[{"publisher":"Elsevier","title":"Cytoplasm's got moves","author":[{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"},{"last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CaHe"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.","lang":"eng"}],"scopus_import":"1","type":"journal_article","citation":{"ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” <i>Developmental Cell</i>, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. <i>Developmental Cell</i>. 2021;56(2):P213-226. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>.","apa":"Shamipour, S., Caballero Mancebo, S., &#38; Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>."},"publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"quality_controlled":"1","_id":"9006","publication_status":"published","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","date_published":"2021-01-25T00:00:00Z","month":"01","intvolume":"        56","oa":1,"issue":"2","date_updated":"2024-03-25T23:30:10Z","page":"P213-226","external_id":{"pmid":["33321104"],"isi":["000613273900009"]},"year":"2021","volume":56,"pmid":1,"status":"public","day":"25","date_created":"2021-01-17T23:01:10Z","publication":"Developmental Cell","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2020.12.002"}],"doi":"10.1016/j.devcel.2020.12.002","oa_version":"Published Version","isi":1,"related_material":{"record":[{"id":"9623","relation":"dissertation_contains","status":"public"}]}},{"_id":"9009","quality_controlled":"1","citation":{"chicago":"Grosser, Joshua A., Margaret E Maes, and Robert W. Nickells. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>.","short":"J.A. Grosser, M.E. Maes, R.W. Nickells, Apoptosis 26 (2021) 132–145.","ista":"Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145.","ieee":"J. A. Grosser, M. E. Maes, and R. W. Nickells, “Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis,” <i>Apoptosis</i>, vol. 26, no. 2. Springer Nature, pp. 132–145, 2021.","ama":"Grosser JA, Maes ME, Nickells RW. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. 2021;26(2):132-145. doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>","mla":"Grosser, Joshua A., et al. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>, vol. 26, no. 2, Springer Nature, 2021, pp. 132–45, doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>.","apa":"Grosser, J. A., Maes, M. E., &#38; Nickells, R. W. (2021). Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>"},"publication_identifier":{"issn":["1360-8185"],"eissn":["1573-675X"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"Recent advancements in live cell imaging technologies have identified the phenomenon of intracellular propagation of late apoptotic events, such as cytochrome c release and caspase activation. The mechanism, prevalence, and speed of apoptosis propagation remain unclear. Additionally, no studies have demonstrated propagation of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome c and SMAC/Diablo release and is affected by cellular morphology, such that cells with processes are more likely to exhibit propagation. The initiation of propagation events is most prevalent in the distal tips of processes, while the rate of propagation is influenced by the 2-dimensional width of the process. Propagation was rarely observed in the cell soma, which exhibited near synchronous recruitment of BAX. Propagation velocity is not affected by mitochondrial volume in segments of processes, but is negatively affected by mitochondrial density. There was no evidence of a propagating wave of increased levels of intracellular calcium ions. Alternatively, we did observe a uniform increase in superoxide build-up in cellular mitochondria, which was released as a propagating wave simultaneously with the propagating recruitment of BAX to the mitochondrial outer membrane."}],"type":"journal_article","publication_status":"published","author":[{"full_name":"Grosser, Joshua A.","last_name":"Grosser","first_name":"Joshua A."},{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E"},{"last_name":"Nickells","first_name":"Robert W.","full_name":"Nickells, Robert W."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"SaSi"}],"date_created":"2021-01-17T23:01:11Z","day":"01","status":"public","volume":26,"pmid":1,"oa_version":"Submitted Version","isi":1,"publication":"Apoptosis","doi":"10.1007/s10495-020-01654-w","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/"}],"date_updated":"2023-08-07T13:32:40Z","oa":1,"issue":"2","date_published":"2021-02-01T00:00:00Z","intvolume":"        26","month":"02","acknowledgement":"This work was supported by National Institute of Health grants R01 EY030123, P30 EY016665, and T32 GM081061, an unrestricted research grant from Research to Prevent Blindness, Inc., and the Frederick A. Davis Endowment from the Department of Ophthalmology and Visual Sciences at the University of Wisconsin-Madison.","year":"2021","page":"132-145","external_id":{"isi":["000606722600001"],"pmid":["33426618"]}},{"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Ötvös, Krisztina","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","last_name":"Ötvös"},{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"last_name":"Vega","first_name":"Andrea","full_name":"Vega, Andrea"},{"full_name":"O’Brien, Jose","last_name":"O’Brien","first_name":"Jose"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"full_name":"Abualia, Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia"},{"full_name":"Antonielli, Livio","last_name":"Antonielli","first_name":"Livio"},{"full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","last_name":"Zhang","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","full_name":"Tan, Shutang"},{"full_name":"Cuesta, Candela","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","orcid":"0000-0003-1923-2410"},{"full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina","last_name":"Artner"},{"full_name":"Bouguyon, Eleonore","first_name":"Eleonore","last_name":"Bouguyon"},{"last_name":"Gojon","first_name":"Alain","full_name":"Gojon, Alain"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."},{"last_name":"Wabnik","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T"},{"full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"file":[{"creator":"dernst","file_size":2358617,"file_id":"9110","content_type":"application/pdf","checksum":"dc55c900f3b061d6c2790b8813d759a3","access_level":"open_access","relation":"main_file","file_name":"2021_Embo_Otvos.pdf","success":1,"date_created":"2021-02-11T12:28:29Z","date_updated":"2021-02-11T12:28:29Z"}],"has_accepted_license":"1","publisher":"Embo Press","project":[{"call_identifier":"FWF","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development"},{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"},{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","_id":"9010","quality_controlled":"1","citation":{"apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>, vol. 40, no. 3, e106862, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>.","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. 2021;40(3). doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","ieee":"K. Ötvös <i>et al.</i>, “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” <i>EMBO Journal</i>, vol. 40, no. 3. Embo Press, 2021.","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>."},"publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"abstract":[{"lang":"eng","text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments."}],"scopus_import":"1","file_date_updated":"2021-02-11T12:28:29Z","type":"journal_article","year":"2021","external_id":{"pmid":[" 33399250"],"isi":["000604645600001"]},"date_updated":"2024-03-25T23:30:22Z","oa":1,"acknowledged_ssus":[{"_id":"Bio"}],"issue":"3","date_published":"2021-02-01T00:00:00Z","intvolume":"        40","month":"02","acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","article_number":"e106862","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","relation":"press_release"}],"record":[{"id":"10303","status":"public","relation":"dissertation_contains"}]},"oa_version":"Published Version","isi":1,"publication":"EMBO Journal","doi":"10.15252/embj.2020106862","ddc":["580"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-01-17T23:01:12Z","status":"public","day":"01","volume":40,"pmid":1},{"oa_version":"Published Version","ec_funded":1,"isi":1,"publication":"Entropy","doi":"10.3390/e23010125","ddc":["530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-01-19T11:12:06Z","day":"19","status":"public","volume":23,"year":"2021","external_id":{"arxiv":["2012.01390"],"isi":["000610122000001"]},"date_updated":"2023-08-07T13:34:18Z","oa":1,"issue":"1","date_published":"2021-01-19T00:00:00Z","intvolume":"        23","month":"01","article_number":"e23010125","acknowledgement":"A.K. was supported by NSF grants DMR-2037654. T.G. acknowledges funding from the Institute of Science and Technology (IST) Austria, and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nWe are indebted to Boris Shklovskii for introducing us to the problem, and Alexander Gorsky and Peter Koroteev for introducing us to the Picard-Fuchs methods. A very special thanks goes to Michael Janas for several years of excellent collaboration on these topics. TG thanks Michael Kreshchuk for introduction to the exact WKB method and great collaboration on related projects. Figure 3 and Figure 4 are reproduced from Reference [25] with friendly permission by the Russian Academy of Sciences. Figure 2, Figure 4, Figure 5, Figure 6, and Figure 8 are reproduced from Reference [26] with friendly permission by IOP Publishing.","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"publication_status":"published","_id":"9020","quality_controlled":"1","publication_identifier":{"eissn":["1099-4300"]},"citation":{"chicago":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>.","ama":"Gulden T, Kamenev A. Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>","ieee":"T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum mechanics,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","short":"T. Gulden, A. Kamenev, Entropy 23 (2021).","ista":"Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum mechanics. Entropy. 23(1), e23010125.","mla":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>, vol. 23, no. 1, e23010125, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>.","apa":"Gulden, T., &#38; Kamenev, A. (2021). Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>"},"abstract":[{"text":"We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels. ","lang":"eng"}],"arxiv":1,"type":"journal_article","file_date_updated":"2021-01-19T11:11:14Z","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes","department":[{"_id":"MaSe"}],"author":[{"full_name":"Gulden, Tobias","last_name":"Gulden","orcid":"0000-0001-6814-7541","id":"1083E038-9F73-11E9-A4B5-532AE6697425","first_name":"Tobias"},{"full_name":"Kamenev, Alex","first_name":"Alex","last_name":"Kamenev"}],"title":"Dynamics of ion channels via non-hermitian quantum mechanics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_id":"9021","creator":"tgulden","file_size":981285,"checksum":"6cd0e706156827c45c740534bd32c179","relation":"main_file","access_level":"open_access","file_name":"Final published paper.pdf","date_created":"2021-01-19T11:11:14Z","date_updated":"2021-01-19T11:11:14Z"}],"has_accepted_license":"1","publisher":"MDPI"},{"project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804"}],"publication_status":"published","_id":"9022","citation":{"ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9022\">10.15479/AT:ISTA:9022</a>","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9022\">https://doi.org/10.15479/AT:ISTA:9022</a>.","apa":"Cipolloni, G. (2021). <i>Fluctuations in the spectrum of random matrices</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9022\">https://doi.org/10.15479/AT:ISTA:9022</a>","mla":"Cipolloni, Giorgio. <i>Fluctuations in the Spectrum of Random Matrices</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9022\">10.15479/AT:ISTA:9022</a>."},"publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2021-01-25T14:19:10Z","type":"dissertation","abstract":[{"lang":"eng","text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices."}],"language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"file":[{"access_level":"open_access","relation":"main_file","checksum":"5a93658a5f19478372523ee232887e2b","content_type":"application/pdf","file_id":"9043","file_size":4127796,"creator":"gcipollo","date_created":"2021-01-25T14:19:03Z","date_updated":"2021-01-25T14:19:03Z","success":1,"file_name":"thesis.pdf"},{"content_type":"application/zip","file_id":"9044","creator":"gcipollo","file_size":12775206,"relation":"source_file","access_level":"closed","checksum":"e8270eddfe6a988e92a53c88d1d19b8c","file_name":"Thesis_files.zip","date_created":"2021-01-25T14:19:10Z","date_updated":"2021-01-25T14:19:10Z"}],"author":[{"full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","last_name":"Cipolloni","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Fluctuations in the spectrum of random matrices","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","ec_funded":1,"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:9022","ddc":["510"],"date_created":"2021-01-21T18:16:54Z","supervisor":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"status":"public","day":"25","year":"2021","page":"380","date_updated":"2023-09-07T13:29:32Z","oa":1,"month":"01","alternative_title":["ISTA Thesis"],"date_published":"2021-01-25T00:00:00Z","acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804."},{"isi":1,"oa_version":"Preprint","ec_funded":1,"doi":"10.1016/j.aim.2021.107595","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.10447"}],"publication":"Advances in Mathematics","date_created":"2021-01-22T17:55:17Z","status":"public","day":"26","volume":380,"year":"2021","external_id":{"isi":["000619676100035"],"arxiv":["1910.10447"]},"date_updated":"2023-08-07T13:34:48Z","keyword":["General Mathematics"],"issue":"3","oa":1,"intvolume":"       380","month":"03","date_published":"2021-03-26T00:00:00Z","acknowledgement":"D. Virosztek was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K124152, and no. KH129601.","article_number":"107595","project":[{"name":"Geometric study of Wasserstein spaces and free probability","_id":"26A455A6-B435-11E9-9278-68D0E5697425","grant_number":"846294","call_identifier":"H2020"}],"publication_status":"published","_id":"9036","quality_controlled":"1","citation":{"apa":"Virosztek, D. (2021). The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>","mla":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>, vol. 380, no. 3, 107595, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>.","short":"D. Virosztek, Advances in Mathematics 380 (2021).","ieee":"D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,” <i>Advances in Mathematics</i>, vol. 380, no. 3. Elsevier, 2021.","ista":"Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence. Advances in Mathematics. 380(3), 107595.","ama":"Virosztek D. The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. 2021;380(3). doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>","chicago":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>."},"publication_identifier":{"issn":["0001-8708"]},"type":"journal_article","abstract":[{"lang":"eng","text":"In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space."}],"arxiv":1,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"LaEr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511","last_name":"Virosztek","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"title":"The metric property of the quantum Jensen-Shannon divergence","publisher":"Elsevier"},{"citation":{"ieee":"G. Ivanov, “No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. London Mathematical Society, pp. 631–641, 2021.","short":"G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641.","ista":"Ivanov G. 2021. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. Bulletin of the London Mathematical Society. 53(2), 631–641.","ama":"Ivanov G. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):631-641. doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>","chicago":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society, 2021. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>.","apa":"Ivanov, G. (2021). No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>","mla":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, London Mathematical Society, 2021, pp. 631–41, doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>."},"publication_identifier":{"eissn":["14692120"],"issn":["00246093"]},"abstract":[{"text":"We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial and convex geometry in Banach spaces. We generalize some results of the paper (Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego, California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg theorem, the selection lemma and the weak  𝜀 ‐net theorem in Banach spaces of type  𝑝>1 . To prove these results, we use the original ideas of Adiprasito, Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon theorem and slightly modified version of the celebrated Maurey lemma.","lang":"eng"}],"scopus_import":"1","arxiv":1,"type":"journal_article","file_date_updated":"2021-08-06T09:59:45Z","_id":"9037","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"London Mathematical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p","author":[{"full_name":"Ivanov, Grigory","last_name":"Ivanov","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"}],"file":[{"success":1,"file_name":"2021_BLMS_Ivanov.pdf","date_updated":"2021-08-06T09:59:45Z","date_created":"2021-08-06T09:59:45Z","file_id":"9796","content_type":"application/pdf","file_size":194550,"creator":"kschuh","checksum":"e6ceaa6470d835eb4c211cbdd38fdfd1","access_level":"open_access","relation":"main_file"}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"article_type":"original","volume":53,"date_created":"2021-01-24T23:01:08Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["510"],"day":"01","status":"public","publication":"Bulletin of the London Mathematical Society","doi":"10.1112/blms.12449","oa_version":"Published Version","isi":1,"date_published":"2021-04-01T00:00:00Z","intvolume":"        53","month":"04","acknowledgement":"I wish to thank Imre Bárány for bringing the problem to my attention. I am grateful to Marton Naszódi and Igor Tsiutsiurupa for useful remarks and help with the text.\r\nThe author acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075‐15‐2019‐1926.","date_updated":"2023-08-07T13:35:20Z","oa":1,"issue":"2","page":"631-641","external_id":{"arxiv":["1912.08561"],"isi":["000607265100001"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2021"},{"date_created":"2021-01-24T23:01:09Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["620"],"day":"07","status":"public","volume":11,"pmid":1,"oa_version":"Published Version","isi":1,"publication":"Nanomaterials","doi":"10.3390/nano11010120","date_updated":"2023-08-07T13:35:50Z","oa":1,"issue":"1","date_published":"2021-01-07T00:00:00Z","intvolume":"        11","month":"01","acknowledgement":"P.A.-M. acknowledges financial support through JAE Intro program from the Superior\r\nCouncil of Scientific Investigations and the Spanish Ministry of Science and Innovation (grant number JAEINT_20_00589). G.Á.-P. and J.T.-G. acknowledge financial support through the Severo Ochoa Program from the Government of the Principality of Asturias (grant numbers PA-20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00).","article_number":"120","year":"2021","external_id":{"isi":["000610636600001"],"pmid":["33430225"]},"_id":"9038","quality_controlled":"1","citation":{"mla":"Aguilar-Merino, Patricia, et al. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” <i>Nanomaterials</i>, vol. 11, no. 1, 120, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/nano11010120\">10.3390/nano11010120</a>.","apa":"Aguilar-Merino, P., Álvarez-Pérez, G., Taboada-Gutiérrez, J., Duan, J., Prieto Gonzalez, I., Álvarez-Prado, L. M., … Alonso-González, P. (2021). Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. <i>Nanomaterials</i>. MDPI. <a href=\"https://doi.org/10.3390/nano11010120\">https://doi.org/10.3390/nano11010120</a>","chicago":"Aguilar-Merino, Patricia, Gonzalo Álvarez-Pérez, Javier Taboada-Gutiérrez, Jiahua Duan, Ivan Prieto Gonzalez, Luis Manuel Álvarez-Prado, Alexey Y. Nikitin, Javier Martín-Sánchez, and Pablo Alonso-González. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” <i>Nanomaterials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/nano11010120\">https://doi.org/10.3390/nano11010120</a>.","ama":"Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, et al. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. <i>Nanomaterials</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.3390/nano11010120\">10.3390/nano11010120</a>","short":"P. Aguilar-Merino, G. Álvarez-Pérez, J. Taboada-Gutiérrez, J. Duan, I. Prieto Gonzalez, L.M. Álvarez-Prado, A.Y. Nikitin, J. Martín-Sánchez, P. Alonso-González, Nanomaterials 11 (2021).","ista":"Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, Duan J, Prieto Gonzalez I, Álvarez-Prado LM, Nikitin AY, Martín-Sánchez J, Alonso-González P. 2021. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. Nanomaterials. 11(1), 120.","ieee":"P. Aguilar-Merino <i>et al.</i>, “Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal,” <i>Nanomaterials</i>, vol. 11, no. 1. MDPI, 2021."},"publication_identifier":{"eissn":["20794991"]},"abstract":[{"text":"Layered materials in which individual atomic layers are bonded by weak van der Waals forces (vdW materials) constitute one of the most prominent platforms for materials research. Particularly, polar vdW crystals, such as hexagonal boron nitride (h-BN), alpha-molybdenum trioxide (α-MoO3) or alpha-vanadium pentoxide (α-V2O5), have received significant attention in nano-optics, since they support phonon polaritons (PhPs)―light coupled to lattice vibrations― with strong electromagnetic confinement and low optical losses. Recently, correlative far- and near-field studies of α-MoO3 have been demonstrated as an effective strategy to accurately extract the permittivity of this material. Here, we use this accurately characterized and low-loss polaritonic material to sense its local dielectric environment, namely silica (SiO2), one of the most widespread substrates in nanotechnology. By studying the propagation of PhPs on α-MoO3 flakes with different thicknesses laying on SiO2 substrates via near-field microscopy (s-SNOM), we extract locally the infrared permittivity of SiO2. Our work reveals PhPs nanoimaging as a versatile method for the quantitative characterization of the local optical properties of dielectric substrates, crucial for understanding and predicting the response of nanomaterials and for the future scalability of integrated nanophotonic devices. ","lang":"eng"}],"scopus_import":"1","file_date_updated":"2021-01-25T08:02:32Z","type":"journal_article","publication_status":"published","title":"Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Aguilar-Merino, Patricia","first_name":"Patricia","last_name":"Aguilar-Merino"},{"full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo","last_name":"Álvarez-Pérez"},{"full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez","first_name":"Javier"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez"},{"full_name":"Álvarez-Prado, Luis Manuel","last_name":"Álvarez-Prado","first_name":"Luis Manuel"},{"first_name":"Alexey Y.","last_name":"Nikitin","full_name":"Nikitin, Alexey Y."},{"last_name":"Martín-Sánchez","first_name":"Javier","full_name":"Martín-Sánchez, Javier"},{"full_name":"Alonso-González, Pablo","last_name":"Alonso-González","first_name":"Pablo"}],"file":[{"date_updated":"2021-01-25T08:02:32Z","date_created":"2021-01-25T08:02:32Z","file_name":"2020_Nanomaterials_Aguilar_Merino.pdf","success":1,"relation":"main_file","checksum":"1edc13eeda83df5cd9fff9504727b1f5","access_level":"open_access","creator":"dernst","file_size":2730267,"file_id":"9042","content_type":"application/pdf"}],"has_accepted_license":"1","publisher":"MDPI","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"NanoFab"}]},{"article_processing_charge":"No","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Public Library of Science","title":"Mechanisms and therapeutic potential of collateral sensitivity to antibiotics","author":[{"full_name":"Römhild, Roderich","last_name":"Römhild","orcid":"0000-0001-9480-5261","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","first_name":"Roderich"},{"last_name":"Andersson","first_name":"Dan I.","full_name":"Andersson, Dan I."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"d745d7f8fcbb9b95fea16a36f94dee31","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9070","file_size":570066,"creator":"dernst","date_created":"2021-02-03T12:13:03Z","date_updated":"2021-02-03T12:13:03Z","success":1,"file_name":"2021_PlosPathogens_Roemhild.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["15537374"],"issn":["15537366"]},"citation":{"mla":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>, vol. 17, no. 1, e1009172, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>.","apa":"Römhild, R., &#38; Andersson, D. I. (2021). Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>","chicago":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>.","ista":"Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172.","short":"R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021).","ieee":"R. Römhild and D. I. Andersson, “Mechanisms and therapeutic potential of collateral sensitivity to antibiotics,” <i>PLoS Pathogens</i>, vol. 17, no. 1. Public Library of Science, 2021.","ama":"Römhild R, Andersson DI. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. 2021;17(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>"},"scopus_import":"1","file_date_updated":"2021-02-03T12:13:03Z","type":"journal_article","_id":"9046","quality_controlled":"1","external_id":{"pmid":["33444399"],"isi":["000610190400007"]},"year":"2021","date_published":"2021-01-14T00:00:00Z","intvolume":"        17","month":"01","acknowledgement":"Our work was supported by the Swedish Research Council (grant 2017-01527) to DIA","article_number":"e1009172","date_updated":"2023-08-07T13:36:55Z","oa":1,"issue":"1","publication":"PLoS Pathogens","doi":"10.1371/journal.ppat.1009172","oa_version":"Published Version","isi":1,"volume":17,"pmid":1,"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-01-31T23:01:21Z","status":"public","day":"14"},{"date_created":"2021-01-31T23:01:21Z","day":"01","status":"public","volume":20,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"8536"}]},"isi":1,"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.04892"}],"doi":"10.1109/TWC.2020.3022922","publication":"IEEE Transactions on Wireless Communications","date_updated":"2023-08-07T13:36:25Z","issue":"1","oa":1,"intvolume":"        20","month":"01","date_published":"2021-01-01T00:00:00Z","acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162, and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei. The authors would like to thank the anonymous reviewers for their comments that helped improving the quality of the manuscript.","year":"2021","external_id":{"isi":["000607808800002"],"arxiv":["1909.04892"]},"page":"18-27","_id":"9047","quality_controlled":"1","publication_identifier":{"issn":["15361276"],"eissn":["15582248"]},"citation":{"apa":"Mondelli, M., Hashemi, S. A., Cioffi, J. M., &#38; Goldsmith, A. (2021). Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>","mla":"Mondelli, Marco, et al. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1, IEEE, 2021, pp. 18–27, doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>.","ieee":"M. Mondelli, S. A. Hashemi, J. M. Cioffi, and A. Goldsmith, “Sublinear latency for simplified successive cancellation decoding of polar codes,” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1. IEEE, pp. 18–27, 2021.","ista":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. 2021. Sublinear latency for simplified successive cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 20(1), 18–27.","short":"M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 20 (2021) 18–27.","ama":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. 2021;20(1):18-27. doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>","chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John M. Cioffi, and Andrea Goldsmith. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>."},"type":"journal_article","abstract":[{"text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block length and μ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 or 1.","lang":"eng"}],"scopus_import":"1","arxiv":1,"publication_status":"published","author":[{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco"},{"full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali","last_name":"Hashemi"},{"full_name":"Cioffi, John M.","first_name":"John M.","last_name":"Cioffi"},{"first_name":"Andrea","last_name":"Goldsmith","full_name":"Goldsmith, Andrea"}],"title":"Sublinear latency for simplified successive cancellation decoding of polar codes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"IEEE","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"MaMo"}]},{"date_published":"2021-01-29T00:00:00Z","intvolume":"       126","month":"01","article_number":"040602","acknowledgement":"S. D. N. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. M. and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement No. 850899).","keyword":["General Physics and Astronomy"],"date_updated":"2023-09-05T12:08:58Z","oa":1,"issue":"4","external_id":{"arxiv":["2008.04894"],"isi":["000613148200001"]},"year":"2021","volume":126,"ddc":["530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-01T09:20:00Z","status":"public","day":"29","publication":"Physical Review Letters","doi":"10.1103/physrevlett.126.040602","ec_funded":1,"oa_version":"Published Version","isi":1,"has_accepted_license":"1","publisher":"American Physical Society","author":[{"first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87","last_name":"De Nicola","orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis","full_name":"Michailidis, Alexios"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"title":"Entanglement view of dynamical quantum phase transitions","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2021-02-03T12:47:04Z","date_updated":"2021-02-03T12:47:04Z","success":1,"file_name":"2021_PhysicalRevLett_DeNicola.pdf","checksum":"d9acbc502390ed7a97e631d23ae19ecd","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9074","file_size":398075,"creator":"dernst"}],"article_processing_charge":"Yes","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"apa":"De Nicola, S., Michailidis, A., &#38; Serbyn, M. (2021). Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>","mla":"De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>, vol. 126, no. 4, 040602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>.","ista":"De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602.","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical quantum phase transitions,” <i>Physical Review Letters</i>, vol. 126, no. 4. American Physical Society, 2021.","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021).","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. 2021;126(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>","chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>."},"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"arxiv":1,"abstract":[{"lang":"eng","text":"The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology."}],"type":"journal_article","file_date_updated":"2021-02-03T12:47:04Z","_id":"9048","quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020"}],"publication_status":"published"},{"publication_status":"published","place":"Klosterneuburg","publication_identifier":{"issn":["2663-337X"]},"citation":{"ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021.","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>.","apa":"Osang, G. F. (2021). <i>Multi-cover persistence and Delaunay mosaics</i>. Institute of Science and Technology Austria, Klosterneuburg. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>","mla":"Osang, Georg F. <i>Multi-Cover Persistence and Delaunay Mosaics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>."},"file_date_updated":"2021-02-03T10:37:28Z","type":"dissertation","abstract":[{"lang":"eng","text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets."}],"_id":"9056","article_processing_charge":"No","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"file_name":"thesis_source.zip","date_created":"2021-02-02T14:09:25Z","date_updated":"2021-02-03T10:37:28Z","creator":"patrickd","file_size":13446994,"content_type":"application/zip","file_id":"9063","relation":"source_file","access_level":"closed","checksum":"bcf27986147cab0533b6abadd74e7629"},{"file_name":"thesis_pdfA2b.pdf","success":1,"date_created":"2021-02-02T14:09:18Z","date_updated":"2021-02-02T14:09:18Z","file_size":5210329,"creator":"patrickd","content_type":"application/pdf","file_id":"9064","relation":"main_file","checksum":"9cc8af266579a464385bbe2aff6af606","access_level":"open_access"}],"title":"Multi-cover persistence and Delaunay mosaics","author":[{"orcid":"0000-0002-8882-5116","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","full_name":"Osang, Georg F"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:9056","related_material":{"record":[{"id":"187","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8703"}]},"oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-02T14:11:06Z","ddc":["006","514","516"],"supervisor":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"status":"public","day":"01","page":"134","year":"2021","month":"02","date_published":"2021-02-01T00:00:00Z","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-07T13:29:01Z","oa":1},{"volume":41,"pmid":1,"ddc":["570"],"date_created":"2021-02-03T12:23:51Z","day":"03","status":"public","publication":"The Journal of Neuroscience","doi":"10.1523/jneurosci.1655-20.2020","oa_version":"Published Version","ec_funded":1,"isi":1,"date_published":"2021-02-03T00:00:00Z","month":"02","intvolume":"        41","acknowledgement":"Work in the I.L.H.-O. laboratory was supported by European Research Council Grant ERC-2015-CoG 681577 and German Research Foundation Ha 4466/10-1, Ha4466/11-1, Ha4466/12-1, SPP 1665, and SFB 936B5. Work in the S.J.B.B. laboratory was supported by Biotechnology and Biological Sciences Research Council BB/P003796/1, Medical Research Council MR/K004387/1 and MR/T033320/1, Wellcome Trust 215199/Z/19/Z and 102386/Z/13/Z, and John Fell Fund. Work in the S.H. laboratory was supported by European Research Council Grants ERC-2016-CoG 725780 LinPro and FWF SFB F78. This work was supported by National Institutes of Health Grant NIMH 1R01MH110553 to N.V.D.M.G. Work in the J.A.C. laboratory was supported by the Ludwig Family Foundation, Simons Foundation SFARI Research Award, and National Institutes of Health/National Institute of Mental Health R01 MH102365 and R01MH113852. The B.V. laboratory was supported by Whitehall Foundation 2017-12-73, National Science Foundation 1736028, National Institutes of Health, National Institute of General Medical Sciences R01GM134363-01, and Halıcıoğlu Data Science Institute Fellowship. This work was supported by the University of California San Diego School of Medicine.","keyword":["General Neuroscience"],"date_updated":"2023-09-05T14:03:17Z","oa":1,"issue":"5","external_id":{"isi":["000616763400002"],"pmid":["33431633"]},"page":"813-822","year":"2021","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"citation":{"ama":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, et al. The logic of developing neocortical circuits in health and disease. <i>The Journal of Neuroscience</i>. 2021;41(5):813-822. doi:<a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">10.1523/jneurosci.1655-20.2020</a>","short":"I.L. Hanganu-Opatz, S.J.B. Butt, S. Hippenmeyer, N.V. De Marco García, J.A. Cardin, B. Voytek, A.R. Muotri, The Journal of Neuroscience 41 (2021) 813–822.","ista":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, De Marco García NV, Cardin JA, Voytek B, Muotri AR. 2021. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 41(5), 813–822.","ieee":"I. L. Hanganu-Opatz <i>et al.</i>, “The logic of developing neocortical circuits in health and disease,” <i>The Journal of Neuroscience</i>, vol. 41, no. 5. Society for Neuroscience, pp. 813–822, 2021.","chicago":"Hanganu-Opatz, Ileana L., Simon J. B. Butt, Simon Hippenmeyer, Natalia V. De Marco García, Jessica A. Cardin, Bradley Voytek, and Alysson R. Muotri. “The Logic of Developing Neocortical Circuits in Health and Disease.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2021. <a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">https://doi.org/10.1523/jneurosci.1655-20.2020</a>.","apa":"Hanganu-Opatz, I. L., Butt, S. J. B., Hippenmeyer, S., De Marco García, N. V., Cardin, J. A., Voytek, B., &#38; Muotri, A. R. (2021). The logic of developing neocortical circuits in health and disease. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">https://doi.org/10.1523/jneurosci.1655-20.2020</a>","mla":"Hanganu-Opatz, Ileana L., et al. “The Logic of Developing Neocortical Circuits in Health and Disease.” <i>The Journal of Neuroscience</i>, vol. 41, no. 5, Society for Neuroscience, 2021, pp. 813–22, doi:<a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">10.1523/jneurosci.1655-20.2020</a>."},"scopus_import":"1","abstract":[{"text":"The sensory and cognitive abilities of the mammalian neocortex are underpinned by intricate columnar and laminar circuits formed from an array of diverse neuronal populations. One approach to determining how interactions between these circuit components give rise to complex behavior is to investigate the rules by which cortical circuits are formed and acquire functionality during development. This review summarizes recent research on the development of the neocortex, from genetic determination in neural stem cells through to the dynamic role that specific neuronal populations play in the earliest circuits of neocortex, and how they contribute to emergent function and cognition. While many of these endeavors take advantage of model systems, consideration will also be given to advances in our understanding of activity in nascent human circuits. Such cross-species perspective is imperative when investigating the mechanisms underlying the dysfunction of early neocortical circuits in neurodevelopmental disorders, so that one can identify targets amenable to therapeutic intervention.","lang":"eng"}],"type":"journal_article","file_date_updated":"2022-05-27T06:59:55Z","_id":"9073","quality_controlled":"1","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020"},{"grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"publication_status":"published","has_accepted_license":"1","publisher":"Society for Neuroscience","author":[{"last_name":"Hanganu-Opatz","first_name":"Ileana L.","full_name":"Hanganu-Opatz, Ileana L."},{"first_name":"Simon J. B.","last_name":"Butt","full_name":"Butt, Simon J. B."},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"first_name":"Natalia V.","last_name":"De Marco García","full_name":"De Marco García, Natalia V."},{"full_name":"Cardin, Jessica A.","last_name":"Cardin","first_name":"Jessica A."},{"full_name":"Voytek, Bradley","last_name":"Voytek","first_name":"Bradley"},{"first_name":"Alysson R.","last_name":"Muotri","full_name":"Muotri, Alysson R."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The logic of developing neocortical circuits in health and disease","file":[{"checksum":"578fd7ed1a0aef74bce61bea2d987b33","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"11414","creator":"dernst","file_size":1031150,"date_created":"2022-05-27T06:59:55Z","date_updated":"2022-05-27T06:59:55Z","success":1,"file_name":"2021_JourNeuroscience_Hanganu.pdf"}],"article_processing_charge":"No","department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"article_type":"original"},{"oa":1,"title":"Simultaneous identification of brain cell type and lineage via single cell RNA sequencing","author":[{"last_name":"Anderson","first_name":"Donovan J.","full_name":"Anderson, Donovan J."},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"McKenna, Aaron","last_name":"McKenna","first_name":"Aaron"},{"last_name":"Shendure","first_name":"Jay","full_name":"Shendure, Jay"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"last_name":"Horwitz","first_name":"Marshall S.","full_name":"Horwitz, Marshall S."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-02-04T07:29:53Z","acknowledgement":"We thank Bill Bolosky, Microsoft Research, for earlier work showing proof of concept in TCGA\r\nbulk RNA-seq data. Supported by the Paul G. Allen Frontiers Group (University of Washington);\r\nNIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant\r\n(C13-002) to SH, and the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation program 725780 LinPro to SH.","publisher":"Cold Spring Harbor Laboratory","date_published":"2021-01-01T00:00:00Z","month":"01","year":"2021","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"article_processing_charge":"No","day":"01","status":"public","_id":"9082","date_created":"2021-02-04T07:23:23Z","abstract":[{"text":"Acquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans.","lang":"eng"}],"type":"preprint","citation":{"mla":"Anderson, Donovan J., et al. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","apa":"Anderson, D. J., Pauler, F., McKenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (n.d.). Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>","chicago":"Anderson, Donovan J., Florian Pauler, Aaron McKenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>.","short":"D.J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, BioRxiv (n.d.).","ieee":"D. J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous identification of brain cell type and lineage via single cell RNA sequencing,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. bioRxiv, <a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","ama":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>"},"ec_funded":1,"oa_version":"Preprint","publication":"bioRxiv","publication_status":"submitted","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.12.31.425016"}],"doi":"10.1101/2020.12.31.425016","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020"}]},{"has_accepted_license":"1","publisher":"SciPost Foundation","file":[{"file_name":"2021_SciPostPhysics_Marchukov.pdf","success":1,"date_updated":"2021-02-09T07:06:22Z","date_created":"2021-02-09T07:06:22Z","file_size":666512,"creator":"dernst","file_id":"9105","content_type":"application/pdf","access_level":"open_access","checksum":"9fd614b7ab49999e7267874df2582f7e","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Shape of a sound wave in a weakly-perturbed Bose gas","author":[{"full_name":"Marchukov, Oleksandr","last_name":"Marchukov","first_name":"Oleksandr"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"article_processing_charge":"No","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"ieee":"O. Marchukov and A. Volosniev, “Shape of a sound wave in a weakly-perturbed Bose gas,” <i>SciPost Physics</i>, vol. 10, no. 2. SciPost Foundation, 2021.","short":"O. Marchukov, A. Volosniev, SciPost Physics 10 (2021).","ista":"Marchukov O, Volosniev A. 2021. Shape of a sound wave in a weakly-perturbed Bose gas. SciPost Physics. 10(2), 025.","ama":"Marchukov O, Volosniev A. Shape of a sound wave in a weakly-perturbed Bose gas. <i>SciPost Physics</i>. 2021;10(2). doi:<a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">10.21468/scipostphys.10.2.025</a>","chicago":"Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” <i>SciPost Physics</i>. SciPost Foundation, 2021. <a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">https://doi.org/10.21468/scipostphys.10.2.025</a>.","apa":"Marchukov, O., &#38; Volosniev, A. (2021). Shape of a sound wave in a weakly-perturbed Bose gas. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">https://doi.org/10.21468/scipostphys.10.2.025</a>","mla":"Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” <i>SciPost Physics</i>, vol. 10, no. 2, 025, SciPost Foundation, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">10.21468/scipostphys.10.2.025</a>."},"publication_identifier":{"issn":["2542-4653"]},"type":"journal_article","file_date_updated":"2021-02-09T07:06:22Z","abstract":[{"lang":"eng","text":"We employ the Gross-Pitaevskii equation to study acoustic emission generated in a uniform Bose gas by a static impurity. The impurity excites a sound-wave packet, which propagates through the gas. We calculate the shape of this wave packet in the limit of long wave lengths, and argue that it is possible to extract properties of the impurity by observing this shape. We illustrate here this possibility for a Bose gas with a trapped impurity atom -- an example of a relevant experimental setup. Presented results are general for all one-dimensional systems described by the nonlinear Schrödinger equation and can also be used in nonatomic systems, e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate the shape of the sound-wave packet for a three-dimensional Bose gas assuming a spherically symmetric perturbation."}],"arxiv":1,"_id":"9093","quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"publication_status":"published","intvolume":"        10","month":"02","date_published":"2021-02-03T00:00:00Z","acknowledgement":"We acknowledge fruitful discussions with Dr. Simos Mistakidis regarding beyond mean-field\r\neffects in our system. We also thank Prof. Maxim Olshanii for valuable suggestions to improve\r\nthe manuscript.O.V.M acknowledges the support from the National Science Foundation\r\nthrough grants No. PHY-1402249, No. PHY-1607221, and No. PHY-1912542 and the\r\nBinational (US-Israel) Science Foundation through grant No. 2015616, as well as by the Israel\r\nScience Foundation (grant No. 1287/17) and from the German Aeronautics and Space Administration\r\n(DLR) through Grant No. 50WM1957. This work has also received funding from\r\nthe DFG Project No.413495248 [VO 2437/1-1] and European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411\r\n(A. G. V.)","article_number":"025","date_updated":"2023-08-07T13:39:37Z","issue":"2","oa":1,"external_id":{"arxiv":["2004.08075"],"isi":["000646783100027"]},"year":"2021","volume":10,"ddc":["530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-04T12:39:24Z","status":"public","day":"03","doi":"10.21468/scipostphys.10.2.025","publication":"SciPost Physics","isi":1,"oa_version":"Published Version","ec_funded":1},{"department":[{"_id":"MiSi"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Rockefeller University Press","has_accepted_license":"1","author":[{"full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Altenburger, LM","first_name":"LM","last_name":"Altenburger"},{"full_name":"Hauschild, R","last_name":"Hauschild","first_name":"R"},{"full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","last_name":"Assen","first_name":"Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87"},{"first_name":"K","last_name":"Rottner","full_name":"Rottner, K"},{"first_name":"Stradal","last_name":"TEB","full_name":"TEB, Stradal"},{"first_name":"A","last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, A"},{"full_name":"Stein, JV","last_name":"Stein","first_name":"JV"},{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse","file":[{"date_created":"2022-05-12T14:16:21Z","date_updated":"2022-05-12T14:16:21Z","file_name":"2021_JournCellBiology_Leithner.pdf","success":1,"checksum":"843ebc153847c8626e13c9c5ce71d533","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":5102328,"file_id":"11367","content_type":"application/pdf"}],"publication_status":"published","scopus_import":"1","abstract":[{"lang":"eng","text":"Dendritic cells (DCs) are crucial for the priming of naive T cells and the initiation of adaptive immunity. Priming is initiated at a heterologous cell–cell contact, the immunological synapse (IS). While it is established that F-actin dynamics regulates signaling at the T cell side of the contact, little is known about the cytoskeletal contribution on the DC side. Here, we show that the DC actin cytoskeleton is decisive for the formation of a multifocal synaptic structure, which correlates with T cell priming efficiency. DC actin at the IS appears in transient foci that are dynamized by the WAVE regulatory complex (WRC). The absence of the WRC in DCs leads to stabilized contacts with T cells, caused by an increase in ICAM1-integrin–mediated cell–cell adhesion. This results in lower numbers of activated and proliferating T cells, demonstrating an important role for DC actin in the regulation of immune synapse functionality."}],"type":"journal_article","file_date_updated":"2022-05-12T14:16:21Z","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"citation":{"mla":"Leithner, Alexander F., et al. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” <i>Journal of Cell Biology</i>, vol. 220, no. 4, e202006081, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202006081\">10.1083/jcb.202006081</a>.","apa":"Leithner, A. F., Altenburger, L., Hauschild, R., Assen, F. P., Rottner, K., TEB, S., … Sixt, M. K. (2021). Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202006081\">https://doi.org/10.1083/jcb.202006081</a>","chicago":"Leithner, Alexander F, LM Altenburger, R Hauschild, Frank P Assen, K Rottner, Stradal TEB, A Diz-Muñoz, JV Stein, and Michael K Sixt. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202006081\">https://doi.org/10.1083/jcb.202006081</a>.","ieee":"A. F. Leithner <i>et al.</i>, “Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse,” <i>Journal of Cell Biology</i>, vol. 220, no. 4. Rockefeller University Press, 2021.","ista":"Leithner AF, Altenburger L, Hauschild R, Assen FP, Rottner K, TEB S, Diz-Muñoz A, Stein J, Sixt MK. 2021. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 220(4), e202006081.","short":"A.F. Leithner, L. Altenburger, R. Hauschild, F.P. Assen, K. Rottner, S. TEB, A. Diz-Muñoz, J. Stein, M.K. Sixt, Journal of Cell Biology 220 (2021).","ama":"Leithner AF, Altenburger L, Hauschild R, et al. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. <i>Journal of Cell Biology</i>. 2021;220(4). doi:<a href=\"https://doi.org/10.1083/jcb.202006081\">10.1083/jcb.202006081</a>"},"quality_controlled":"1","_id":"9094","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","external_id":{"isi":["000626365700001"],"pmid":["33533935"]},"year":"2021","article_number":"e202006081","date_published":"2021-04-05T00:00:00Z","intvolume":"       220","month":"04","oa":1,"issue":"4","date_updated":"2023-09-05T13:57:53Z","publication":"Journal of Cell Biology","doi":"10.1083/jcb.202006081","oa_version":"Published Version","isi":1,"volume":220,"pmid":1,"status":"public","day":"05","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"ddc":["570"],"date_created":"2021-02-05T10:08:04Z"},{"has_accepted_license":"1","publisher":"Springer Nature","file":[{"content_type":"application/pdf","file_id":"9106","file_size":2885056,"creator":"dernst","access_level":"open_access","relation":"main_file","checksum":"e8a68df48750712671f5c47b0228e531","success":1,"file_name":"2021_ScientificReports_Pandey.pdf","date_created":"2021-02-09T07:33:23Z","date_updated":"2021-02-09T07:33:23Z"}],"title":"Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis","author":[{"full_name":"Pandey, Rakesh","last_name":"Pandey","first_name":"Rakesh"},{"full_name":"Al-Nuaimi, Yusur","last_name":"Al-Nuaimi","first_name":"Yusur"},{"full_name":"Mishra, Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","first_name":"Rajiv Kumar","last_name":"Mishra"},{"last_name":"Spurgeon","first_name":"Sarah K.","full_name":"Spurgeon, Sarah K."},{"full_name":"Goodfellow, Marc","last_name":"Goodfellow","first_name":"Marc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Pandey, Rakesh, Yusur Al-Nuaimi, Rajiv Kumar Mishra, Sarah K. Spurgeon, and Marc Goodfellow. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17 and IL-15 in a Network Involved in the Pathogenesis of Psoriasis.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-020-80507-7\">https://doi.org/10.1038/s41598-020-80507-7</a>.","ama":"Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. <i>Scientific Reports</i>. 2021;11. doi:<a href=\"https://doi.org/10.1038/s41598-020-80507-7\">10.1038/s41598-020-80507-7</a>","ieee":"R. Pandey, Y. Al-Nuaimi, R. K. Mishra, S. K. Spurgeon, and M. Goodfellow, “Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis,” <i>Scientific Reports</i>, vol. 11. Springer Nature, 2021.","ista":"Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. 2021. Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. Scientific Reports. 11, 2204.","short":"R. Pandey, Y. Al-Nuaimi, R.K. Mishra, S.K. Spurgeon, M. Goodfellow, Scientific Reports 11 (2021).","mla":"Pandey, Rakesh, et al. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17 and IL-15 in a Network Involved in the Pathogenesis of Psoriasis.” <i>Scientific Reports</i>, vol. 11, 2204, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-020-80507-7\">10.1038/s41598-020-80507-7</a>.","apa":"Pandey, R., Al-Nuaimi, Y., Mishra, R. K., Spurgeon, S. K., &#38; Goodfellow, M. (2021). Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-80507-7\">https://doi.org/10.1038/s41598-020-80507-7</a>"},"publication_identifier":{"eissn":["20452322"]},"file_date_updated":"2021-02-09T07:33:23Z","type":"journal_article","abstract":[{"lang":"eng","text":"Psoriasis is a chronic inflammatory skin disease clinically characterized by the appearance of red colored, well-demarcated plaques with thickened skin and with silvery scales. Recent studies have established the involvement of a complex signalling network of interactions between cytokines, immune cells and skin cells called keratinocytes. Keratinocytes form the cells of the outermost layer of the skin (epidermis). Visible plaques in psoriasis are developed due to the fast proliferation and unusual differentiation of keratinocyte cells. Despite that, the exact mechanism of the appearance of these plaques in the cytokine-immune cell network is not clear. A mathematical model embodying interactions between key immune cells believed to be involved in psoriasis, keratinocytes and relevant cytokines has been developed. The complex network formed of these interactions poses several challenges. Here, we choose to study subnetworks of this complex network and initially focus on interactions involving TNFα, IL-23/IL-17, and IL-15. These are chosen based on known evidence of their therapeutic efficacy. In addition, we explore the role of IL-15 in the pathogenesis of psoriasis and its potential as a future drug target for a novel treatment option. We perform steady state analyses for these subnetworks and demonstrate that the interactions between cells, driven by cytokines could cause the emergence of a psoriasis state (hyper-proliferation of keratinocytes) when levels of TNFα, IL-23/IL-17 or IL-15 are increased. The model results explain and support the clinical potentiality of anti-cytokine treatments. Interestingly, our results suggest different dynamic scenarios underpin the pathogenesis of psoriasis, depending upon the dominant cytokines of subnetworks. We observed that the increase in the level of IL-23/IL-17 and IL-15 could lead to psoriasis via a bistable route, whereas an increase in the level of TNFα would lead to a monotonic and gradual disease progression. Further, we demonstrate how this insight, bistability, could be exploited to improve the current therapies and develop novel treatment strategies for psoriasis."}],"scopus_import":"1","_id":"9097","quality_controlled":"1","publication_status":"published","month":"01","intvolume":"        11","date_published":"2021-01-26T00:00:00Z","article_number":"2204","acknowledgement":"RP acknowledges the Department of Science and Technology, India for the support through the DST-INSPIRE Faculty Award (DST/INSPIRE/04/2015/001939). This work was supported by the Engineering and Physical Sciences Research Council (EPSRC), United Kingdom (Grant numbers EP/J018295/1, EP/J018392/1, EP/N014391/1). The contribution of RP was also supported by the later Grant. This work was generously supported by the Welcome Trust Institutional Strategic Support Award (204909/Z/16/Z) too. The contribution of MG was supported by the EPSRC via EP/N014391/1 and a Wellcome Trust Institutional Strategic Support Award (WT105618MA). The contribution of YA was generously supported by the Wellcome Trust Institutional Strategic Support Award (WT105618MA).","date_updated":"2022-08-19T07:22:23Z","oa":1,"year":"2021","volume":11,"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-07T23:01:12Z","status":"public","day":"26","doi":"10.1038/s41598-020-80507-7","publication":"Scientific Reports","oa_version":"Published Version"},{"arxiv":1,"abstract":[{"text":"We study properties of the volume of projections of the n-dimensional\r\ncross-polytope $\\crosp^n = \\{ x \\in \\R^n \\mid |x_1| + \\dots + |x_n| \\leqslant 1\\}.$ We prove that the projection of $\\crosp^n$ onto a k-dimensional coordinate subspace has the maximum possible volume for k=2 and for k=3.\r\nWe obtain the exact lower bound on the volume of such a projection onto a two-dimensional plane. Also, we show that there exist local maxima which are not global ones for the volume of a projection of $\\crosp^n$ onto a k-dimensional subspace for any n>k⩾2.","lang":"eng"}],"scopus_import":"1","type":"journal_article","publication_identifier":{"issn":["0012365X"]},"citation":{"chicago":"Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” <i>Discrete Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.disc.2021.112312\">https://doi.org/10.1016/j.disc.2021.112312</a>.","ieee":"G. Ivanov, “On the volume of projections of the cross-polytope,” <i>Discrete Mathematics</i>, vol. 344, no. 5. Elsevier, 2021.","short":"G. Ivanov, Discrete Mathematics 344 (2021).","ista":"Ivanov G. 2021. On the volume of projections of the cross-polytope. Discrete Mathematics. 344(5), 112312.","ama":"Ivanov G. On the volume of projections of the cross-polytope. <i>Discrete Mathematics</i>. 2021;344(5). doi:<a href=\"https://doi.org/10.1016/j.disc.2021.112312\">10.1016/j.disc.2021.112312</a>","mla":"Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” <i>Discrete Mathematics</i>, vol. 344, no. 5, 112312, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.disc.2021.112312\">10.1016/j.disc.2021.112312</a>.","apa":"Ivanov, G. (2021). On the volume of projections of the cross-polytope. <i>Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disc.2021.112312\">https://doi.org/10.1016/j.disc.2021.112312</a>"},"quality_controlled":"1","_id":"9098","publication_status":"published","publisher":"Elsevier","title":"On the volume of projections of the cross-polytope","author":[{"full_name":"Ivanov, Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"UlWa"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"volume":344,"status":"public","day":"01","date_created":"2021-02-07T23:01:12Z","publication":"Discrete Mathematics","doi":"10.1016/j.disc.2021.112312","main_file_link":[{"url":"https://arxiv.org/abs/1808.09165","open_access":"1"}],"oa_version":"Preprint","isi":1,"article_number":"112312","acknowledgement":"Research was supported by the Russian Foundation for Basic Research, project 18-01-00036A (Theorems 1.5 and 5.3) and by the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926 (Theorems 1.2 and 7.3).","date_published":"2021-05-01T00:00:00Z","month":"05","intvolume":"       344","oa":1,"issue":"5","date_updated":"2023-08-07T13:40:37Z","external_id":{"arxiv":["1808.09165"],"isi":["000633365200001"]},"year":"2021"},{"date_created":"2021-02-07T23:01:13Z","status":"public","day":"01","volume":116,"isi":1,"ec_funded":1,"oa_version":"Preprint","doi":"10.1007/s00013-020-01564-y","main_file_link":[{"url":"https://arxiv.org/abs/2001.07762","open_access":"1"}],"publication":"Archiv der Mathematik","date_updated":"2023-08-07T13:42:38Z","issue":"5","oa":1,"intvolume":"       116","month":"05","date_published":"2021-05-01T00:00:00Z","acknowledgement":"I would like to thank Piotr Achinger, Daniel Huybrechts, Katrina Honigs, Marcin Lara, and Maciek Zdanowicz for the mathematical discussions, Tamas Hausel for hosting me in his research group at IST Austria, and the referees for their valuable suggestions. This research has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie Grant Agreement No. 754411.","year":"2021","page":"515-527","external_id":{"isi":["000612580200001"],"arxiv":["2001.07762"]},"_id":"9099","quality_controlled":"1","publication_identifier":{"issn":["0003889X"],"eissn":["14208938"]},"citation":{"mla":"Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived Autoequivalences.” <i>Archiv Der Mathematik</i>, vol. 116, no. 5, Springer Nature, 2021, pp. 515–27, doi:<a href=\"https://doi.org/10.1007/s00013-020-01564-y\">10.1007/s00013-020-01564-y</a>.","apa":"Srivastava, T. K. (2021). Lifting automorphisms on Abelian varieties as derived autoequivalences. <i>Archiv Der Mathematik</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00013-020-01564-y\">https://doi.org/10.1007/s00013-020-01564-y</a>","chicago":"Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived Autoequivalences.” <i>Archiv Der Mathematik</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00013-020-01564-y\">https://doi.org/10.1007/s00013-020-01564-y</a>.","short":"T.K. Srivastava, Archiv Der Mathematik 116 (2021) 515–527.","ista":"Srivastava TK. 2021. Lifting automorphisms on Abelian varieties as derived autoequivalences. Archiv der Mathematik. 116(5), 515–527.","ieee":"T. K. Srivastava, “Lifting automorphisms on Abelian varieties as derived autoequivalences,” <i>Archiv der Mathematik</i>, vol. 116, no. 5. Springer Nature, pp. 515–527, 2021.","ama":"Srivastava TK. Lifting automorphisms on Abelian varieties as derived autoequivalences. <i>Archiv der Mathematik</i>. 2021;116(5):515-527. doi:<a href=\"https://doi.org/10.1007/s00013-020-01564-y\">10.1007/s00013-020-01564-y</a>"},"type":"journal_article","arxiv":1,"abstract":[{"lang":"eng","text":"We show that on an Abelian variety over an algebraically closed field of positive characteristic, the obstruction to lifting an automorphism to a field of characteristic zero as a morphism vanishes if and only if it vanishes for lifting it as a derived autoequivalence. We also compare the deformation space of these two types of deformations."}],"scopus_import":"1","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Lifting automorphisms on Abelian varieties as derived autoequivalences","author":[{"first_name":"Tanya K","id":"4D046628-F248-11E8-B48F-1D18A9856A87","last_name":"Srivastava","full_name":"Srivastava, Tanya K"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"TaHa"}]},{"publisher":"Wiley","has_accepted_license":"1","title":"Speciation in marine environments: Diving under the surface","author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"file_name":"2021_JourEvolBiology_Faria.pdf","date_created":"2021-02-09T09:04:02Z","date_updated":"2021-02-09T09:04:02Z","content_type":"application/pdf","file_id":"9108","file_size":561340,"creator":"dernst","checksum":"5755856a5368d4b4cdd6fad5ab27f4d1","access_level":"open_access","relation":"main_file"}],"department":[{"_id":"NiBa"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity."}],"type":"journal_article","file_date_updated":"2021-02-09T09:04:02Z","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"citation":{"mla":"Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:<a href=\"https://doi.org/10.1111/jeb.13756\">10.1111/jeb.13756</a>.","apa":"Faria, R., Johannesson, K., &#38; Stankowski, S. (2021). Speciation in marine environments: Diving under the surface. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13756\">https://doi.org/10.1111/jeb.13756</a>","chicago":"Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13756\">https://doi.org/10.1111/jeb.13756</a>.","ieee":"R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments: Diving under the surface,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1. Wiley, pp. 4–15, 2021.","short":"R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15.","ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.","ama":"Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. <i>Journal of Evolutionary Biology</i>. 2021;34(1):4-15. doi:<a href=\"https://doi.org/10.1111/jeb.13756\">10.1111/jeb.13756</a>"},"quality_controlled":"1","_id":"9100","publication_status":"published","acknowledgement":"We would like to thank all the participants in the speciation symposium of the Marine Evolution Conference in Sweden for the interesting discussions and to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary Biology, respectively, for the encouragement and support in putting together this special issue, and to all reviewers involved. RF was financed by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement Number 706376 and is currently financed by the FEDER Funds through the Operational Competitiveness Factors Program COMPETE and by National Funds through the Foundation for Science and Technology (FCT) within the scope of the project ‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded to Roger K. Butlin.","date_published":"2021-01-18T00:00:00Z","month":"01","intvolume":"        34","oa":1,"issue":"1","date_updated":"2023-08-07T13:42:08Z","external_id":{"isi":["000608367500001"]},"page":"4-15","year":"2021","volume":34,"day":"18","status":"public","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-07T23:01:13Z","publication":"Journal of Evolutionary Biology","doi":"10.1111/jeb.13756","oa_version":"Published Version","isi":1}]