ama":"Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. 2023;27(6):433-457. doi:10.7155/jgaa.00629","ieee":"A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,” Journal of Graph Algorithms and Applications, vol. 27, no. 6. Brown University, pp. 433–457, 2023.","short":"A.M. Arroyo Guevara, S. Felsner, Journal of Graph Algorithms and Applications 27 (2023) 433–457.","mla":"Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing Number.” Journal of Graph Algorithms and Applications, vol. 27, no. 6, Brown University, 2023, pp. 433–57, doi:10.7155/jgaa.00629."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Brown University","quality_controlled":"1","acknowledgement":"This work was initiated during the Workshop on Geometric Graphs in November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during the workshop. The first author has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No 754411. The second author has been supported by the German Research Foundation DFG Project FE 340/12-1. An extended abstract of this paper has been published in the proceedings of WALCOM 2022 in the Springer LNCS series, vol. 13174, pages 383–395.","page":"433-457","date_created":"2023-08-06T22:01:11Z","doi":"10.7155/jgaa.00629","date_published":"2023-07-01T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"Journal of Graph Algorithms and Applications","day":"01"},{"volume":2023,"publication_status":"published","publication_identifier":{"isbn":["9781611977554"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2111.14759"}],"scopus_import":"1","intvolume":" 2023","month":"01","abstract":[{"text":"We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in two different settings. In the first one, G is given to us in the form of randomly ordered adjacency lists while in the second one, we are given the adjacency matrix of G. In each of the two settings we derive a deterministic algorithm that w.h.p. either finds a Hamilton cycle or returns a certificate that such a cycle does not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and respectively, each being best possible in its own setting.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"MaKw"}],"date_updated":"2023-09-25T09:13:41Z","conference":{"start_date":"2023-01-22","location":"Florence, Italy","end_date":"2023-01-25","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","status":"public","_id":"14344","page":"2286-2323","date_created":"2023-09-17T22:01:10Z","date_published":"2023-01-01T00:00:00Z","doi":"10.1137/1.9781611977554.ch88","year":"2023","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","oa":1,"publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","external_id":{"arxiv":["2111.14759"]},"article_processing_charge":"No","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","full_name":"Anastos, Michael","last_name":"Anastos"}],"title":"Fast algorithms for solving the Hamilton cycle problem with high probability","citation":{"chicago":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 2023:2286–2323. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch88.","ista":"Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.","mla":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2023, Society for Industrial and Applied Mathematics, 2023, pp. 2286–323, doi:10.1137/1.9781611977554.ch88.","ama":"Anastos M. Fast algorithms for solving the Hamilton cycle problem with high probability. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:10.1137/1.9781611977554.ch88","apa":"Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem with high probability. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch88","short":"M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.","ieee":"M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high probability,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, vol. 2023, pp. 2286–2323."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"review","_id":"12710","file_date_updated":"2023-09-26T10:51:56Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-09-26T10:56:46Z","intvolume":" 35","month":"03","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes."}],"volume":35,"issue":"13","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-09-26T10:51:56Z","file_size":2898063,"date_created":"2023-09-26T10:51:56Z","file_name":"2023_AdvancedMaterials_Schamberger.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14373","checksum":"5c04d68130e97a0ecd1ca27fbc15a246","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"article_number":"2206110","title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales","article_processing_charge":"No","external_id":{"isi":["000941068900001"],"pmid":["36461812"]},"author":[{"first_name":"Barbara","full_name":"Schamberger, Barbara","last_name":"Schamberger"},{"first_name":"Ricardo","last_name":"Ziege","full_name":"Ziege, Ricardo"},{"first_name":"Karine","full_name":"Anselme, Karine","last_name":"Anselme"},{"first_name":"Martine","last_name":"Ben Amar","full_name":"Ben Amar, Martine"},{"last_name":"Bykowski","full_name":"Bykowski, Michał","first_name":"Michał"},{"first_name":"André P.G.","full_name":"Castro, André P.G.","last_name":"Castro"},{"last_name":"Cipitria","full_name":"Cipitria, Amaia","first_name":"Amaia"},{"first_name":"Rhoslyn A.","last_name":"Coles","full_name":"Coles, Rhoslyn A."},{"last_name":"Dimova","full_name":"Dimova, Rumiana","first_name":"Rumiana"},{"full_name":"Eder, Michaela","last_name":"Eder","first_name":"Michaela"},{"last_name":"Ehrig","full_name":"Ehrig, Sebastian","first_name":"Sebastian"},{"last_name":"Escudero","full_name":"Escudero, Luis M.","first_name":"Luis M."},{"full_name":"Evans, Myfanwy E.","last_name":"Evans","first_name":"Myfanwy E."},{"last_name":"Fernandes","full_name":"Fernandes, Paulo R.","first_name":"Paulo R."},{"full_name":"Fratzl, Peter","last_name":"Fratzl","first_name":"Peter"},{"first_name":"Liesbet","last_name":"Geris","full_name":"Geris, Liesbet"},{"full_name":"Gierlinger, Notburga","last_name":"Gierlinger","first_name":"Notburga"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"full_name":"Iglič, Aleš","last_name":"Iglič","first_name":"Aleš"},{"first_name":"Jacob J.K.","last_name":"Kirkensgaard","full_name":"Kirkensgaard, Jacob J.K."},{"last_name":"Kollmannsberger","full_name":"Kollmannsberger, Philip","first_name":"Philip"},{"first_name":"Łucja","full_name":"Kowalewska, Łucja","last_name":"Kowalewska"},{"first_name":"Nicholas A.","last_name":"Kurniawan","full_name":"Kurniawan, Nicholas A."},{"first_name":"Ioannis","last_name":"Papantoniou","full_name":"Papantoniou, Ioannis"},{"last_name":"Pieuchot","full_name":"Pieuchot, Laurent","first_name":"Laurent"},{"last_name":"Pires","full_name":"Pires, Tiago H.V.","first_name":"Tiago H.V."},{"first_name":"Lars D.","full_name":"Renner, Lars D.","last_name":"Renner"},{"first_name":"Andrew O.","last_name":"Sageman-Furnas","full_name":"Sageman-Furnas, Andrew O."},{"last_name":"Schröder-Turk","full_name":"Schröder-Turk, Gerd E.","first_name":"Gerd E."},{"first_name":"Anupam","last_name":"Sengupta","full_name":"Sengupta, Anupam"},{"first_name":"Vikas R.","last_name":"Sharma","full_name":"Sharma, Vikas R."},{"full_name":"Tagua, Antonio","last_name":"Tagua","first_name":"Antonio"},{"full_name":"Tomba, Caterina","last_name":"Tomba","first_name":"Caterina"},{"full_name":"Trepat, Xavier","last_name":"Trepat","first_name":"Xavier"},{"first_name":"Sarah L.","last_name":"Waters","full_name":"Waters, Sarah L."},{"first_name":"Edwina F.","full_name":"Yeo, Edwina F.","last_name":"Yeo"},{"last_name":"Roschger","full_name":"Roschger, Andreas","first_name":"Andreas"},{"first_name":"Cécile M.","last_name":"Bidan","full_name":"Bidan, Cécile M."},{"last_name":"Dunlop","full_name":"Dunlop, John W.C.","first_name":"John W.C."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials, vol. 35, no. 13, 2206110, Wiley, 2023, doi:10.1002/adma.202206110.","ama":"Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 2023;35(13). doi:10.1002/adma.202206110","apa":"Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro, A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202206110","short":"B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro, A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans, P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K. Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou, L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk, A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo, A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023).","ieee":"B. Schamberger et al., “Curvature in biological systems: Its quantification, emergence, and implications across the scales,” Advanced Materials, vol. 35, no. 13. Wiley, 2023.","chicago":"Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar, Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202206110.","ista":"Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 35(13), 2206110."},"oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F. acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD. A.S. acknowledges that this work was partially supported by the ATTRACT Investigator Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research Fund. The author thanks Gerardo Ceada for his help in the graphical representations. N.A.K. acknowledges support from the European Research Council (grant 851960) and the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands Organization for Scientific Research (024.003.013). M.B.A. acknowledges support from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project “Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft (DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation (PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science.","date_created":"2023-03-05T23:01:06Z","doi":"10.1002/adma.202206110","date_published":"2023-03-29T00:00:00Z","publication":"Advanced Materials","day":"29","year":"2023","isi":1,"has_accepted_license":"1"},{"doi":"10.1126/science.adh9059","date_published":"2023-09-22T00:00:00Z","date_created":"2023-08-01T08:26:15Z","page":"1357-1363","day":"22","publication":"Science","year":"2023","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"acknowledgement":"We acknowledge funding from the European Union’s Horizon 2020 Research and Innovation Program [European Research Council grants 820008 (Ra.K.) and 101045223 (A.P.) and Marie Skłodowska-Curie grants 812868 (J.G.) and 101022777 (T.-P.R.)], the Academy of Finland [Center of Excellence Programme LIBER grant 346107 (A.P.), Flagship Programme PREIN grant 320165 (A.P.), and Postdoctoral Researcher grant 340103 (T.-P.R.)], Zuckerman STEM Leadership Program Fellowship (J.R.C.), President’s PhD Scholarship (M.O.), and the EPSRC [Established Career Fellowship grant EP/R00188X/1 (M.J.F.)].","title":"Disequilibrating azoarenes by visible-light sensitization under confinement","author":[{"first_name":"Julius","full_name":"Gemen, Julius","last_name":"Gemen"},{"last_name":"Church","full_name":"Church, Jonathan R.","first_name":"Jonathan R."},{"first_name":"Tero-Petri","last_name":"Ruoko","full_name":"Ruoko, Tero-Petri"},{"last_name":"Durandin","full_name":"Durandin, Nikita","first_name":"Nikita"},{"last_name":"Białek","full_name":"Białek, Michał J.","first_name":"Michał J."},{"first_name":"Maren","full_name":"Weissenfels, Maren","last_name":"Weissenfels"},{"first_name":"Moran","last_name":"Feller","full_name":"Feller, Moran"},{"first_name":"Miri","last_name":"Kazes","full_name":"Kazes, Miri"},{"last_name":"Borin","full_name":"Borin, Veniamin A.","first_name":"Veniamin A."},{"last_name":"Odaybat","full_name":"Odaybat, Magdalena","first_name":"Magdalena"},{"first_name":"Rishir","full_name":"Kalepu, Rishir","last_name":"Kalepu"},{"last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael","first_name":"Yael"},{"first_name":"Dan","full_name":"Oron, Dan","last_name":"Oron"},{"first_name":"Matthew J.","last_name":"Fuchter","full_name":"Fuchter, Matthew J."},{"first_name":"Arri","full_name":"Priimagi, Arri","last_name":"Priimagi"},{"last_name":"Schapiro","full_name":"Schapiro, Igor","first_name":"Igor"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Gemen et al., “Disequilibrating azoarenes by visible-light sensitization under confinement,” Science, vol. 381, no. 6664. American Association for the Advancement of Science, pp. 1357–1363, 2023.","short":"J. Gemen, J.R. Church, T.-P. Ruoko, N. Durandin, M.J. Białek, M. Weissenfels, M. Feller, M. Kazes, V.A. Borin, M. Odaybat, R. Kalepu, Y. Diskin-Posner, D. Oron, M.J. Fuchter, A. Priimagi, I. Schapiro, R. Klajn, Science 381 (2023) 1357–1363.","ama":"Gemen J, Church JR, Ruoko T-P, et al. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 2023;381(6664):1357-1363. doi:10.1126/science.adh9059","apa":"Gemen, J., Church, J. R., Ruoko, T.-P., Durandin, N., Białek, M. J., Weissenfels, M., … Klajn, R. (2023). Disequilibrating azoarenes by visible-light sensitization under confinement. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adh9059","mla":"Gemen, Julius, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science, vol. 381, no. 6664, American Association for the Advancement of Science, 2023, pp. 1357–63, doi:10.1126/science.adh9059.","ista":"Gemen J, Church JR, Ruoko T-P, Durandin N, Białek MJ, Weissenfels M, Feller M, Kazes M, Borin VA, Odaybat M, Kalepu R, Diskin-Posner Y, Oron D, Fuchter MJ, Priimagi A, Schapiro I, Klajn R. 2023. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 381(6664), 1357–1363.","chicago":"Gemen, Julius, Jonathan R. Church, Tero-Petri Ruoko, Nikita Durandin, Michał J. Białek, Maren Weissenfels, Moran Feller, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adh9059."},"issue":"6664","volume":381,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"]},"publication_status":"published","month":"09","intvolume":" 381","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv-2023-gq2h0","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation."}],"department":[{"_id":"RaKl"}],"date_updated":"2023-10-03T08:11:26Z","status":"public","type":"journal_article","article_type":"original","_id":"13340"},{"_id":"12705","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-10-03T11:31:51Z","department":[{"_id":"AnSa"}],"abstract":[{"text":"The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04810"}],"scopus_import":"1","intvolume":" 158","month":"02","publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"language":[{"iso":"eng"}],"volume":158,"issue":"7","article_number":"074905","citation":{"chicago":"Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0134271.","ista":"Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.","mla":"Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics, vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:10.1063/5.0134271.","apa":"Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli, E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0134271","ama":"Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 2023;158(7). doi:10.1063/5.0134271","short":"V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).","ieee":"V. Sorichetti et al., “Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks,” Journal of Chemical Physics, vol. 158, no. 7. American Institute of Physics, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["36813705"],"isi":["000936943800002"],"arxiv":["2211.04810"]},"author":[{"id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","first_name":"Valerio","last_name":"Sorichetti","full_name":"Sorichetti, Valerio","orcid":"0000-0002-9645-6576"},{"last_name":"Ninarello","full_name":"Ninarello, Andrea","first_name":"Andrea"},{"first_name":"José","full_name":"Ruiz-Franco, José","last_name":"Ruiz-Franco"},{"first_name":"Virginie","full_name":"Hugouvieux, Virginie","last_name":"Hugouvieux"},{"first_name":"Emanuela","full_name":"Zaccarelli, Emanuela","last_name":"Zaccarelli"},{"first_name":"Cristian","last_name":"Micheletti","full_name":"Micheletti, Cristian"},{"last_name":"Kob","full_name":"Kob, Walter","first_name":"Walter"},{"first_name":"Lorenzo","full_name":"Rovigatti, Lorenzo","last_name":"Rovigatti"}],"title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","acknowledgement":"We thank Michael Lang for helpful discussions. We acknowledge financial support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC) and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir” French Government program, managed by the French National Research Agency (ANR). W.K. is a senior member of the Institut Universitaire de France.","oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","year":"2023","isi":1,"publication":"Journal of Chemical Physics","day":"21","date_created":"2023-03-05T23:01:05Z","date_published":"2023-02-21T00:00:00Z","doi":"10.1063/5.0134271"},{"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Katoen, Joost P","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P"},{"full_name":"Mohr, Stefanie","last_name":"Mohr","first_name":"Stefanie"},{"first_name":"Maximilian","last_name":"Weininger","full_name":"Weininger, Maximilian"},{"first_name":"Tobias","last_name":"Winkler","full_name":"Winkler, Tobias"}],"external_id":{"isi":["000946174300001"]},"article_processing_charge":"No","title":"Stochastic games with lexicographic objectives","citation":{"mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design, Springer Nature, 2023, doi:10.1007/s10703-023-00411-4.","short":"K. Chatterjee, J.P. Katoen, S. Mohr, M. Weininger, T. Winkler, Formal Methods in System Design (2023).","ieee":"K. Chatterjee, J. P. Katoen, S. Mohr, M. Weininger, and T. Winkler, “Stochastic games with lexicographic objectives,” Formal Methods in System Design. Springer Nature, 2023.","apa":"Chatterjee, K., Katoen, J. P., Mohr, S., Weininger, M., & Winkler, T. (2023). Stochastic games with lexicographic objectives. Formal Methods in System Design. Springer Nature. https://doi.org/10.1007/s10703-023-00411-4","ama":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. Stochastic games with lexicographic objectives. Formal Methods in System Design. 2023. doi:10.1007/s10703-023-00411-4","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Stefanie Mohr, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design. Springer Nature, 2023. https://doi.org/10.1007/s10703-023-00411-4.","ista":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. 2023. Stochastic games with lexicographic objectives. Formal Methods in System Design."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"Tobias Winkler and Joost-Pieter Katoen are supported by the DFG RTG 2236 UnRAVeL and the innovation programme under the Marie Skłodowska-Curie grant agreement No. 101008233 (Mission). Krishnendu Chatterjee is supported by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) Project ICT15-003. Maximilian Weininger is supported by the DFG projects 383882557 Statistical Unbounded Verification (SUV) and 427755713 Group-By Objectives in Probabilistic Verification (GOPro). Stefanie Mohr is supported by the DFG RTG 2428 CONVEY. Open Access funding enabled and organized by Projekt DEAL.","date_published":"2023-03-08T00:00:00Z","doi":"10.1007/s10703-023-00411-4","date_created":"2023-03-19T23:00:59Z","isi":1,"year":"2023","day":"08","publication":"Formal Methods in System Design","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":"12738","department":[{"_id":"KrCh"}],"date_updated":"2023-10-03T11:36:13Z","ddc":["000"],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s10703-023-00411-4","open_access":"1"}],"month":"03","abstract":[{"lang":"eng","text":"We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"8272"}]},"ec_funded":1,"publication_identifier":{"eissn":["1572-8102"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}]},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"publisher":"Zenodo","month":"07","abstract":[{"lang":"eng","text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"oa_version":"Published Version","date_created":"2023-09-06T08:39:25Z","date_published":"2023-07-11T00:00:00Z","doi":"10.5281/ZENODO.8133960","related_material":{"record":[{"status":"public","id":"14274","relation":"used_in_publication"}]},"year":"2023","has_accepted_license":"1","day":"11","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":"research_data_reference","status":"public","_id":"14279","article_processing_charge":"No","author":[{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"}],"department":[{"_id":"EdHa"}],"title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","citation":{"chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133960.","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960.","mla":"Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo, 2023, doi:10.5281/ZENODO.8133960.","ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960","apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960","ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.","short":"M.C. Ucar, (2023)."},"date_updated":"2023-10-03T11:42:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"]},{"title":"Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices","external_id":{"isi":["000724652500001"],"arxiv":["1912.04100"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications on Pure and Applied Mathematics 76 (2023) 946–1034.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices,” Communications on Pure and Applied Mathematics, vol. 76, no. 5. Wiley, pp. 946–1034, 2023.","ama":"Cipolloni G, Erdös L, Schröder DJ. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 2023;76(5):946-1034. doi:10.1002/cpa.22028","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.22028","mla":"Cipolloni, Giorgio, et al. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics, vol. 76, no. 5, Wiley, 2023, pp. 946–1034, doi:10.1002/cpa.22028.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 76(5), 946–1034.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics. Wiley, 2023. https://doi.org/10.1002/cpa.22028."},"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"date_created":"2021-12-05T23:01:41Z","date_published":"2023-05-01T00:00:00Z","doi":"10.1002/cpa.22028","page":"946-1034","publication":"Communications on Pure and Applied Mathematics","day":"01","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"L.E. would like to thank Nathanaël Berestycki and D.S.would like to thank Nina Holden for valuable discussions on the Gaussian freefield.G.C. and L.E. are partially supported by ERC Advanced Grant No. 338804.G.C. received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Skłodowska-Curie Grant Agreement No.665385. D.S. is supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.","department":[{"_id":"LaEr"}],"file_date_updated":"2023-10-04T09:21:48Z","ddc":["510"],"date_updated":"2023-10-04T09:22:55Z","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","_id":"10405","ec_funded":1,"volume":76,"issue":"5","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-10-04T09:21:48Z","file_size":803440,"date_created":"2023-10-04T09:21:48Z","file_name":"2023_CommPureMathematics_Cipolloni.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"8346bc2642afb4ccb7f38979f41df5d9","file_id":"14388","success":1}],"publication_status":"published","publication_identifier":{"issn":["0010-3640"],"eissn":["1097-0312"]},"intvolume":" 76","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32]. "}]},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"title":"Where do mistakes lead? A survey of games with incompetent players","author":[{"last_name":"Graham","full_name":"Graham, Thomas","first_name":"Thomas"},{"last_name":"Kleshnina","full_name":"Kleshnina, Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Jerzy A.","last_name":"Filar","full_name":"Filar, Jerzy A."}],"article_processing_charge":"No","external_id":{"isi":["000753777100001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Graham, Thomas, Maria Kleshnina, and Jerzy A. Filar. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” Dynamic Games and Applications. Springer Nature, 2023. https://doi.org/10.1007/s13235-022-00425-3.","ista":"Graham T, Kleshnina M, Filar JA. 2023. Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. 13, 231–264.","mla":"Graham, Thomas, et al. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” Dynamic Games and Applications, vol. 13, Springer Nature, 2023, pp. 231–64, doi:10.1007/s13235-022-00425-3.","ieee":"T. Graham, M. Kleshnina, and J. A. Filar, “Where do mistakes lead? A survey of games with incompetent players,” Dynamic Games and Applications, vol. 13. Springer Nature, pp. 231–264, 2023.","short":"T. Graham, M. Kleshnina, J.A. Filar, Dynamic Games and Applications 13 (2023) 231–264.","apa":"Graham, T., Kleshnina, M., & Filar, J. A. (2023). Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. Springer Nature. https://doi.org/10.1007/s13235-022-00425-3","ama":"Graham T, Kleshnina M, Filar JA. Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. 2023;13:231-264. doi:10.1007/s13235-022-00425-3"},"publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"The authors would like to acknowledge stimulating email discussions with Dr Wayne Lobb of W.A. Lobb LLC on the topic of evolutionary games. We also thank Dr Thomas Taimre for his input to the material in Sect. 3.\r\nThe authors would like to acknowledge partial support from the Australian Research Council under the Discovery grant DP180101602 and support by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411.","date_published":"2023-03-01T00:00:00Z","doi":"10.1007/s13235-022-00425-3","date_created":"2022-02-20T23:01:32Z","page":"231-264","day":"01","publication":"Dynamic Games and Applications","has_accepted_license":"1","isi":1,"year":"2023","status":"public","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)"},"_id":"10770","file_date_updated":"2022-02-21T08:54:17Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-10-04T09:24:30Z","month":"03","intvolume":" 13","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Mathematical models often aim to describe a complicated mechanism in a cohesive and simple manner. However, reaching perfect balance between being simple enough or overly simplistic is a challenging task. Frequently, game-theoretic models have an underlying assumption that players, whenever they choose to execute a specific action, do so perfectly. In fact, it is rare that action execution perfectly coincides with intentions of individuals, giving rise to behavioural mistakes. The concept of incompetence of players was suggested to address this issue in game-theoretic settings. Under the assumption of incompetence, players have non-zero probabilities of executing a different strategy from the one they chose, leading to stochastic outcomes of the interactions. In this article, we survey results related to the concept of incompetence in classic as well as evolutionary game theory and provide several new results. We also suggest future extensions of the model and argue why it is important to take into account behavioural mistakes when analysing interactions among players in both economic and biological settings."}],"volume":13,"ec_funded":1,"file":[{"date_created":"2022-02-21T08:54:17Z","file_name":"2022_DynamicGamesApplic_Graham.pdf","creator":"dernst","date_updated":"2022-02-21T08:54:17Z","file_size":1890512,"checksum":"cd53b07e96f9030ddb348f305e5b58c7","file_id":"10781","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2153-0785"],"eissn":["2153-0793"]},"publication_status":"published"},{"publication_status":"published","publication_identifier":{"issn":["0926-2601"],"eissn":["1572-929X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2023_PotentialAnalysis_DelloSchiavo.pdf","date_created":"2023-10-04T09:18:59Z","file_size":806391,"date_updated":"2023-10-04T09:18:59Z","creator":"dernst","success":1,"file_id":"14387","checksum":"625526482be300ca7281c91c30d41725","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"volume":58,"abstract":[{"text":"We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 58","month":"03","date_updated":"2023-10-04T09:19:12Z","ddc":["510"],"department":[{"_id":"JaMa"}],"file_date_updated":"2023-10-04T09:18:59Z","_id":"10145","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","year":"2023","has_accepted_license":"1","isi":1,"publication":"Potential Analysis","day":"01","page":"573-615","date_created":"2021-10-17T22:01:17Z","date_published":"2023-03-01T00:00:00Z","doi":"10.1007/s11118-021-09951-y","acknowledgement":"The author is grateful to Professors Sergio Albeverio and Andreas Eberle, and to Dr. Kohei Suzuki, for fruitful conversations on the subject of the present work, and for respectively pointing out the references [1, 13], and [3, 20]. Finally, he is especially grateful to an anonymous Reviewer for their very careful reading and their suggestions which improved the readability of the paper.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"chicago":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis. Springer Nature, 2023. https://doi.org/10.1007/s11118-021-09951-y.","ista":"Dello Schiavo L. 2023. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 58, 573–615.","mla":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis, vol. 58, Springer Nature, 2023, pp. 573–615, doi:10.1007/s11118-021-09951-y.","apa":"Dello Schiavo, L. (2023). Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-021-09951-y","ama":"Dello Schiavo L. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 2023;58:573-615. doi:10.1007/s11118-021-09951-y","ieee":"L. Dello Schiavo, “Ergodic decomposition of Dirichlet forms via direct integrals and applications,” Potential Analysis, vol. 58. Springer Nature, pp. 573–615, 2023.","short":"L. Dello Schiavo, Potential Analysis 58 (2023) 573–615."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2003.01366"],"isi":["000704213400001"]},"author":[{"orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo"}],"title":"Ergodic decomposition of Dirichlet forms via direct integrals and applications","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}]},{"file_date_updated":"2023-10-04T09:37:26Z","department":[{"_id":"MaKw"}],"ddc":["510"],"date_updated":"2023-10-04T09:38:45Z","status":"public","type":"journal_article","article_type":"original","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":"11706","volume":62,"issue":"4","file":[{"file_size":1362334,"date_updated":"2023-10-04T09:37:26Z","creator":"dernst","file_name":"2023_RandomStructureAlgorithms_Liebenau.pdf","date_created":"2023-10-04T09:37:26Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14389","checksum":"3a5969d0c512aef01c30f3dc81c6d59b"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1042-9832"],"eissn":["1098-2418"]},"publication_status":"published","month":"07","intvolume":" 62","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. ","lang":"eng"}],"title":"Asymmetric Ramsey properties of random graphs involving cliques and cycles","author":[{"full_name":"Liebenau, Anita","last_name":"Liebenau","first_name":"Anita"},{"last_name":"Mattos","full_name":"Mattos, Letícia","first_name":"Letícia"},{"first_name":"Walner","id":"12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd","full_name":"Mendonca Dos Santos, Walner","last_name":"Mendonca Dos Santos"},{"full_name":"Skokan, Jozef","last_name":"Skokan","first_name":"Jozef"}],"external_id":{"isi":["000828530400001"]},"article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. 2023. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 62(4), 1035–1055.","chicago":"Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” Random Structures and Algorithms. Wiley, 2023. https://doi.org/10.1002/rsa.21106.","ama":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 2023;62(4):1035-1055. doi:10.1002/rsa.21106","apa":"Liebenau, A., Mattos, L., Mendonca dos Santos, W., & Skokan, J. (2023). Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. Wiley. https://doi.org/10.1002/rsa.21106","ieee":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric Ramsey properties of random graphs involving cliques and cycles,” Random Structures and Algorithms, vol. 62, no. 4. Wiley, pp. 1035–1055, 2023.","short":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures and Algorithms 62 (2023) 1035–1055.","mla":"Liebenau, Anita, et al. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” Random Structures and Algorithms, vol. 62, no. 4, Wiley, 2023, pp. 1035–55, doi:10.1002/rsa.21106."},"date_published":"2023-07-01T00:00:00Z","doi":"10.1002/rsa.21106","date_created":"2022-07-31T22:01:49Z","page":"1035-1055","day":"01","publication":"Random Structures and Algorithms","has_accepted_license":"1","isi":1,"year":"2023","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"This work was started at the thematic program GRAPHS@IMPA (January–March 2018), in Rio de Janeiro. We thank IMPA and the organisers for the hospitality and for providing a pleasant research environment. We thank Rob Morris for helpful discussions, and the anonymous referees for their careful reading and many helpful suggestions. Open Access funding enabled and organized by Projekt DEAL.\r\nA. Liebenau was supported by an ARC DECRA Fellowship Grant DE170100789. L. Mattos was supported by CAPES and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). W. Mendonça was supported by CAPES project 88882.332408/2010-01."},{"abstract":[{"lang":"eng","text":"We establish precise right-tail small deviation estimates for the largest eigenvalue of real symmetric and complex Hermitian matrices whose entries are independent random variables with uniformly bounded moments. The proof relies on a Green function comparison along a continuous interpolating matrix flow for a long time. Less precise estimates are also obtained in the left tail."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2112.12093"}],"month":"05","intvolume":" 29","publication_identifier":{"issn":["1350-7265"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":29,"issue":"2","ec_funded":1,"_id":"12707","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-10-04T10:21:07Z","department":[{"_id":"LaEr"}],"quality_controlled":"1","publisher":"Bernoulli Society for Mathematical Statistics and Probability","oa":1,"isi":1,"year":"2023","day":"01","publication":"Bernoulli","page":"1063-1079","doi":"10.3150/22-BEJ1490","date_published":"2023-05-01T00:00:00Z","date_created":"2023-03-05T23:01:05Z","project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"citation":{"ista":"Erdös L, Xu Y. 2023. Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. 29(2), 1063–1079.","chicago":"Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest Eigenvalue of Wigner Matrices.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2023. https://doi.org/10.3150/22-BEJ1490.","ama":"Erdös L, Xu Y. Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. 2023;29(2):1063-1079. doi:10.3150/22-BEJ1490","apa":"Erdös, L., & Xu, Y. (2023). Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/22-BEJ1490","short":"L. Erdös, Y. Xu, Bernoulli 29 (2023) 1063–1079.","ieee":"L. Erdös and Y. Xu, “Small deviation estimates for the largest eigenvalue of Wigner matrices,” Bernoulli, vol. 29, no. 2. 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B., Zagórski, M. P., & Kicheva, A. (2023). Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-01977-w","ama":"Bocanegra L, Singh A, Hannezo EB, Zagórski MP, Kicheva A. Cell cycle dynamics control fluidity of the developing mouse neuroepithelium. Nature Physics. 2023;19:1050-1058. doi:10.1038/s41567-023-01977-w","short":"L. Bocanegra, A. Singh, E.B. Hannezo, M.P. Zagórski, A. Kicheva, Nature Physics 19 (2023) 1050–1058.","ieee":"L. Bocanegra, A. Singh, E. B. Hannezo, M. P. Zagórski, and A. Kicheva, “Cell cycle dynamics control fluidity of the developing mouse neuroepithelium,” Nature Physics, vol. 19. 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Springer Nature, 2023. https://doi.org/10.1038/s41567-023-01977-w."},"title":"Cell cycle dynamics control fluidity of the developing mouse neuroepithelium","external_id":{"isi":["000964029300003"]},"article_processing_charge":"No","author":[{"id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Bocanegra, Laura","last_name":"Bocanegra"},{"full_name":"Singh, Amrita","last_name":"Singh","first_name":"Amrita","id":"76250f9f-3a21-11eb-9a80-a6180a0d7958"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Zagórski","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"acknowledgement":"We thank S. Hippenmeyer for the reagents and C. P. Heisenberg, J. Briscoe and K. Page for comments on the manuscript. This work was supported by IST Austria; the European Research Council under Horizon 2020 research and innovation programme grant no. 680037 and Horizon Europe grant 101044579 (A.K.); Austrian Science Fund (FWF): F78 (Stem Cell Modulation) (A.K.); ISTFELLOW postdoctoral program (A.S.); Narodowe Centrum Nauki, Poland SONATA, 2017/26/D/NZ2/00454 (M.Z.); and the Polish National Agency for Academic Exchange (M.Z.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature Physics","day":"01","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-04-16T22:01:09Z","doi":"10.1038/s41567-023-01977-w","date_published":"2023-07-01T00:00:00Z","page":"1050-1058","_id":"12837","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2023-10-04T11:14:05Z","department":[{"_id":"EdHa"},{"_id":"AnKi"}],"file_date_updated":"2023-10-04T11:13:28Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues."}],"intvolume":" 19","month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":5532285,"date_updated":"2023-10-04T11:13:28Z","creator":"dernst","file_name":"2023_NaturePhysics_Boncanegra.pdf","date_created":"2023-10-04T11:13:28Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14392","checksum":"858225a4205b74406e5045006cdd853f"}],"publication_status":"published","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"ec_funded":1,"volume":19,"related_material":{"record":[{"relation":"dissertation_contains","id":"13081","status":"public"}]}},{"date_published":"2023-05-23T00:00:00Z","doi":"10.15479/at:ista:13081","date_created":"2023-05-23T19:10:42Z","page":"93","day":"23","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","title":"Epithelial dynamics during mouse neural tube development","author":[{"full_name":"Bocanegra, Laura","last_name":"Bocanegra","id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081.","ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:10.15479/at:ista:13081","apa":"Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023.","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081.","ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria."},"related_material":{"record":[{"status":"public","id":"9349","relation":"part_of_dissertation"},{"status":"public","id":"12837","relation":"part_of_dissertation"}]},"file":[{"date_created":"2023-05-25T06:32:12Z","file_name":"Thesis_final_LauraBocanegra.docx","date_updated":"2023-05-25T06:32:12Z","file_size":25615534,"creator":"lbocaneg","file_id":"13089","checksum":"74f3f89e59a0189bee53ebfad9c1b9af","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"},{"date_created":"2023-05-25T06:32:16Z","file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf","date_updated":"2023-05-25T06:32:16Z","file_size":12386046,"creator":"lbocaneg","file_id":"13090","checksum":"c6cdef6323eacfb4b7a8af20f32eae97","embargo":"2024-05-31","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2023-05-25T06:32:16Z","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"ddc":["570"],"supervisor":[{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva"}],"date_updated":"2023-10-04T11:14:04Z","status":"public","type":"dissertation","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"13081"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” Environmental Science and Pollution Research, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:10.1007/s11356-023-26844-2.","ieee":"V. Filipović Marijić et al., “Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish,” Environmental Science and Pollution Research, vol. 30. Springer Nature, pp. 63510–63521, 2023.","short":"V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić, M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental Science and Pollution Research 30 (2023) 63510–63521.","apa":"Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić, I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. Springer Nature. https://doi.org/10.1007/s11356-023-26844-2","ama":"Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 2023;30:63510-63521. doi:10.1007/s11356-023-26844-2","chicago":"Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović, Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” Environmental Science and Pollution Research. Springer Nature, 2023. https://doi.org/10.1007/s11356-023-26844-2.","ista":"Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I, Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 30, 63510–63521."},"title":"Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish","external_id":{"isi":["000970917900012"],"pmid":["37055686"]},"article_processing_charge":"No","author":[{"last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka","first_name":"Vlatka"},{"first_name":"Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","full_name":"Krasnici, Nesrete","last_name":"Krasnici"},{"full_name":"Valić, Damir","last_name":"Valić","first_name":"Damir"},{"first_name":"Damir","full_name":"Kapetanović, Damir","last_name":"Kapetanović"},{"last_name":"Vardić Smrzlić","full_name":"Vardić Smrzlić, Irena","first_name":"Irena"},{"last_name":"Jordanova","full_name":"Jordanova, Maja","first_name":"Maja"},{"full_name":"Rebok, Katerina","last_name":"Rebok","first_name":"Katerina"},{"first_name":"Sheriban","last_name":"Ramani","full_name":"Ramani, Sheriban"},{"last_name":"Kostov","full_name":"Kostov, Vasil","first_name":"Vasil"},{"full_name":"Nastova, Rodne","last_name":"Nastova","first_name":"Rodne"},{"last_name":"Dragun","full_name":"Dragun, Zrinka","first_name":"Zrinka"}],"acknowledgement":"The authors are grateful to Dr. Nevenka Mikac for the opportunity to perform metal measurements on HR ICP-MS. This research was funded by the Ministry of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721 and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian bilateral projects: “The assessment of availability and effects of metals on fish in the rivers under the impact of mining activities” and “Bacterial and parasitical communities of chub as indicators of the status of environment exposed to mining activities.”","publisher":"Springer Nature","quality_controlled":"1","publication":"Environmental Science and Pollution Research","day":"01","year":"2023","isi":1,"date_created":"2023-04-23T22:01:03Z","doi":"10.1007/s11356-023-26844-2","date_published":"2023-05-01T00:00:00Z","page":"63510-63521","_id":"12863","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-10-04T11:23:10Z","department":[{"_id":"LifeSc"}],"oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems."}],"intvolume":" 30","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1614-7499"],"issn":["0944-1344"]},"volume":30},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Khatoniar M, Yama N, Ghazaryan A, et al. Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities. Advanced Optical Materials. 2023;11(13). doi:10.1002/adom.202202631","apa":"Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., Majumdar, K., & Menon, V. (2023). Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities. Advanced Optical Materials. Wiley. https://doi.org/10.1002/adom.202202631","short":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, K. Majumdar, V. Menon, Advanced Optical Materials 11 (2023).","ieee":"M. Khatoniar et al., “Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities,” Advanced Optical Materials, vol. 11, no. 13. Wiley, 2023.","mla":"Khatoniar, Mandeep, et al. “Optical Manipulation of Layer–Valley Coherence via Strong Exciton–Photon Coupling in Microcavities.” Advanced Optical Materials, vol. 11, no. 13, 2202631, Wiley, 2023, doi:10.1002/adom.202202631.","ista":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Majumdar K, Menon V. 2023. Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities. Advanced Optical Materials. 11(13), 2202631.","chicago":"Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan Ghaemi, Kausik Majumdar, and Vinod Menon. “Optical Manipulation of Layer–Valley Coherence via Strong Exciton–Photon Coupling in Microcavities.” Advanced Optical Materials. Wiley, 2023. https://doi.org/10.1002/adom.202202631."},"title":"Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities","external_id":{"isi":["000963866700001"],"arxiv":["2211.08755"]},"article_processing_charge":"No","author":[{"last_name":"Khatoniar","full_name":"Khatoniar, Mandeep","first_name":"Mandeep"},{"first_name":"Nicholas","last_name":"Yama","full_name":"Yama, Nicholas"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan"},{"first_name":"Sriram","full_name":"Guddala, Sriram","last_name":"Guddala"},{"first_name":"Pouyan","last_name":"Ghaemi","full_name":"Ghaemi, Pouyan"},{"first_name":"Kausik","full_name":"Majumdar, Kausik","last_name":"Majumdar"},{"first_name":"Vinod","last_name":"Menon","full_name":"Menon, Vinod"}],"article_number":"2202631","publication":"Advanced Optical Materials","day":"04","year":"2023","isi":1,"date_created":"2023-04-16T22:01:09Z","doi":"10.1002/adom.202202631","date_published":"2023-07-04T00:00:00Z","acknowledgement":"The authors acknowledge insightful discussions with Prof. Wang Yao and graphics by Rezlind Bushati. M.K. and N.Y. acknowledge support from NSF grants NSF DMR-1709996 and NSF OMA 1936276. S.G. was supported by the Army Research Office Multidisciplinary University Research Initiative program (W911NF-17-1-0312) and V.M.M. by the Army Research Office grant (W911NF-22-1-0091). K.M acknowledges the SPARC program that supported his collaboration with the CUNY team. The authors acknowledge the Nanofabrication facility at the CUNY Advanced Science Research Center where the cavity devices were fabricated.","oa":1,"quality_controlled":"1","publisher":"Wiley","date_updated":"2023-10-04T11:15:17Z","department":[{"_id":"MiLe"}],"_id":"12836","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2195-1071"]},"volume":11,"issue":"13","oa_version":"Preprint","abstract":[{"text":"Coherent control and manipulation of quantum degrees of freedom such as spins forms the basis of emerging quantum technologies. In this context, the robust valley degree of freedom and the associated valley pseudospin found in two-dimensional transition metal dichalcogenides is a highly attractive platform. Valley polarization and coherent superposition of valley states have been observed in these systems even up to room temperature. Control of valley coherence is an important building block for the implementation of valley qubit. Large magnetic fields or high-power lasers have been used in the past to demonstrate the control (initialization and rotation) of the valley coherent states. Here, the control of layer–valley coherence via strong coupling of valley excitons in bilayer WS2 to microcavity photons is demonstrated by exploiting the pseudomagnetic field arising in optical cavities owing to the transverse electric–transverse magnetic (TE–TM)mode splitting. The use of photonic structures to generate pseudomagnetic fields which can be used to manipulate exciton-polaritons presents an attractive approach to control optical responses without the need for large magnets or high-intensity optical pump powers.","lang":"eng"}],"intvolume":" 11","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.08755"}],"scopus_import":"1"},{"issue":"5","volume":62,"ec_funded":1,"file":[{"file_size":1240995,"date_updated":"2023-10-04T11:34:10Z","creator":"dernst","file_name":"2023_CalculusEquations_Gladbach.pdf","date_created":"2023-10-04T11:34:10Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14393","checksum":"359bee38d94b7e0aa73925063cb8884d"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0944-2669"],"eissn":["1432-0835"]},"publication_status":"published","month":"04","intvolume":" 62","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This paper deals with the large-scale behaviour of dynamical optimal transport on Zd\r\n-periodic graphs with general lower semicontinuous and convex energy densities. Our main contribution is a homogenisation result that describes the effective behaviour of the discrete problems in terms of a continuous optimal transport problem. The effective energy density can be explicitly expressed in terms of a cell formula, which is a finite-dimensional convex programming problem that depends non-trivially on the local geometry of the discrete graph and the discrete energy density. Our homogenisation result is derived from a Γ\r\n-convergence result for action functionals on curves of measures, which we prove under very mild growth conditions on the energy density. We investigate the cell formula in several cases of interest, including finite-volume discretisations of the Wasserstein distance, where non-trivial limiting behaviour occurs."}],"department":[{"_id":"JaMa"}],"file_date_updated":"2023-10-04T11:34:10Z","ddc":["510"],"date_updated":"2023-10-04T11:34:49Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12959","doi":"10.1007/s00526-023-02472-z","date_published":"2023-04-28T00:00:00Z","date_created":"2023-05-14T22:01:00Z","day":"28","publication":"Calculus of Variations and Partial Differential Equations","has_accepted_license":"1","isi":1,"year":"2023","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117). J.M and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—350398276. We thank the anonymous reviewer for the careful reading and for useful suggestions. Open access funding provided by Austrian Science Fund (FWF).","title":"Homogenisation of dynamical optimal transport on periodic graphs","author":[{"last_name":"Gladbach","full_name":"Gladbach, Peter","first_name":"Peter"},{"first_name":"Eva","full_name":"Kopfer, Eva","last_name":"Kopfer"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Portinale","full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000980588900001"],"arxiv":["2110.15321"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Gladbach, Peter, et al. “Homogenisation of Dynamical Optimal Transport on Periodic Graphs.” Calculus of Variations and Partial Differential Equations, vol. 62, no. 5, 143, Springer Nature, 2023, doi:10.1007/s00526-023-02472-z.","ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of dynamical optimal transport on periodic graphs,” Calculus of Variations and Partial Differential Equations, vol. 62, no. 5. Springer Nature, 2023.","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Calculus of Variations and Partial Differential Equations 62 (2023).","ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of dynamical optimal transport on periodic graphs. Calculus of Variations and Partial Differential Equations. 2023;62(5). doi:10.1007/s00526-023-02472-z","apa":"Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2023). Homogenisation of dynamical optimal transport on periodic graphs. Calculus of Variations and Partial Differential Equations. Springer Nature. https://doi.org/10.1007/s00526-023-02472-z","chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of Dynamical Optimal Transport on Periodic Graphs.” Calculus of Variations and Partial Differential Equations. Springer Nature, 2023. https://doi.org/10.1007/s00526-023-02472-z.","ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2023. Homogenisation of dynamical optimal transport on periodic graphs. Calculus of Variations and Partial Differential Equations. 62(5), 143."},"project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"}],"article_number":"143"},{"abstract":[{"lang":"eng","text":"Cu2–xS and Cu2–xSe have recently been reported as promising thermoelectric (TE) materials for medium-temperature applications. In contrast, Cu2–xTe, another member of the copper chalcogenide family, typically exhibits low Seebeck coefficients that limit its potential to achieve a superior thermoelectric figure of merit, zT, particularly in the low-temperature range where this material could be effective. To address this, we investigated the TE performance of Cu1.5–xTe–Cu2Se nanocomposites by consolidating surface-engineered Cu1.5Te nanocrystals. This surface engineering strategy allows for precise adjustment of Cu/Te ratios and results in a reversible phase transition at around 600 K in Cu1.5–xTe–Cu2Se nanocomposites, as systematically confirmed by in situ high-temperature X-ray diffraction combined with differential scanning calorimetry analysis. The phase transition leads to a conversion from metallic-like to semiconducting-like TE properties. Additionally, a layer of Cu2Se generated around Cu1.5–xTe nanoparticles effectively inhibits Cu1.5–xTe grain growth, minimizing thermal conductivity and decreasing hole concentration. These properties indicate that copper telluride based compounds have a promising thermoelectric potential, translated into a high dimensionless zT of 1.3 at 560 K."}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"05","intvolume":" 17","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"9","volume":17,"_id":"12915","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-10-04T11:29:22Z","department":[{"_id":"MaIb"}],"acknowledgement":"The authors acknowledge support from the projects ENE2016-77798-C4-3-R and NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/and by “ERDF A way of making Europe”, and by the “European Union”. K.X. and B.N. thank the China Scholarship Council (CSC) for scholarship support. The authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246. ICN2 is supported by the Severo Ochoa program from the Spanish MCIN/AEI (Grant No.: CEX2021-001214-S). IREC and ICN2 are funded by the CERCA Programme/Generalitat de Catalunya. J.L. acknowledges support from the Natural Science Foundation of Sichuan province (2022NSFSC1229). Part of the present work was performed in the frameworks of Universitat de Barcelona Nanoscience Ph.D. program and Universitat Autònoma de Barcelona Materials Science Ph.D. program. Y.L. acknowledges funding from the National Natural Science Foundation of China (Grant No. 22209034) and the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grants No. 2022LCX002). K.H.L. acknowledges the financial support of the National Natural Science Foundation of China (Grant No. 22208293).","quality_controlled":"1","publisher":"American Chemical Society","isi":1,"year":"2023","day":"09","publication":"ACS Nano","page":"8442-8452","date_published":"2023-05-09T00:00:00Z","doi":"10.1021/acsnano.3c00495","date_created":"2023-05-07T22:01:04Z","citation":{"chicago":"Xing, Congcong, Yu Zhang, Ke Xiao, Xu Han, Yu Liu, Bingfei Nan, Maria Garcia Ramon, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se Nanocomposites.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.3c00495.","ista":"Xing C, Zhang Y, Xiao K, Han X, Liu Y, Nan B, Ramon MG, Lim KH, Li J, Arbiol J, Poudel B, Nozariasbmarz A, Li W, Ibáñez M, Cabot A. 2023. Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. ACS Nano. 17(9), 8442–8452.","mla":"Xing, Congcong, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se Nanocomposites.” ACS Nano, vol. 17, no. 9, American Chemical Society, 2023, pp. 8442–52, doi:10.1021/acsnano.3c00495.","apa":"Xing, C., Zhang, Y., Xiao, K., Han, X., Liu, Y., Nan, B., … Cabot, A. (2023). Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c00495","ama":"Xing C, Zhang Y, Xiao K, et al. Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. ACS Nano. 2023;17(9):8442-8452. doi:10.1021/acsnano.3c00495","short":"C. Xing, Y. Zhang, K. Xiao, X. Han, Y. Liu, B. Nan, M.G. Ramon, K.H. Lim, J. Li, J. Arbiol, B. Poudel, A. Nozariasbmarz, W. Li, M. Ibáñez, A. Cabot, ACS Nano 17 (2023) 8442–8452.","ieee":"C. Xing et al., “Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites,” ACS Nano, vol. 17, no. 9. American Chemical Society, pp. 8442–8452, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Xing","full_name":"Xing, Congcong","first_name":"Congcong"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"first_name":"Xu","last_name":"Han","full_name":"Han, Xu"},{"orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","last_name":"Liu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nan, Bingfei","last_name":"Nan","first_name":"Bingfei"},{"last_name":"Ramon","full_name":"Ramon, Maria Garcia","first_name":"Maria Garcia","id":"1ffff7cd-ed76-11ed-8d5f-be5e7c364eb9"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"first_name":"Junshan","last_name":"Li","full_name":"Li, Junshan"},{"first_name":"Jordi","full_name":"Arbiol, Jordi","last_name":"Arbiol"},{"full_name":"Poudel, Bed","last_name":"Poudel","first_name":"Bed"},{"first_name":"Amin","full_name":"Nozariasbmarz, Amin","last_name":"Nozariasbmarz"},{"full_name":"Li, Wenjie","last_name":"Li","first_name":"Wenjie"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"external_id":{"isi":["000976063200001"],"pmid":["37071412"]},"article_processing_charge":"No","title":"Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites"}]