[{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","file_date_updated":"2023-02-03T10:56:39Z","doi":"10.1007/978-1-0716-2887-4_12","date_published":"2023-01-19T00:00:00Z","intvolume":"      2608","has_accepted_license":"1","editor":[{"last_name":"Margadant","full_name":"Margadant, Coert","first_name":"Coert"}],"pmid":1,"day":"19","publication":"Cell Migration in Three Dimensions","volume":2608,"title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","page":"183-205","quality_controlled":"1","date_created":"2023-01-29T23:00:58Z","citation":{"ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. <i>Cell Migration in Three Dimensions</i>. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in <i>Cell Migration in Three Dimensions</i>, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","apa":"Hannezo, E. B., &#38; Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), <i>Cell Migration in Three Dimensions</i> (Vol. 2608, pp. 183–205). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>."},"oa":1,"status":"public","author":[{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele","first_name":"Colinda L.G.J."}],"scopus_import":"1","abstract":[{"lang":"eng","text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis."}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-03T10:58:56Z","series_title":"MIMB","department":[{"_id":"EdHa"}],"year":"2023","month":"01","publication_identifier":{"isbn":["9781071628867"],"eisbn":["9781071628874"],"eissn":["1940-6029"]},"external_id":{"pmid":["36653709"]},"publication_status":"published","alternative_title":["Methods in Molecular Biology"],"_id":"12428","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12500","creator":"dernst","file_name":"2023_MIMB_Hannezo.pdf","date_created":"2023-02-03T10:56:39Z","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","file_size":826598,"success":1,"date_updated":"2023-02-03T10:56:39Z","access_level":"open_access","content_type":"application/pdf"}],"ddc":["570"],"type":"book_chapter","publisher":"Springer Nature"},{"department":[{"_id":"JuFi"}],"article_type":"original","publication_identifier":{"eissn":["1522-2616"],"issn":["0025-584X"]},"isi":1,"month":"04","year":"2023","oa_version":"Published Version","type":"journal_article","ddc":["510"],"file":[{"file_name":"2023_MathNachrichten_Agresti.pdf","relation":"main_file","file_id":"14067","creator":"dernst","date_updated":"2023-08-16T11:40:02Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-08-16T11:40:02Z","checksum":"6f099f1d064173784d1a27716a2cc795","file_size":449280,"success":1}],"publication_status":"published","external_id":{"isi":["000914134900001"],"arxiv":["2104.05063"]},"issue":"4","_id":"12429","publisher":"Wiley","status":"public","author":[{"last_name":"Agresti","full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio"},{"first_name":"Nick","last_name":"Lindemulder","full_name":"Lindemulder, Nick"},{"full_name":"Veraar, Mark","last_name":"Veraar","first_name":"Mark"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"lang":"eng","text":"In this paper, we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement is that we can allow general interpolation couples. The abstract results are applied to regularity problems for fractional evolution equations and stochastic evolution equations, where uniform trace estimates on the half-line are shown."}],"scopus_import":"1","date_updated":"2023-08-16T11:41:42Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On the trace embedding and its applications to evolution equations","page":"1319-1350","citation":{"ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.","short":"A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023) 1319–1350.","ieee":"A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its applications to evolution equations,” <i>Mathematische Nachrichten</i>, vol. 296, no. 4. Wiley, pp. 1319–1350, 2023.","ama":"Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications to evolution equations. <i>Mathematische Nachrichten</i>. 2023;296(4):1319-1350. doi:<a href=\"https://doi.org/10.1002/mana.202100192\">10.1002/mana.202100192</a>","chicago":"Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding and Its Applications to Evolution Equations.” <i>Mathematische Nachrichten</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/mana.202100192\">https://doi.org/10.1002/mana.202100192</a>.","apa":"Agresti, A., Lindemulder, N., &#38; Veraar, M. (2023). On the trace embedding and its applications to evolution equations. <i>Mathematische Nachrichten</i>. Wiley. <a href=\"https://doi.org/10.1002/mana.202100192\">https://doi.org/10.1002/mana.202100192</a>","mla":"Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution Equations.” <i>Mathematische Nachrichten</i>, vol. 296, no. 4, Wiley, 2023, pp. 1319–50, doi:<a href=\"https://doi.org/10.1002/mana.202100192\">10.1002/mana.202100192</a>."},"date_created":"2023-01-29T23:00:59Z","arxiv":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"article_processing_charge":"No","doi":"10.1002/mana.202100192","file_date_updated":"2023-08-16T11:40:02Z","intvolume":"       296","has_accepted_license":"1","date_published":"2023-04-01T00:00:00Z","acknowledgement":"The first author has been partially supported by the Nachwuchsring—Network for the promotion of young scientists—at TU Kaiserslautern. The second and third authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","day":"01","publication":"Mathematische Nachrichten","volume":296},{"scopus_import":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2110.00458","open_access":"1"}],"abstract":[{"lang":"eng","text":"We study the time evolution of the Nelson model in a mean-field limit in which N nonrelativistic bosons weakly couple (with respect to the particle number) to a positive or zero mass quantized scalar field. Our main result is the derivation of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove the convergence of the approximate wave function to the many-body wave function in norm, with a convergence rate proportional to the number of corrections taken into account in the approximation. We prove an analogous result for the unitary propagator. As an application, we derive a simple system of partial differential equations describing the time evolution of the first- and second-order approximations to the one-particle reduced density matrices of the particles and the quantum field, respectively."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-08-16T11:47:27Z","status":"public","author":[{"first_name":"Marco","full_name":"Falconi, Marco","last_name":"Falconi"},{"last_name":"Leopold","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes"},{"first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P","last_name":"Petrat","orcid":"0000-0002-9166-5889"}],"publication_status":"published","external_id":{"isi":["000909760300001"],"arxiv":["2110.00458"]},"issue":"4","_id":"12430","oa_version":"Preprint","type":"journal_article","publisher":"World Scientific Publishing","article_type":"original","department":[{"_id":"RoSe"}],"year":"2023","month":"01","publication_identifier":{"issn":["0129-055X"]},"isi":1,"date_published":"2023-01-09T00:00:00Z","intvolume":"        35","day":"09","publication":"Reviews in Mathematical Physics","volume":35,"article_processing_charge":"No","doi":"10.1142/S0129055X2350006X","quality_controlled":"1","arxiv":1,"date_created":"2023-01-29T23:00:59Z","citation":{"mla":"Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” <i>Reviews in Mathematical Physics</i>, vol. 35, no. 4, 2350006, World Scientific Publishing, 2023, doi:<a href=\"https://doi.org/10.1142/S0129055X2350006X\">10.1142/S0129055X2350006X</a>.","apa":"Falconi, M., Leopold, N. K., Mitrouskas, D. J., &#38; Petrat, S. P. (2023). Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129055X2350006X\">https://doi.org/10.1142/S0129055X2350006X</a>","chicago":"Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2023. <a href=\"https://doi.org/10.1142/S0129055X2350006X\">https://doi.org/10.1142/S0129055X2350006X</a>.","ama":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. <i>Reviews in Mathematical Physics</i>. 2023;35(4). doi:<a href=\"https://doi.org/10.1142/S0129055X2350006X\">10.1142/S0129055X2350006X</a>","ista":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 35(4), 2350006.","short":"M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical Physics 35 (2023).","ieee":"M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov dynamics and higher-order corrections for the regularized Nelson model,” <i>Reviews in Mathematical Physics</i>, vol. 35, no. 4. World Scientific Publishing, 2023."},"oa":1,"article_number":"2350006","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model"},{"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"month":"04","year":"2023","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093"}],"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031308284"]},"_id":"12467","external_id":{"arxiv":["2301.11175"]},"publication_status":"published","alternative_title":["LNCS"],"file":[{"relation":"main_file","creator":"esarac","file_id":"12468","file_name":"qsl.pdf","date_created":"2023-01-31T07:22:21Z","checksum":"981025aed580b6b27c426cb8856cf63e","success":1,"file_size":449027,"date_updated":"2023-01-31T07:22:21Z","content_type":"application/pdf","access_level":"open_access"},{"file_name":"2023_LNCS_HenzingerT.pdf","file_id":"13153","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-06-19T10:28:09Z","file_size":1048171,"checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","success":1,"date_created":"2023-06-19T10:28:09Z"}],"oa_version":"Published Version","type":"conference","ddc":["000"],"publisher":"Springer Nature","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","full_name":"Sarac, Naci E","last_name":"Sarac"}],"status":"public","scopus_import":"1","abstract":[{"text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"date_updated":"2023-07-14T11:20:27Z","title":"Quantitative safety and liveness","page":"349-370","conference":{"end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22","name":"FOSSACS: Foundations of Software Science and Computation Structures"},"arxiv":1,"quality_controlled":"1","date_created":"2023-01-31T07:23:56Z","citation":{"mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” <i>26th International Conference Foundations of Software Science and Computation Structures</i>, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:<a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">10.1007/978-3-031-30829-1_17</a>.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2023). Quantitative safety and liveness. In <i>26th International Conference Foundations of Software Science and Computation Structures</i> (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">https://doi.org/10.1007/978-3-031-30829-1_17</a>","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In <i>26th International Conference Foundations of Software Science and Computation Structures</i>, 13992:349–70. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">https://doi.org/10.1007/978-3-031-30829-1_17</a>.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: <i>26th International Conference Foundations of Software Science and Computation Structures</i>. Vol 13992. Springer Nature; 2023:349-370. doi:<a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">10.1007/978-3-031-30829-1_17</a>","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in <i>26th International Conference Foundations of Software Science and Computation Structures</i>, Paris, France, 2023, vol. 13992, pp. 349–370.","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370."},"oa":1,"ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-06-19T10:28:09Z","doi":"10.1007/978-3-031-30829-1_17","date_published":"2023-04-21T00:00:00Z","intvolume":"     13992","has_accepted_license":"1","volume":13992,"publication":"26th International Conference Foundations of Software Science and Computation Structures","day":"21","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093."},{"date_published":"2023-03-16T00:00:00Z","has_accepted_license":"1","intvolume":"        14","pmid":1,"publication":"Frontiers in Microbiology","acknowledgement":"We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad, B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz, E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25 to MAF) and the Academy of Finland (343022 to LV). ","day":"16","volume":14,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2023-04-17T07:49:09Z","doi":"10.3389/fmicb.2023.1119002","quality_controlled":"1","citation":{"ieee":"L. Viljakainen <i>et al.</i>, “Antiviral immune response reveals host-specific virus infections in natural ant populations,” <i>Frontiers in Microbiology</i>, vol. 14. Frontiers, 2023.","ista":"Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 14, 1119002.","short":"L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T. Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).","ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. <i>Frontiers in Microbiology</i>. 2023;14. doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1119002\">10.3389/fmicb.2023.1119002</a>","mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” <i>Frontiers in Microbiology</i>, vol. 14, 1119002, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1119002\">10.3389/fmicb.2023.1119002</a>.","chicago":"Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” <i>Frontiers in Microbiology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fmicb.2023.1119002\">https://doi.org/10.3389/fmicb.2023.1119002</a>.","apa":"Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2023.1119002\">https://doi.org/10.3389/fmicb.2023.1119002</a>"},"date_created":"2023-01-31T08:13:40Z","oa":1,"article_number":"1119002","title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","scopus_import":"1","abstract":[{"text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-01T12:39:58Z","status":"public","author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"first_name":"Jaana","last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana"},{"orcid":"0000-0001-7425-2372","full_name":"Oh, Jinook","last_name":"Oh","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","first_name":"Jinook"},{"first_name":"Lassi","full_name":"Tolonen, Lassi","last_name":"Tolonen"},{"last_name":"Eder","full_name":"Eder, Thomas","first_name":"Thomas"},{"full_name":"Rattei, Thomas","last_name":"Rattei","first_name":"Thomas"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"external_id":{"isi":["000961542100001"],"pmid":["PPR559293 "]},"publication_status":"published","_id":"12469","ddc":["570"],"file":[{"date_updated":"2023-04-17T07:49:09Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-04-17T07:49:09Z","file_size":4866332,"checksum":"cd52292963acce1111634d9fac08c699","success":1,"file_name":"2023_FrontMicrobiology_Viljakainen.pdf","relation":"main_file","creator":"dernst","file_id":"12843"}],"oa_version":"Published Version","type":"journal_article","publisher":"Frontiers","article_type":"original","department":[{"_id":"SyCr"}],"project":[{"grant_number":"M02076","_id":"25DF61D8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Viral pathogens and social immunity in ants"}],"month":"03","year":"2023","publication_identifier":{"eissn":["1664-302X"]},"isi":1},{"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","page":"201","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"date_created":"2023-01-31T15:10:53Z","citation":{"ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","apa":"Michalska, J. M. (2023). <i>A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>.","mla":"Michalska, Julia M. <i>A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>."},"oa":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","ec_funded":1,"doi":"10.15479/at:ista:12470","file_date_updated":"2023-07-27T22:30:54Z","degree_awarded":"PhD","has_accepted_license":"1","date_published":"2023-01-09T00:00:00Z","day":"09","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"publication_identifier":{"isbn":[" 978-3-99078-026-8"],"issn":["2663-337X"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24"}],"year":"2023","month":"01","oa_version":"Published Version","ddc":["610"],"file":[{"file_name":"20230109_PhD_thesis_JM_final.pdf","relation":"main_file","creator":"cchlebak","file_id":"12471","date_updated":"2023-07-27T22:30:54Z","content_type":"application/pdf","embargo":"2023-07-09","access_level":"open_access","date_created":"2023-01-31T15:11:42Z","file_size":41771714,"checksum":"1a2306e5f59f52df598e7ecfadf921ac"},{"file_size":66983464,"checksum":"0bebbdee0773443959e1f6ab8caf281f","embargo_to":"open_access","date_created":"2023-01-31T15:11:51Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-07-10T22:30:04Z","file_id":"12472","creator":"cchlebak","relation":"source_file","file_name":"20230109_PhD_thesis_JM_final.docx"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"publication_status":"published","_id":"12470","publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"}],"status":"public","author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","last_name":"Michalska"}],"related_material":{"record":[{"id":"11943","relation":"part_of_dissertation","status":"public"},{"id":"11950","relation":"part_of_dissertation","status":"public"}]},"abstract":[{"text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy.","lang":"eng"}],"date_updated":"2023-08-31T12:26:58Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}]},{"title":"Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression","article_number":"1049255","oa":1,"date_created":"2023-02-02T08:13:28Z","citation":{"chicago":"Guet, Calin C, L Bruneaux, P Oikonomou, M Aldana, and P Cluzel. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of <i>Mar</i> Operon Expression.” <i>Frontiers in Microbiology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fmicb.2023.1049255\">https://doi.org/10.3389/fmicb.2023.1049255</a>.","apa":"Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., &#38; Cluzel, P. (2023). Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2023.1049255\">https://doi.org/10.3389/fmicb.2023.1049255</a>","mla":"Guet, Calin C., et al. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of <i>Mar</i> Operon Expression.” <i>Frontiers in Microbiology</i>, vol. 14, 1049255, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1049255\">10.3389/fmicb.2023.1049255</a>.","ista":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. 2023. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression. Frontiers in Microbiology. 14, 1049255.","short":"C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in Microbiology 14 (2023).","ieee":"C. C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, and P. Cluzel, “Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression,” <i>Frontiers in Microbiology</i>, vol. 14. Frontiers, 2023.","ama":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression. <i>Frontiers in Microbiology</i>. 2023;14. doi:<a href=\"https://doi.org/10.3389/fmicb.2023.1049255\">10.3389/fmicb.2023.1049255</a>"},"quality_controlled":"1","doi":"10.3389/fmicb.2023.1049255","file_date_updated":"2023-07-31T07:16:34Z","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":14,"acknowledgement":"This work was supported by NIH P50 award P50GM081892-02 to the University of Chicago, a catalyst grant from the Chicago Biomedical Consortium with support from The Searle Funds at The Chicago Community Trust to PC, and a Yen Fellowship to CCG. MA was partially supported by PAPIIT-UNAM grant IN-11322.","publication":"Frontiers in Microbiology","day":"20","pmid":1,"intvolume":"        14","has_accepted_license":"1","date_published":"2023-06-20T00:00:00Z","isi":1,"publication_identifier":{"eissn":["1664-302X"]},"year":"2023","month":"06","department":[{"_id":"CaGu"}],"article_type":"original","publisher":"Frontiers","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-07-31T07:16:34Z","checksum":"7dd322347512afaa5daf72a0154f2f07","file_size":6452841,"success":1,"date_created":"2023-07-31T07:16:34Z","file_name":"2023_FrontiersMicrobiology_Guet.pdf","creator":"dernst","file_id":"13322","relation":"main_file"}],"type":"journal_article","ddc":["570"],"oa_version":"Published Version","_id":"12478","external_id":{"isi":["001030002600001"],"pmid":["37485524"]},"publication_status":"published","author":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"first_name":"L","full_name":"Bruneaux, L","last_name":"Bruneaux"},{"first_name":"P","full_name":"Oikonomou, P","last_name":"Oikonomou"},{"first_name":"M","full_name":"Aldana, M","last_name":"Aldana"},{"last_name":"Cluzel","full_name":"Cluzel, P","first_name":"P"}],"status":"public","date_updated":"2023-08-02T06:25:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype.","lang":"eng"}],"scopus_import":"1"},{"publication_identifier":{"issn":["2194-0401"],"eissn":["2194-041X"]},"year":"2023","month":"11","project":[{"grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","name":"Bridging Scales in Random Materials"}],"department":[{"_id":"JuFi"}],"article_type":"original","publisher":"Springer Nature","oa_version":"Submitted Version","ddc":["510"],"type":"journal_article","_id":"12486","external_id":{"arxiv":["2207.08293"]},"publication_status":"epub_ahead","author":[{"first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti"}],"status":"public","date_updated":"2023-12-18T07:53:45Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"This paper is concerned with the problem of regularization by noise of systems of reaction–diffusion equations with mass control. It is known that strong solutions to such systems of PDEs may blow-up in finite time. Moreover, for many systems of practical interest, establishing whether the blow-up occurs or not is an open question. Here we prove that a suitable multiplicative noise of transport type has a regularizing effect. More precisely, for both a sufficiently noise intensity and a high spectrum, the blow-up of strong solutions is delayed up to an arbitrary large time. Global existence is shown for the case of exponentially decreasing mass. The proofs combine and extend recent developments in regularization by noise and in the Lp(Lq)-approach to stochastic PDEs, highlighting new connections between the two areas."}],"main_file_link":[{"url":"https://doi.org/10.1007/s40072-023-00319-4","open_access":"1"}],"scopus_import":"1","title":"Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations","oa":1,"citation":{"chicago":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s40072-023-00319-4\">https://doi.org/10.1007/s40072-023-00319-4</a>.","apa":"Agresti, A. (2023). Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40072-023-00319-4\">https://doi.org/10.1007/s40072-023-00319-4</a>","mla":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s40072-023-00319-4\">10.1007/s40072-023-00319-4</a>.","ista":"Agresti A. 2023. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations.","ieee":"A. Agresti, “Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations,” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature, 2023.","short":"A. Agresti, Stochastics and Partial Differential Equations: Analysis and Computations (2023).","ama":"Agresti A. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s40072-023-00319-4\">10.1007/s40072-023-00319-4</a>"},"date_created":"2023-02-02T10:45:47Z","arxiv":1,"doi":"10.1007/s40072-023-00319-4","article_processing_charge":"No","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"28","publication":"Stochastics and Partial Differential Equations: Analysis and Computations","acknowledgement":"The author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).\r\nThe author thanks Lorenzo Dello Schiavo, Lucio Galeati and Mark Veraar for helpful comments. The author acknowledges Caterina Balzotti for her support in creating the picture. The author\r\nthanks the anonymous referee for helpful comments. ","has_accepted_license":"1","date_published":"2023-11-28T00:00:00Z"},{"scopus_import":"1","abstract":[{"text":"Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.</jats:p><jats:sec><jats:title>Significance statement</jats:title><jats:p>We fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-13T11:11:24Z","status":"public","author":[{"last_name":"Scarpetta","full_name":"Scarpetta, Silvia","first_name":"Silvia"},{"first_name":"Niccolò","full_name":"Morrisi, Niccolò","last_name":"Morrisi"},{"first_name":"Carlotta","last_name":"Mutti","full_name":"Mutti, Carlotta"},{"full_name":"Azzi, Nicoletta","last_name":"Azzi","first_name":"Nicoletta"},{"last_name":"Trippi","full_name":"Trippi, Irene","first_name":"Irene"},{"full_name":"Ciliento, Rosario","last_name":"Ciliento","first_name":"Rosario"},{"full_name":"Apicella, Ilenia","last_name":"Apicella","first_name":"Ilenia"},{"last_name":"Messuti","full_name":"Messuti, Giovanni","first_name":"Giovanni"},{"first_name":"Marianna","full_name":"Angiolelli, Marianna","last_name":"Angiolelli"},{"full_name":"Lombardi, Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Liborio","full_name":"Parrino, Liborio","last_name":"Parrino"},{"last_name":"Vaudano","full_name":"Vaudano, Anna Elisabetta","first_name":"Anna Elisabetta"}],"publication_status":"published","external_id":{"pmid":["37766992"],"isi":["001082331200001"]},"_id":"12487","issue":"10","type":"journal_article","oa_version":"Published Version","ddc":["570"],"file":[{"date_created":"2023-10-09T07:23:46Z","checksum":"f499836af172ecc9865de4bb41fa99d1","success":1,"file_size":4872708,"date_updated":"2023-10-09T07:23:46Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"14412","file_name":"2023_iScience_Scarpetta.pdf"}],"publisher":"Elsevier","article_type":"original","department":[{"_id":"GaTk"}],"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Functional Advantages of Critical Brain Dynamics","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318"}],"month":"10","year":"2023","publication_identifier":{"eissn":["2589-0042"]},"isi":1,"date_published":"2023-10-20T00:00:00Z","has_accepted_license":"1","intvolume":"        26","pmid":1,"day":"20","publication":"iScience","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411, and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318. IA acknowledges financial support from the MIUR PRIN 2017WZFTZP.","volume":26,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"Yes","file_date_updated":"2023-10-09T07:23:46Z","doi":"10.1016/j.isci.2023.107840","quality_controlled":"1","date_created":"2023-02-02T10:50:17Z","citation":{"apa":"Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R., … Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2023.107840\">https://doi.org/10.1016/j.isci.2023.107840</a>","chicago":"Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” <i>IScience</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.isci.2023.107840\">https://doi.org/10.1016/j.isci.2023.107840</a>.","mla":"Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” <i>IScience</i>, vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107840\">10.1016/j.isci.2023.107840</a>.","ama":"Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. <i>iScience</i>. 2023;26(10):107840. doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107840\">10.1016/j.isci.2023.107840</a>","short":"S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.","ieee":"S. Scarpetta <i>et al.</i>, “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” <i>iScience</i>, vol. 26, no. 10. Elsevier, p. 107840, 2023.","ista":"Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I, Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 26(10), 107840."},"oa":1,"title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","page":"107840"},{"day":"02","degree_awarded":"PhD","has_accepted_license":"1","date_published":"2023-02-02T00:00:00Z","doi":"10.15479/at:ista:12491","file_date_updated":"2024-02-08T23:30:04Z","article_processing_charge":"No","oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_created":"2023-02-02T14:50:20Z","citation":{"chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>.","apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>","mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>"},"page":"187","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","date_updated":"2024-02-08T23:30:05Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8586"}]},"author":[{"first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","full_name":"Zens, Bettina"}],"status":"public","supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","ddc":["570"],"file":[{"date_updated":"2024-02-08T23:30:04Z","access_level":"open_access","embargo":"2024-02-07","content_type":"application/pdf","date_created":"2023-02-07T13:07:38Z","checksum":"069d87f025e0799bf9e3c375664264f2","file_size":23082464,"file_name":"PhDThesis_BettinaZens_2023_final.pdf","relation":"main_file","file_id":"12527","creator":"bzens"},{"file_name":"PhDThesis_BettinaZens_2023_final.docx","file_id":"12528","creator":"bzens","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-02-08T23:30:04Z","checksum":"8c66ed203495d6e078ed1002a866520c","file_size":106169509,"embargo_to":"open_access","date_created":"2023-02-07T13:09:05Z"}],"oa_version":"Published Version","_id":"12491","publication_status":"published","alternative_title":["ISTA Thesis"],"publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"year":"2023","month":"02","project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"department":[{"_id":"GradSch"},{"_id":"FlSc"}]},{"month":"03","year":"2023","contributor":[{"contributor_type":"researcher","first_name":"Mélanie","last_name":"Berbon"},{"last_name":"Vallet","contributor_type":"researcher","first_name":"Alicia"},{"first_name":"Axelle","contributor_type":"researcher","last_name":"Grelard"},{"last_name":"Morvan","first_name":"Estelle","contributor_type":"researcher"},{"last_name":"Bardiaux","contributor_type":"researcher","first_name":"Benjamin"},{"last_name":"Lichtenecker","contributor_type":"researcher","first_name":"Roman"},{"last_name":"Ernst","contributor_type":"researcher","first_name":"Matthias"},{"contributor_type":"researcher","first_name":"Antoine","last_name":"Loquet"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","contributor_type":"contact_person","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"contributor_type":"researcher","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","last_name":"Becker"}],"title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"oa":1,"publisher":"Institute of Science and Technology Austria","_id":"12497","date_created":"2023-02-03T08:08:02Z","citation":{"apa":"Becker, L. M., &#38; Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12497\">https://doi.org/10.15479/AT:ISTA:12497</a>","chicago":"Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12497\">https://doi.org/10.15479/AT:ISTA:12497</a>.","mla":"Becker, Lea Marie, and Paul Schanda. <i>Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12497\">10.15479/AT:ISTA:12497</a>.","ama":"Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12497\">10.15479/AT:ISTA:12497</a>","short":"L.M. Becker, P. Schanda, (2023).","ieee":"L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023.","ista":"Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12497\">10.15479/AT:ISTA:12497</a>."},"ddc":["572"],"type":"research_data","file":[{"file_size":87018103,"checksum":"fd9a28620a81a82991fb70f4fd6591d9","date_created":"2023-03-23T10:03:16Z","access_level":"open_access","content_type":"application/zip","date_updated":"2023-03-24T09:34:20Z","file_id":"12743","creator":"lbecker","relation":"main_file","file_name":"Research_Data.zip"},{"date_updated":"2023-03-24T09:42:03Z","access_level":"open_access","content_type":"text/plain","date_created":"2023-03-24T07:13:55Z","file_size":747,"checksum":"30ebdfb600af118fcf8518b6efe0b7e9","file_name":"README.txt","relation":"main_file","file_id":"12755","creator":"dernst"}],"oa_version":"Published Version","file_date_updated":"2023-03-24T09:42:03Z","doi":"10.15479/AT:ISTA:12497","article_processing_charge":"No","author":[{"orcid":"0000-0002-6401-5151","last_name":"Becker","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:14:06Z","day":"23","date_published":"2023-03-23T00:00:00Z","abstract":[{"text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and  HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture.","lang":"eng"}],"related_material":{"record":[{"id":"12675","relation":"used_in_publication","status":"public"}]},"keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"has_accepted_license":"1"},{"page":"318-328","title":"A multivariate view of the speciation continuum","oa":1,"date_created":"2023-02-05T23:00:59Z","citation":{"ieee":"D. I. Bolnick <i>et al.</i>, “A multivariate view of the speciation continuum,” <i>Evolution: International journal of organic evolution</i>, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. <i>Evolution: International journal of organic evolution</i>. 2023;77(1):318-328. doi:<a href=\"https://doi.org/10.1093/evolut/qpac004\">10.1093/evolut/qpac004</a>","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” <i>Evolution: International Journal of Organic Evolution</i>, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:<a href=\"https://doi.org/10.1093/evolut/qpac004\">10.1093/evolut/qpac004</a>.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” <i>Evolution: International Journal of Organic Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolut/qpac004\">https://doi.org/10.1093/evolut/qpac004</a>.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. <i>Evolution: International Journal of Organic Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpac004\">https://doi.org/10.1093/evolut/qpac004</a>"},"quality_controlled":"1","doi":"10.1093/evolut/qpac004","article_processing_charge":"No","volume":77,"day":"01","publication":"Evolution: International journal of organic evolution","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","pmid":1,"intvolume":"        77","date_published":"2023-01-01T00:00:00Z","isi":1,"publication_identifier":{"eissn":["1558-5646"]},"year":"2023","month":"01","department":[{"_id":"NiBa"}],"article_type":"original","publisher":"Oxford University Press","oa_version":"Published Version","type":"journal_article","issue":"1","_id":"12514","external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"publication_status":"published","author":[{"last_name":"Bolnick","full_name":"Bolnick, Daniel I.","first_name":"Daniel I."},{"first_name":"Amanda K.","last_name":"Hund","full_name":"Hund, Amanda K."},{"first_name":"Patrik","full_name":"Nosil, Patrik","last_name":"Nosil"},{"last_name":"Peng","full_name":"Peng, Foen","first_name":"Foen"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Swapna","full_name":"Subramanian, Swapna","last_name":"Subramanian"},{"last_name":"Wolf","full_name":"Wolf, Jochen B.W.","first_name":"Jochen B.W."},{"last_name":"Yukilevich","full_name":"Yukilevich, Roman","first_name":"Roman"}],"status":"public","date_updated":"2023-08-01T12:58:30Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1093/evolut/qpac004","open_access":"1"}],"scopus_import":"1"},{"oa":1,"article_number":"1097467","quality_controlled":"1","date_created":"2023-02-05T23:01:00Z","citation":{"chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” <i>Frontiers in Neuroanatomy</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fnana.2022.1097467\">https://doi.org/10.3389/fnana.2022.1097467</a>.","apa":"Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., &#38; Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. <i>Frontiers in Neuroanatomy</i>. Frontiers. <a href=\"https://doi.org/10.3389/fnana.2022.1097467\">https://doi.org/10.3389/fnana.2022.1097467</a>","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” <i>Frontiers in Neuroanatomy</i>, vol. 16, 1097467, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fnana.2022.1097467\">10.3389/fnana.2022.1097467</a>.","ieee":"I. Ortiz-Leal <i>et al.</i>, “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” <i>Frontiers in Neuroanatomy</i>, vol. 16. Frontiers, 2023.","ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).","ama":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. <i>Frontiers in Neuroanatomy</i>. 2023;16. doi:<a href=\"https://doi.org/10.3389/fnana.2022.1097467\">10.3389/fnana.2022.1097467</a>"},"title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","pmid":1,"publication":"Frontiers in Neuroanatomy","day":"10","acknowledgement":"This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study.","volume":16,"date_published":"2023-01-10T00:00:00Z","intvolume":"        16","has_accepted_license":"1","file_date_updated":"2023-02-06T07:56:14Z","doi":"10.3389/fnana.2022.1097467","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","publisher":"Frontiers","external_id":{"isi":["000919786900001"],"pmid":["36704406"]},"publication_status":"published","_id":"12515","file":[{"date_created":"2023-02-06T07:56:14Z","file_size":21943473,"checksum":"49cd40f3bda6f267079427042e7d15e3","success":1,"date_updated":"2023-02-06T07:56:14Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"12518","creator":"dernst","file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf"}],"type":"journal_article","ddc":["570"],"oa_version":"Published Version","month":"01","year":"2023","publication_identifier":{"eissn":["1662-5129"]},"isi":1,"article_type":"original","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-16T11:37:52Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues."}],"status":"public","author":[{"full_name":"Ortiz-Leal, Irene","last_name":"Ortiz-Leal","first_name":"Irene"},{"last_name":"Torres","full_name":"Torres, Mateo V.","first_name":"Mateo V."},{"last_name":"Vargas Barroso","full_name":"Vargas Barroso, Victor M","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luis Eusebio","full_name":"Fidalgo, Luis Eusebio","last_name":"Fidalgo"},{"first_name":"Ana María","last_name":"López-Beceiro","full_name":"López-Beceiro, Ana María"},{"first_name":"Jorge A.","last_name":"Larriva-Sahd","full_name":"Larriva-Sahd, Jorge A."},{"full_name":"Sánchez-Quinteiro, Pablo","last_name":"Sánchez-Quinteiro","first_name":"Pablo"}]},{"article_type":"original","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"month":"02","year":"2023","publication_identifier":{"issn":["2056-3744"]},"isi":1,"publication_status":"published","external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"issue":"1","_id":"12521","ddc":["570"],"oa_version":"Published Version","type":"journal_article","file":[{"file_id":"14068","creator":"dernst","relation":"main_file","file_name":"2023_EvLetters_Mrnjavac.pdf","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_size":2592189,"success":1,"date_created":"2023-08-16T11:43:33Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-08-16T11:43:33Z"}],"publisher":"Oxford University Press","status":"public","author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"scopus_import":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-16T11:44:32Z","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","quality_controlled":"1","citation":{"chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>.","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., &#38; Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>.","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” <i>Evolution Letters</i>, vol. 7, no. 1. Oxford University Press, 2023.","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. 2023;7(1). doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>"},"date_created":"2023-02-06T13:59:12Z","oa":1,"article_number":"qrac004","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"file_date_updated":"2023-08-16T11:43:33Z","doi":"10.1093/evlett/qrac004","date_published":"2023-02-01T00:00:00Z","intvolume":"         7","has_accepted_license":"1","pmid":1,"day":"01","publication":"Evolution Letters","acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","volume":7},{"degree_awarded":"MS","has_accepted_license":"1","date_published":"2023-02-08T00:00:00Z","day":"08","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"},"article_processing_charge":"No","doi":"10.15479/at:ista:12531","file_date_updated":"2024-02-09T23:30:03Z","date_created":"2023-02-09T07:45:05Z","citation":{"apa":"Kirillova, K. (2023). <i>Panoramic functional gradients across the mouse retina</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>.","mla":"Kirillova, Kseniia. <i>Panoramic Functional Gradients across the Mouse Retina</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>.","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023."},"oa":1,"title":"Panoramic functional gradients across the mouse retina","page":"46","abstract":[{"text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.","lang":"eng"}],"date_updated":"2024-02-09T23:30:04Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"status":"public","author":[{"full_name":"Kirillova, Kseniia","last_name":"Kirillova","first_name":"Kseniia","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ddc":["570"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","access_level":"open_access","embargo":"2024-02-08","date_updated":"2024-02-09T23:30:03Z","checksum":"57d8da3a6c749eb1556b7435fe266a5f","file_size":8369317,"date_created":"2023-02-09T08:03:32Z","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","creator":"cchlebak","file_id":"12532","relation":"main_file"},{"file_size":11204408,"checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","embargo_to":"open_access","date_created":"2023-02-10T09:32:06Z","access_level":"closed","content_type":"application/x-zip-compressed","date_updated":"2024-02-09T23:30:03Z","file_id":"12535","creator":"cchlebak","relation":"source_file","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip"}],"type":"dissertation","alternative_title":["ISTA Master's Thesis"],"publication_status":"published","_id":"12531","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Jösch, Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publication_identifier":{"issn":["2791-4585"]},"year":"2023","month":"02"},{"date_updated":"2023-02-20T07:02:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics.","lang":"eng"}],"scopus_import":"1","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543"},{"id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto","last_name":"Cappellaro","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev"}],"status":"public","publisher":"American Physical Society","file":[{"file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","relation":"main_file","file_id":"12546","creator":"dernst","date_updated":"2023-02-13T10:38:10Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-02-13T10:38:10Z","success":1,"file_size":865150,"checksum":"6068b62874c0099628a108bb9c5c6bd2"}],"type":"journal_article","oa_version":"Published Version","ddc":["530"],"_id":"12534","issue":"1","publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"year":"2023","month":"01","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"department":[{"_id":"MiLe"}],"article_type":"original","volume":5,"acknowledgement":"We thank Rafael Barfknecht for help at the initial stages of this project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","day":"20","publication":"Physical Review Research","has_accepted_license":"1","intvolume":"         5","date_published":"2023-01-20T00:00:00Z","doi":"10.1103/physrevresearch.5.013029","file_date_updated":"2023-02-13T10:38:10Z","ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"013029","oa":1,"date_created":"2023-02-10T09:02:26Z","citation":{"mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” <i>Physical Review Research</i>, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevresearch.5.013029\">10.1103/physrevresearch.5.013029</a>.","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., &#38; Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.5.013029\">https://doi.org/10.1103/physrevresearch.5.013029</a>","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” <i>Physical Review Research</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevresearch.5.013029\">https://doi.org/10.1103/physrevresearch.5.013029</a>.","ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. <i>Physical Review Research</i>. 2023;5(1). doi:<a href=\"https://doi.org/10.1103/physrevresearch.5.013029\">10.1103/physrevresearch.5.013029</a>","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” <i>Physical Review Research</i>, vol. 5, no. 1. American Physical Society, 2023.","ista":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029."},"quality_controlled":"1","title":"Dissipative dynamics of an impurity with spin-orbit coupling"},{"abstract":[{"text":"In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-01T13:10:27Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"status":"public","author":[{"first_name":"Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana","last_name":"Villalba Requena"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"type":"journal_article","oa_version":"None","publication_status":"published","external_id":{"isi":["000994473300001"]},"issue":"3","_id":"12542","publisher":"Elsevier","department":[{"_id":"SiHi"}],"article_type":"letter_note","publication_identifier":{"eissn":["1097-4199"]},"isi":1,"year":"2023","month":"02","intvolume":"       111","date_published":"2023-02-01T00:00:00Z","publication":"Neuron","day":"01","volume":111,"article_processing_charge":"No","doi":"10.1016/j.neuron.2023.01.006","citation":{"mla":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” <i>Neuron</i>, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.01.006\">10.1016/j.neuron.2023.01.006</a>.","apa":"Villalba Requena, A., &#38; Hippenmeyer, S. (2023). Going back in time with TEMPO. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.01.006\">https://doi.org/10.1016/j.neuron.2023.01.006</a>","chicago":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” <i>Neuron</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.neuron.2023.01.006\">https://doi.org/10.1016/j.neuron.2023.01.006</a>.","ama":"Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. <i>Neuron</i>. 2023;111(3):291-293. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.01.006\">10.1016/j.neuron.2023.01.006</a>","ieee":"A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” <i>Neuron</i>, vol. 111, no. 3. Elsevier, pp. 291–293, 2023.","ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293.","short":"A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293."},"date_created":"2023-02-12T23:00:58Z","quality_controlled":"1","title":"Going back in time with TEMPO","page":"291-293"},{"page":"450-460","title":"Pathogen evasion of social immunity","oa":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"date_created":"2023-02-12T23:00:59Z","citation":{"mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” <i>Nature Ecology and Evolution</i>, vol. 7, Springer Nature, 2023, pp. 450–60, doi:<a href=\"https://doi.org/10.1038/s41559-023-01981-6\">10.1038/s41559-023-01981-6</a>.","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41559-023-01981-6\">https://doi.org/10.1038/s41559-023-01981-6</a>.","apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-023-01981-6\">https://doi.org/10.1038/s41559-023-01981-6</a>","short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","ieee":"M. Stock <i>et al.</i>, “Pathogen evasion of social immunity,” <i>Nature Ecology and Evolution</i>, vol. 7. Springer Nature, pp. 450–460, 2023.","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460.","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. <i>Nature Ecology and Evolution</i>. 2023;7:450-460. doi:<a href=\"https://doi.org/10.1038/s41559-023-01981-6\">10.1038/s41559-023-01981-6</a>"},"quality_controlled":"1","doi":"10.1038/s41559-023-01981-6","file_date_updated":"2023-08-16T11:54:59Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","ec_funded":1,"day":"01","acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","publication":"Nature Ecology and Evolution","volume":7,"pmid":1,"has_accepted_license":"1","intvolume":"         7","date_published":"2023-03-01T00:00:00Z","publication_identifier":{"eissn":["2397-334X"]},"isi":1,"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","call_identifier":"H2020","grant_number":"771402"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}],"year":"2023","month":"03","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"article_type":"original","publisher":"Springer Nature","type":"journal_article","oa_version":"Published Version","ddc":["570"],"file":[{"date_updated":"2023-08-16T11:54:59Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-08-16T11:54:59Z","checksum":"8244f4650a0e7aeea488d1bcd4a31702","file_size":1600499,"success":1,"file_name":"2023_NatureEcoEvo_Stock.pdf","relation":"main_file","creator":"dernst","file_id":"14069"}],"external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"publication_status":"published","_id":"12543","status":"public","author":[{"full_name":"Stock, Miriam","last_name":"Stock","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","full_name":"Milutinovic, Barbara"},{"full_name":"Hönigsberger, Michaela","last_name":"Hönigsberger","id":"953894f3-25bd-11ec-8556-f70a9d38ef60","first_name":"Michaela"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V","last_name":"Grasse"},{"full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer","id":"39523C54-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"last_name":"Kampleitner","full_name":"Kampleitner, Niklas","first_name":"Niklas","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha"},{"full_name":"Schmitt, Thomas","last_name":"Schmitt","first_name":"Thomas"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"date_updated":"2023-08-16T11:55:48Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/"}]},"abstract":[{"text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts.","lang":"eng"}],"scopus_import":"1"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No","doi":"10.1021/acs.jcim.2c01346","file_date_updated":"2023-08-16T12:21:13Z","intvolume":"        63","has_accepted_license":"1","date_published":"2023-02-13T00:00:00Z","acknowledgement":"P.K. acknowledges support from the University of California Multicampus Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant No.1760485). H.E. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access is funded by the Austrian Science Fund (FWF).","publication":"Journal of Chemical Information and Modeling","day":"13","volume":63,"pmid":1,"title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","page":"973-985","date_created":"2023-02-12T23:00:59Z","citation":{"ista":"Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 63(3), 973–985.","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","ieee":"P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives,” <i>Journal of Chemical Information and Modeling</i>, vol. 63, no. 3. American Chemical Society, pp. 973–985, 2023.","ama":"Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. <i>Journal of Chemical Information and Modeling</i>. 2023;63(3):973-985. doi:<a href=\"https://doi.org/10.1021/acs.jcim.2c01346\">10.1021/acs.jcim.2c01346</a>","mla":"Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” <i>Journal of Chemical Information and Modeling</i>, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85, doi:<a href=\"https://doi.org/10.1021/acs.jcim.2c01346\">10.1021/acs.jcim.2c01346</a>.","chicago":"Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” <i>Journal of Chemical Information and Modeling</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jcim.2c01346\">https://doi.org/10.1021/acs.jcim.2c01346</a>.","apa":"Koehl, P., Akopyan, A., &#38; Edelsbrunner, H. (2023). Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. <i>Journal of Chemical Information and Modeling</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jcim.2c01346\">https://doi.org/10.1021/acs.jcim.2c01346</a>"},"quality_controlled":"1","oa":1,"status":"public","author":[{"full_name":"Koehl, Patrice","last_name":"Koehl","first_name":"Patrice"},{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"abstract":[{"lang":"eng","text":"Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software."}],"scopus_import":"1","date_updated":"2023-08-16T12:22:07Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"article_type":"original","publication_identifier":{"issn":["1549-9596"],"eissn":["1549-960X"]},"isi":1,"project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"year":"2023","month":"02","oa_version":"Published Version","type":"journal_article","ddc":["510","540"],"file":[{"file_name":"2023_JCIM_Koehl.pdf","relation":"main_file","creator":"dernst","file_id":"14070","date_updated":"2023-08-16T12:21:13Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-08-16T12:21:13Z","file_size":8069223,"success":1,"checksum":"7d20562269edff1e31b9d6019d4983b0"}],"publication_status":"published","external_id":{"pmid":["36638318"],"isi":["000920370700001"]},"_id":"12544","issue":"3","publisher":"American Chemical Society"},{"abstract":[{"lang":"eng","text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts."}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T13:15:48Z","author":[{"full_name":"Forghani, Mohammad","last_name":"Forghani","first_name":"Mohammad"},{"full_name":"Claramunt, Christophe","last_name":"Claramunt","first_name":"Christophe"},{"id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","first_name":"Farid","full_name":"Karimipour, Farid","last_name":"Karimipour","orcid":"0000-0001-6746-4174"},{"first_name":"Georg","last_name":"Heiler","full_name":"Heiler, Georg"}],"status":"public","_id":"12548","external_id":{"isi":["000971492200145"]},"publication_status":"published","type":"conference","file":[{"relation":"main_file","creator":"fkarimip","file_id":"12549","file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","date_created":"2023-02-14T07:58:26Z","file_size":1183339,"checksum":"c253bee25e6dfe484f96662daa119cb6","success":1,"date_updated":"2023-02-14T07:58:26Z","content_type":"application/pdf","access_level":"open_access"}],"oa_version":"Submitted Version","ddc":["600"],"publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"HeEd"}],"year":"2023","month":"02","isi":1,"publication_identifier":{"eissn":["2375-9259"],"eisbn":["9798350346091"]},"date_published":"2023-02-08T00:00:00Z","has_accepted_license":"1","publication":"2022 IEEE International Conference on Data Mining Workshops","day":"08","article_processing_charge":"No","file_date_updated":"2023-02-14T07:58:26Z","doi":"10.1109/icdmw58026.2022.00093","conference":{"end_date":"2022-12-01","location":"Orlando, FL, United States","name":"ICDMW: Conference on Data Mining Workshops","start_date":"2022-11-28"},"quality_controlled":"1","citation":{"chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In <i>2022 IEEE International Conference on Data Mining Workshops</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">https://doi.org/10.1109/icdmw58026.2022.00093</a>.","apa":"Forghani, M., Claramunt, C., Karimipour, F., &#38; Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In <i>2022 IEEE International Conference on Data Mining Workshops</i>. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">https://doi.org/10.1109/icdmw58026.2022.00093</a>","mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” <i>2022 IEEE International Conference on Data Mining Workshops</i>, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:<a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">10.1109/icdmw58026.2022.00093</a>.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in <i>2022 IEEE International Conference on Data Mining Workshops</i>, Orlando, FL, United States, 2023.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: <i>2022 IEEE International Conference on Data Mining Workshops</i>. Institute of Electrical and Electronics Engineers; 2023. doi:<a href=\"https://doi.org/10.1109/icdmw58026.2022.00093\">10.1109/icdmw58026.2022.00093</a>"},"date_created":"2023-02-14T07:56:21Z","article_number":"00093","oa":1,"title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic"}]