[{"date_updated":"2023-08-16T11:41:42Z","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).","publication_identifier":{"eissn":["1522-2616"],"issn":["0025-584X"]},"title":"On the trace embedding and its applications to evolution equations","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","isi":1,"scopus_import":"1","page":"1319-1350","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"citation":{"short":"A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023) 1319–1350.","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>.","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>.","ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.","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>","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>","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."},"publication":"Mathematische Nachrichten","ddc":["510"],"issue":"4","license":"https://creativecommons.org/licenses/by-nc/4.0/","department":[{"_id":"JuFi"}],"doi":"10.1002/mana.202100192","author":[{"orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio","last_name":"Agresti","first_name":"Antonio"},{"full_name":"Lindemulder, Nick","first_name":"Nick","last_name":"Lindemulder"},{"last_name":"Veraar","first_name":"Mark","full_name":"Veraar, Mark"}],"date_created":"2023-01-29T23:00:59Z","type":"journal_article","intvolume":"       296","file":[{"checksum":"6f099f1d064173784d1a27716a2cc795","success":1,"relation":"main_file","file_id":"14067","content_type":"application/pdf","access_level":"open_access","file_size":449280,"date_updated":"2023-08-16T11:40:02Z","date_created":"2023-08-16T11:40:02Z","file_name":"2023_MathNachrichten_Agresti.pdf","creator":"dernst"}],"publisher":"Wiley","_id":"12429","date_published":"2023-04-01T00:00:00Z","volume":296,"year":"2023","oa":1,"arxiv":1,"abstract":[{"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.","lang":"eng"}],"publication_status":"published","article_type":"original","file_date_updated":"2023-08-16T11:40:02Z","day":"01","oa_version":"Published Version","external_id":{"isi":["000914134900001"],"arxiv":["2104.05063"]},"has_accepted_license":"1","month":"04"},{"status":"public","scopus_import":"1","isi":1,"publication":"Reviews in Mathematical Physics","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>.","ista":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 35(4), 2350006.","chicago":"Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” <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>.","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.","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>","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>"},"issue":"4","department":[{"_id":"RoSe"}],"publication_identifier":{"issn":["0129-055X"]},"date_updated":"2023-08-16T11:47:27Z","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","article_number":"2350006","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"year":"2023","date_published":"2023-01-09T00:00:00Z","volume":35,"arxiv":1,"article_type":"original","publication_status":"published","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."}],"day":"09","external_id":{"arxiv":["2110.00458"],"isi":["000909760300001"]},"oa_version":"Preprint","month":"01","doi":"10.1142/S0129055X2350006X","author":[{"last_name":"Falconi","first_name":"Marco","full_name":"Falconi, Marco"},{"first_name":"Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822"},{"full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","last_name":"Mitrouskas"},{"last_name":"Petrat","first_name":"Sören P","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P"}],"date_created":"2023-01-29T23:00:59Z","intvolume":"        35","type":"journal_article","publisher":"World Scientific Publishing","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2110.00458","open_access":"1"}],"_id":"12430"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"conference":{"start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27","name":"FOSSACS: Foundations of Software Science and Computation Structures"},"quality_controlled":"1","article_processing_charge":"No","title":"Quantitative safety and liveness","date_updated":"2025-09-09T12:21:08Z","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031308284"],"eissn":["1611-3349"]},"license":"https://creativecommons.org/licenses/by/4.0/","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"ddc":["000"],"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"page":"349-370","citation":{"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>.","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.","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>.","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.","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>","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>","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."},"publication":"26th International Conference Foundations of Software Science and Computation Structures","isi":1,"scopus_import":"1","status":"public","_id":"12467","publisher":"Springer Nature","file":[{"date_updated":"2023-01-31T07:22:21Z","date_created":"2023-01-31T07:22:21Z","file_name":"qsl.pdf","creator":"esarac","content_type":"application/pdf","access_level":"open_access","file_size":449027,"relation":"main_file","checksum":"981025aed580b6b27c426cb8856cf63e","success":1,"file_id":"12468"},{"content_type":"application/pdf","access_level":"open_access","file_size":1048171,"success":1,"relation":"main_file","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","file_id":"13153","date_updated":"2023-06-19T10:28:09Z","file_name":"2023_LNCS_HenzingerT.pdf","date_created":"2023-06-19T10:28:09Z","creator":"dernst"}],"intvolume":"     13992","type":"conference","date_created":"2023-01-31T07:23:56Z","author":[{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","first_name":"Nicolas Adrien"},{"last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E"}],"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093"}],"doi":"10.1007/978-3-031-30829-1_17","has_accepted_license":"1","month":"04","oa_version":"Published Version","ec_funded":1,"external_id":{"isi":["001288609300017"],"arxiv":["2301.11175"]},"day":"21","file_date_updated":"2023-06-19T10:28:09Z","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"}],"publication_status":"published","alternative_title":["LNCS"],"arxiv":1,"volume":13992,"date_published":"2023-04-21T00:00:00Z","year":"2023","oa":1},{"date_published":"2023-03-16T00:00:00Z","volume":14,"oa":1,"year":"2023","file_date_updated":"2023-04-17T07:49:09Z","abstract":[{"lang":"eng","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."}],"article_type":"original","publication_status":"published","oa_version":"Published Version","external_id":{"isi":["000961542100001"],"pmid":["37007485"]},"day":"16","has_accepted_license":"1","month":"03","author":[{"full_name":"Viljakainen, Lumi","last_name":"Viljakainen","first_name":"Lumi"},{"orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias","last_name":"Fürst","first_name":"Matthias"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse"},{"full_name":"Jurvansuu, Jaana","first_name":"Jaana","last_name":"Jurvansuu"},{"first_name":"Jinook","last_name":"Oh","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","full_name":"Oh, Jinook","orcid":"0000-0001-7425-2372"},{"full_name":"Tolonen, Lassi","last_name":"Tolonen","first_name":"Lassi"},{"first_name":"Thomas","last_name":"Eder","full_name":"Eder, Thomas"},{"full_name":"Rattei, Thomas","first_name":"Thomas","last_name":"Rattei"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia"}],"date_created":"2023-01-31T08:13:40Z","doi":"10.3389/fmicb.2023.1119002","project":[{"name":"Viral pathogens and social immunity in ants","call_identifier":"FWF","_id":"25DF61D8-B435-11E9-9278-68D0E5697425","grant_number":"M02076"}],"intvolume":"        14","type":"journal_article","file":[{"file_id":"12843","relation":"main_file","checksum":"cd52292963acce1111634d9fac08c699","success":1,"access_level":"open_access","file_size":4866332,"content_type":"application/pdf","date_created":"2023-04-17T07:49:09Z","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","creator":"dernst","date_updated":"2023-04-17T07:49:09Z"}],"_id":"12469","publisher":"Frontiers","status":"public","citation":{"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>.","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>.","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).","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>","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>","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."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"Frontiers in Microbiology","isi":1,"scopus_import":"1","corr_author":"1","ddc":["570"],"pmid":1,"department":[{"_id":"SyCr"}],"title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","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). ","date_updated":"2025-04-23T08:54:27Z","publication_identifier":{"eissn":["1664-302X"]},"article_processing_charge":"Yes (via OA deal)","article_number":"1119002","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1"},{"month":"06","has_accepted_license":"1","external_id":{"pmid":["37485524"],"isi":["001030002600001"]},"oa_version":"Published Version","day":"20","file_date_updated":"2023-07-31T07:16:34Z","publication_status":"published","article_type":"original","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"}],"year":"2023","oa":1,"volume":14,"date_published":"2023-06-20T00:00:00Z","_id":"12478","publisher":"Frontiers","file":[{"creator":"dernst","file_name":"2023_FrontiersMicrobiology_Guet.pdf","date_created":"2023-07-31T07:16:34Z","date_updated":"2023-07-31T07:16:34Z","file_id":"13322","checksum":"7dd322347512afaa5daf72a0154f2f07","success":1,"relation":"main_file","file_size":6452841,"access_level":"open_access","content_type":"application/pdf"}],"intvolume":"        14","type":"journal_article","date_created":"2023-02-02T08:13:28Z","author":[{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bruneaux, L","first_name":"L","last_name":"Bruneaux"},{"full_name":"Oikonomou, P","first_name":"P","last_name":"Oikonomou"},{"last_name":"Aldana","first_name":"M","full_name":"Aldana, M"},{"full_name":"Cluzel, P","first_name":"P","last_name":"Cluzel"}],"doi":"10.3389/fmicb.2023.1049255","pmid":1,"department":[{"_id":"CaGu"}],"ddc":["570"],"corr_author":"1","publication":"Frontiers in Microbiology","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"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>.","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).","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>","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>","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."},"scopus_import":"1","isi":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes","article_number":"1049255","title":"Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression","publication_identifier":{"eissn":["1664-302X"]},"date_updated":"2024-10-09T21:03:59Z","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."},{"oa":1,"year":"2023","volume":26,"date_published":"2023-10-20T00:00:00Z","file_date_updated":"2023-10-09T07:23:46Z","article_type":"original","publication_status":"published","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"}],"external_id":{"pmid":["37766992"],"isi":["001082331200001"]},"ec_funded":1,"oa_version":"Published Version","day":"20","month":"10","has_accepted_license":"1","date_created":"2023-02-02T10:50:17Z","author":[{"full_name":"Scarpetta, Silvia","last_name":"Scarpetta","first_name":"Silvia"},{"full_name":"Morrisi, Niccolò","first_name":"Niccolò","last_name":"Morrisi"},{"full_name":"Mutti, Carlotta","last_name":"Mutti","first_name":"Carlotta"},{"last_name":"Azzi","first_name":"Nicoletta","full_name":"Azzi, Nicoletta"},{"last_name":"Trippi","first_name":"Irene","full_name":"Trippi, Irene"},{"full_name":"Ciliento, Rosario","last_name":"Ciliento","first_name":"Rosario"},{"first_name":"Ilenia","last_name":"Apicella","full_name":"Apicella, Ilenia"},{"full_name":"Messuti, Giovanni","first_name":"Giovanni","last_name":"Messuti"},{"last_name":"Angiolelli","first_name":"Marianna","full_name":"Angiolelli, Marianna"},{"first_name":"Fabrizio","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249"},{"full_name":"Parrino, Liborio","first_name":"Liborio","last_name":"Parrino"},{"last_name":"Vaudano","first_name":"Anna Elisabetta","full_name":"Vaudano, Anna Elisabetta"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics"}],"doi":"10.1016/j.isci.2023.107840","intvolume":"        26","type":"journal_article","file":[{"file_id":"14412","relation":"main_file","success":1,"checksum":"f499836af172ecc9865de4bb41fa99d1","file_size":4872708,"access_level":"open_access","content_type":"application/pdf","date_created":"2023-10-09T07:23:46Z","file_name":"2023_iScience_Scarpetta.pdf","creator":"dernst","date_updated":"2023-10-09T07:23:46Z"}],"_id":"12487","publisher":"Elsevier","status":"public","publication":"iScience","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"page":"107840","citation":{"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.","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.","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>.","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>.","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.","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>","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>"},"scopus_import":"1","isi":1,"issue":"10","ddc":["570"],"pmid":1,"department":[{"_id":"GaTk"}],"title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","publication_identifier":{"eissn":["2589-0042"]},"date_updated":"2025-04-14T07:44:00Z","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.","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1"},{"status":"public","date_published":"2023-03-23T00:00:00Z","year":"2023","oa":1,"keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"citation":{"short":"L.M. Becker, P. Schanda, (2023).","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>.","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>.","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>.","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.","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>","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>"},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"related_material":{"record":[{"status":"public","id":"12675","relation":"used_in_publication"}]},"file_date_updated":"2023-03-24T09:42:03Z","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","corr_author":"1","ddc":["572"],"day":"23","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"has_accepted_license":"1","month":"03","date_created":"2023-02-03T08:08:02Z","author":[{"orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie","last_name":"Becker","first_name":"Lea Marie"},{"last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","date_updated":"2024-10-21T06:01:38Z","doi":"10.15479/AT:ISTA:12497","article_processing_charge":"No","type":"research_data","file":[{"file_id":"12743","relation":"main_file","checksum":"fd9a28620a81a82991fb70f4fd6591d9","access_level":"open_access","file_size":87018103,"content_type":"application/zip","date_created":"2023-03-23T10:03:16Z","file_name":"Research_Data.zip","creator":"lbecker","date_updated":"2023-03-24T09:34:20Z"},{"creator":"dernst","file_name":"README.txt","date_created":"2023-03-24T07:13:55Z","date_updated":"2023-03-24T09:42:03Z","file_id":"12755","relation":"main_file","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","access_level":"open_access","file_size":747,"content_type":"text/plain"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"contributor_type":"researcher","last_name":"Berbon","first_name":"Mélanie"},{"contributor_type":"researcher","last_name":"Vallet","first_name":"Alicia"},{"contributor_type":"researcher","last_name":"Grelard","first_name":"Axelle"},{"first_name":"Estelle","last_name":"Morvan","contributor_type":"researcher"},{"first_name":"Benjamin","last_name":"Bardiaux","contributor_type":"researcher"},{"first_name":"Roman","contributor_type":"researcher","last_name":"Lichtenecker"},{"last_name":"Ernst","contributor_type":"researcher","first_name":"Matthias"},{"contributor_type":"researcher","last_name":"Loquet","first_name":"Antoine"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","contributor_type":"contact_person"},{"first_name":"Lea Marie","contributor_type":"researcher","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151"}],"_id":"12497","publisher":"Institute of Science and Technology Austria"},{"issue":"1","ddc":["570"],"pmid":1,"department":[{"_id":"NiBa"}],"status":"public","scopus_import":"1","isi":1,"publication":"Evolution: International journal of organic evolution","citation":{"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.","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>.","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.","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>.","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>","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>","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."},"page":"318-328","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1558-5646"]},"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.","date_updated":"2026-06-18T17:26:56Z","title":"A multivariate view of the speciation continuum","article_processing_charge":"No","day":"01","external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"oa_version":"Published Version","month":"01","year":"2023","oa":1,"volume":77,"date_published":"2023-01-01T00:00:00Z","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","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."}],"publisher":"Oxford University Press","main_file_link":[{"url":"https://doi.org/10.1093/evolut/qpac004","open_access":"1"}],"_id":"12514","doi":"10.1093/evolut/qpac004","author":[{"last_name":"Bolnick","first_name":"Daniel I.","full_name":"Bolnick, Daniel I."},{"last_name":"Hund","first_name":"Amanda K.","full_name":"Hund, Amanda K."},{"full_name":"Nosil, Patrik","last_name":"Nosil","first_name":"Patrik"},{"last_name":"Peng","first_name":"Foen","full_name":"Peng, Foen"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Subramanian, Swapna","last_name":"Subramanian","first_name":"Swapna"},{"first_name":"Jochen B.W.","last_name":"Wolf","full_name":"Wolf, Jochen B.W."},{"full_name":"Yukilevich, Roman","first_name":"Roman","last_name":"Yukilevich"}],"date_created":"2023-02-05T23:00:59Z","type":"journal_article","intvolume":"        77"},{"doi":"10.3389/fnana.2022.1097467","date_created":"2023-02-05T23:01:00Z","author":[{"full_name":"Ortiz-Leal, Irene","first_name":"Irene","last_name":"Ortiz-Leal"},{"first_name":"Mateo V.","last_name":"Torres","full_name":"Torres, Mateo V."},{"first_name":"Victor M","last_name":"Vargas Barroso","full_name":"Vargas Barroso, Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fidalgo","first_name":"Luis Eusebio","full_name":"Fidalgo, Luis Eusebio"},{"full_name":"López-Beceiro, Ana María","last_name":"López-Beceiro","first_name":"Ana María"},{"full_name":"Larriva-Sahd, Jorge A.","first_name":"Jorge A.","last_name":"Larriva-Sahd"},{"first_name":"Pablo","last_name":"Sánchez-Quinteiro","full_name":"Sánchez-Quinteiro, Pablo"}],"type":"journal_article","intvolume":"        16","file":[{"file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf","date_created":"2023-02-06T07:56:14Z","creator":"dernst","date_updated":"2023-02-06T07:56:14Z","file_size":21943473,"access_level":"open_access","content_type":"application/pdf","file_id":"12518","checksum":"49cd40f3bda6f267079427042e7d15e3","relation":"main_file","success":1}],"publisher":"Frontiers","_id":"12515","oa":1,"year":"2023","date_published":"2023-01-10T00:00:00Z","volume":16,"article_type":"original","publication_status":"published","abstract":[{"text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.","lang":"eng"}],"file_date_updated":"2023-02-06T07:56:14Z","day":"10","external_id":{"isi":["000919786900001"],"pmid":["36704406"]},"oa_version":"Published Version","month":"01","has_accepted_license":"1","publication_identifier":{"eissn":["1662-5129"]},"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.","date_updated":"2023-08-16T11:37:52Z","title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","article_number":"1097467","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","scopus_import":"1","isi":1,"publication":"Frontiers in Neuroanatomy","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” <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>.","ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” <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>.","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.","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>","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>"},"ddc":["570"],"pmid":1,"department":[{"_id":"PeJo"}]},{"_id":"12534","publisher":"American Physical Society","file":[{"date_created":"2023-02-13T10:38:10Z","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","creator":"dernst","date_updated":"2023-02-13T10:38:10Z","file_id":"12546","relation":"main_file","success":1,"checksum":"6068b62874c0099628a108bb9c5c6bd2","file_size":865150,"access_level":"open_access","content_type":"application/pdf"}],"intvolume":"         5","type":"journal_article","author":[{"last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","first_name":"Alberto"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem"}],"date_created":"2023-02-10T09:02:26Z","doi":"10.1103/physrevresearch.5.013029","project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"month":"01","has_accepted_license":"1","ec_funded":1,"oa_version":"Published Version","day":"20","file_date_updated":"2023-02-13T10:38:10Z","article_type":"original","publication_status":"published","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"}],"year":"2023","oa":1,"volume":5,"date_published":"2023-01-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","article_number":"013029","title":"Dissipative dynamics of an impurity with spin-orbit coupling","publication_identifier":{"issn":["2643-1564"]},"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).","date_updated":"2025-04-14T07:48:54Z","department":[{"_id":"MiLe"}],"issue":"1","ddc":["530"],"corr_author":"1","publication":"Physical Review Research","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"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>.","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.","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>.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","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>","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>","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."},"scopus_import":"1","status":"public"},{"_id":"12542","publisher":"Elsevier","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2023.01.006","open_access":"1"}],"type":"journal_article","intvolume":"       111","date_created":"2023-02-12T23:00:58Z","author":[{"orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","last_name":"Villalba Requena","first_name":"Ana"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon"}],"doi":"10.1016/j.neuron.2023.01.006","month":"02","external_id":{"pmid":["36731425"],"isi":["000994473300001"]},"oa_version":"Published Version","OA_place":"publisher","day":"01","publication_status":"published","article_type":"letter_note","abstract":[{"lang":"eng","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."}],"oa":1,"year":"2023","volume":111,"date_published":"2023-02-01T00:00:00Z","OA_type":"free access","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","title":"Going back in time with TEMPO","publication_identifier":{"eissn":["1097-4199"]},"date_updated":"2026-06-18T17:27:44Z","pmid":1,"department":[{"_id":"SiHi"}],"issue":"3","corr_author":"1","ddc":["570"],"publication":"Neuron","citation":{"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>","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>","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.","short":"A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293.","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>.","ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293.","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>."},"page":"291-293","scopus_import":"1","isi":1,"status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Pathogen evasion of social immunity","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.","date_updated":"2025-04-14T07:47:53Z","publication_identifier":{"eissn":["2397-334X"]},"article_processing_charge":"No","ddc":["570"],"corr_author":"1","pmid":1,"department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"status":"public","page":"450-460","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” <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>.","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460.","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” <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>.","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.","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>","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>"},"publication":"Nature Ecology and Evolution","isi":1,"scopus_import":"1","file":[{"file_id":"14069","checksum":"8244f4650a0e7aeea488d1bcd4a31702","relation":"main_file","success":1,"file_size":1600499,"access_level":"open_access","content_type":"application/pdf","file_name":"2023_NatureEcoEvo_Stock.pdf","date_created":"2023-08-16T11:54:59Z","creator":"dernst","date_updated":"2023-08-16T11:54:59Z"}],"_id":"12543","publisher":"Springer Nature","author":[{"id":"42462816-F248-11E8-B48F-1D18A9856A87","full_name":"Stock, Miriam","last_name":"Stock","first_name":"Miriam"},{"orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","last_name":"Milutinovic","first_name":"Barbara"},{"full_name":"Hönigsberger, Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60","last_name":"Hönigsberger","first_name":"Michaela"},{"first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","last_name":"Wiesenhofer","full_name":"Wiesenhofer, Florian","id":"39523C54-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Niklas","last_name":"Kampleitner","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87","full_name":"Kampleitner, Niklas"},{"last_name":"Narasimhan","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","last_name":"Schmitt","full_name":"Schmitt, Thomas"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-02-12T23:00:59Z","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}],"doi":"10.1038/s41559-023-01981-6","type":"journal_article","intvolume":"         7","oa_version":"Published Version","external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"ec_funded":1,"day":"01","has_accepted_license":"1","month":"03","volume":7,"date_published":"2023-03-01T00:00:00Z","year":"2023","oa":1,"related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/"}]},"file_date_updated":"2023-08-16T11:54:59Z","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"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"article_type":"original","publication_status":"published"},{"abstract":[{"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.","lang":"eng"}],"publication_status":"published","article_type":"original","file_date_updated":"2023-08-16T12:21:13Z","date_published":"2023-02-13T00:00:00Z","volume":63,"year":"2023","oa":1,"has_accepted_license":"1","month":"02","day":"13","oa_version":"Published Version","external_id":{"pmid":["36638318"],"isi":["000920370700001"]},"ec_funded":1,"intvolume":"        63","type":"journal_article","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183"},{"grant_number":"Z00342","call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"doi":"10.1021/acs.jcim.2c01346","date_created":"2023-02-12T23:00:59Z","author":[{"last_name":"Koehl","first_name":"Patrice","full_name":"Koehl, Patrice"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan"},{"first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"publisher":"American Chemical Society","_id":"12544","file":[{"date_updated":"2023-08-16T12:21:13Z","date_created":"2023-08-16T12:21:13Z","file_name":"2023_JCIM_Koehl.pdf","creator":"dernst","checksum":"7d20562269edff1e31b9d6019d4983b0","relation":"main_file","success":1,"file_id":"14070","content_type":"application/pdf","file_size":8069223,"access_level":"open_access"}],"isi":1,"scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"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>","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>","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.","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","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>.","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>.","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."},"page":"973-985","publication":"Journal of Chemical Information and Modeling","status":"public","pmid":1,"department":[{"_id":"HeEd"}],"ddc":["510","540"],"corr_author":"1","issue":"3","article_processing_charge":"No","date_updated":"2025-04-15T07:16:52Z","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_identifier":{"eissn":["1549-960X"],"issn":["1549-9596"]},"title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"year":"2023","date_published":"2023-01-24T00:00:00Z","volume":107,"arxiv":1,"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front."}],"day":"24","external_id":{"pmid":["36797971"],"isi":["000963909800006"],"arxiv":["2301.01856"]},"oa_version":"Preprint","month":"01","doi":"10.1103/PhysRevE.107.014608","author":[{"last_name":"Rojas Vega","first_name":"Mauricio Nicolas","full_name":"Rojas Vega, Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d"},{"last_name":"De Castro","first_name":"Pablo","full_name":"De Castro, Pablo"},{"first_name":"Rodrigo","last_name":"Soto","full_name":"Soto, Rodrigo"}],"date_created":"2023-02-12T23:00:59Z","type":"journal_article","intvolume":"       107","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01856"}],"publisher":"American Physical Society","_id":"12545","status":"public","scopus_import":"1","isi":1,"publication":"Physical Review E","citation":{"chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">https://doi.org/10.1103/PhysRevE.107.014608</a>.","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608.","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” <i>Physical Review E</i>, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">10.1103/PhysRevE.107.014608</a>.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. <i>Physical Review E</i>. 2023;107(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">10.1103/PhysRevE.107.014608</a>","apa":"Rojas Vega, M. N., De Castro, P., &#38; Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">https://doi.org/10.1103/PhysRevE.107.014608</a>","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” <i>Physical Review E</i>, vol. 107, no. 1. American Physical Society, 2023."},"issue":"1","pmid":1,"department":[{"_id":"GradSch"}],"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","date_updated":"2025-03-06T14:01:47Z","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","article_number":"014608","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"oa_version":"None","external_id":{"pmid":["36695533"],"isi":["000957721600001"]},"day":"01","month":"03","date_published":"2023-03-01T00:00:00Z","volume":129,"year":"2023","abstract":[{"text":"Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons.","lang":"eng"}],"publication_status":"published","article_type":"original","_id":"12562","publisher":"American Physiological Society","date_created":"2023-02-15T14:46:14Z","author":[{"last_name":"Ladle","first_name":"David R.","full_name":"Ladle, David R."},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1152/jn.00172.2022","intvolume":"       129","type":"journal_article","issue":"3","pmid":1,"department":[{"_id":"SiHi"}],"status":"public","keyword":["Physiology","General Neuroscience"],"citation":{"short":"D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.","chicago":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” <i>Journal of Neurophysiology</i>. American Physiological Society, 2023. <a href=\"https://doi.org/10.1152/jn.00172.2022\">https://doi.org/10.1152/jn.00172.2022</a>.","mla":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” <i>Journal of Neurophysiology</i>, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:<a href=\"https://doi.org/10.1152/jn.00172.2022\">10.1152/jn.00172.2022</a>.","ista":"Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512.","apa":"Ladle, D. R., &#38; Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. <i>Journal of Neurophysiology</i>. American Physiological Society. <a href=\"https://doi.org/10.1152/jn.00172.2022\">https://doi.org/10.1152/jn.00172.2022</a>","ama":"Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. <i>Journal of Neurophysiology</i>. 2023;129(3):501-512. doi:<a href=\"https://doi.org/10.1152/jn.00172.2022\">10.1152/jn.00172.2022</a>","ieee":"D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” <i>Journal of Neurophysiology</i>, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023."},"page":"501-512","publication":"Journal of Neurophysiology","isi":1,"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","title":"Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons","acknowledgement":"The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University.","date_updated":"2024-10-21T06:01:28Z","publication_identifier":{"issn":["0022-3077"],"eissn":["1522-1598"]},"article_processing_charge":"No"},{"_id":"12563","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2003.11351"}],"publisher":"Society for Industrial and Applied Mathematics","intvolume":"        52","type":"journal_article","author":[{"last_name":"Krokhin","first_name":"Andrei","full_name":"Krokhin, Andrei"},{"full_name":"Opršal, Jakub","id":"ec596741-c539-11ec-b829-c79322a91242","orcid":"0000-0003-1245-3456","first_name":"Jakub","last_name":"Opršal"},{"first_name":"Marcin","last_name":"Wrochna","full_name":"Wrochna, Marcin"},{"full_name":"Živný, Stanislav","first_name":"Stanislav","last_name":"Živný"}],"date_created":"2023-02-16T07:03:52Z","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"doi":"10.1137/20m1378223","month":"01","external_id":{"isi":["000955000000001"],"arxiv":["2003.11351"]},"ec_funded":1,"oa_version":"Preprint","day":"01","publication_status":"published","article_type":"original","abstract":[{"text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems.","lang":"eng"}],"arxiv":1,"year":"2023","oa":1,"volume":52,"date_published":"2023-01-01T00:00:00Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","title":"Topology and adjunction in promise constraint satisfaction","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","date_updated":"2025-05-14T10:51:32Z","department":[{"_id":"UlWa"}],"issue":"1","publication":"SIAM Journal on Computing","citation":{"ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. <i>SIAM Journal on Computing</i>. 2023;52(1):38-79. doi:<a href=\"https://doi.org/10.1137/20m1378223\">10.1137/20m1378223</a>","apa":"Krokhin, A., Opršal, J., Wrochna, M., &#38; Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20m1378223\">https://doi.org/10.1137/20m1378223</a>","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” <i>SIAM Journal on Computing</i>, vol. 52, no. 1. Society for Industrial and Applied Mathematics, pp. 38–79, 2023.","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/20m1378223\">https://doi.org/10.1137/20m1378223</a>.","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” <i>SIAM Journal on Computing</i>, vol. 52, no. 1, Society for Industrial and Applied Mathematics, 2023, pp. 38–79, doi:<a href=\"https://doi.org/10.1137/20m1378223\">10.1137/20m1378223</a>."},"page":"38-79","scopus_import":"1","isi":1,"keyword":["General Mathematics","General Computer Science"],"status":"public"},{"article_number":"113733","article_processing_charge":"Yes (via OA deal)","date_updated":"2025-04-14T07:49:16Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","publication_identifier":{"issn":["0304-3975"]},"title":"Wait-free approximate agreement on graphs","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. <i>Theoretical Computer Science</i>. 2023;948(2). doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">10.1016/j.tcs.2023.113733</a>","apa":"Alistarh, D.-A., Ellen, F., &#38; Rybicki, J. (2023). Wait-free approximate agreement on graphs. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">https://doi.org/10.1016/j.tcs.2023.113733</a>","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” <i>Theoretical Computer Science</i>, vol. 948, no. 2. Elsevier, 2023.","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” <i>Theoretical Computer Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">https://doi.org/10.1016/j.tcs.2023.113733</a>.","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” <i>Theoretical Computer Science</i>, vol. 948, no. 2, 113733, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">10.1016/j.tcs.2023.113733</a>.","ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023)."},"publication":"Theoretical Computer Science","status":"public","department":[{"_id":"DaAl"}],"corr_author":"1","ddc":["000"],"issue":"2","intvolume":"       948","type":"journal_article","project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"},{"call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605"}],"doi":"10.1016/j.tcs.2023.113733","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Ellen, Faith","last_name":"Ellen","first_name":"Faith"},{"orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","last_name":"Rybicki","first_name":"Joel"}],"date_created":"2023-02-19T23:00:55Z","publisher":"Elsevier","_id":"12566","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":602333,"relation":"main_file","success":1,"checksum":"b27c5290f2f1500c403494364ee39c9f","file_id":"12570","date_updated":"2023-02-20T07:30:20Z","creator":"dernst","date_created":"2023-02-20T07:30:20Z","file_name":"2023_TheoreticalCompScience_Alistarh.pdf"}],"abstract":[{"lang":"eng","text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among  processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs."}],"publication_status":"published","article_type":"original","file_date_updated":"2023-02-20T07:30:20Z","volume":948,"date_published":"2023-02-28T00:00:00Z","oa":1,"year":"2023","has_accepted_license":"1","month":"02","day":"28","oa_version":"Published Version","ec_funded":1,"external_id":{"isi":["000934262700001"]}},{"file":[{"content_type":"application/pdf","access_level":"open_access","file_size":2823025,"success":1,"checksum":"69a35dcd3e0249f902ab881b06ee2e58","relation":"main_file","file_id":"12569","date_updated":"2023-02-20T07:09:27Z","creator":"dernst","file_name":"2023_IJMS_Mrestani.pdf","date_created":"2023-02-20T07:09:27Z"}],"publisher":"MDPI","_id":"12567","doi":"10.3390/ijms24032128","date_created":"2023-02-19T23:00:56Z","author":[{"last_name":"Mrestani","first_name":"Achmed","full_name":"Mrestani, Achmed"},{"last_name":"Lichter","first_name":"Katharina","orcid":"0000-0002-1485-0351","full_name":"Lichter, Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d"},{"last_name":"Sirén","first_name":"Anna Leena","full_name":"Sirén, Anna Leena"},{"first_name":"Manfred","last_name":"Heckmann","full_name":"Heckmann, Manfred"},{"full_name":"Paul, Mila M.","first_name":"Mila M.","last_name":"Paul"},{"last_name":"Pauli","first_name":"Martin","full_name":"Pauli, Martin"}],"type":"journal_article","intvolume":"        24","day":"21","oa_version":"Published Version","external_id":{"isi":["000930324700001"],"pmid":["36768451"]},"has_accepted_license":"1","month":"01","volume":24,"date_published":"2023-01-21T00:00:00Z","oa":1,"year":"2023","abstract":[{"lang":"eng","text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations."}],"article_type":"original","publication_status":"published","file_date_updated":"2023-02-20T07:09:27Z","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","date_updated":"2025-04-23T08:48:27Z","publication_identifier":{"eissn":["1422-0067"]},"title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","article_number":"2128","article_processing_charge":"No","ddc":["570"],"issue":"3","pmid":1,"department":[{"_id":"PeJo"}],"status":"public","isi":1,"scopus_import":"1","citation":{"mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 3, 2128, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/ijms24032128\">10.3390/ijms24032128</a>.","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” <i>International Journal of Molecular Sciences</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/ijms24032128\">https://doi.org/10.3390/ijms24032128</a>.","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 3. MDPI, 2023.","ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. <i>International Journal of Molecular Sciences</i>. 2023;24(3). doi:<a href=\"https://doi.org/10.3390/ijms24032128\">10.3390/ijms24032128</a>","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., &#38; Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms24032128\">https://doi.org/10.3390/ijms24032128</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"International Journal of Molecular Sciences"},{"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","OA_type":"green","title":"Cross-client label propagation for transductive and semi-supervised federated learning","date_updated":"2025-02-04T08:32:19Z","publication_identifier":{"issn":["2835-8856"]},"article_processing_charge":"No","corr_author":"1","ddc":["004"],"department":[{"_id":"ChLa"}],"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Scott JA, Yeo MX, Lampert C. Cross-client label propagation for transductive and semi-supervised federated learning. In: <i>Transactions in Machine Learning</i>. Curran Associates; 2023.","apa":"Scott, J. A., Yeo, M. X., &#38; Lampert, C. (2023). Cross-client label propagation for transductive and semi-supervised federated learning. In <i>Transactions in Machine Learning</i>. Curran Associates.","ieee":"J. A. Scott, M. X. Yeo, and C. Lampert, “Cross-client label propagation for transductive and semi-supervised federated learning,” in <i>Transactions in Machine Learning</i>, 2023.","short":"J.A. Scott, M.X. Yeo, C. Lampert, in:, Transactions in Machine Learning, Curran Associates, 2023.","chicago":"Scott, Jonathan A, Michelle X Yeo, and Christoph Lampert. “Cross-Client Label Propagation for Transductive and Semi-Supervised Federated Learning.” In <i>Transactions in Machine Learning</i>. Curran Associates, 2023.","ista":"Scott JA, Yeo MX, Lampert C. 2023. Cross-client label propagation for transductive and semi-supervised federated learning. Transactions in Machine Learning. , TMLR, .","mla":"Scott, Jonathan A., et al. “Cross-Client Label Propagation for Transductive and Semi-Supervised Federated Learning.” <i>Transactions in Machine Learning</i>, Curran Associates, 2023."},"publication":"Transactions in Machine Learning","file":[{"file_id":"18990","success":1,"checksum":"aa322ad91cbd229f5cafe6733a119bd1","relation":"main_file","access_level":"open_access","file_size":553717,"content_type":"application/pdf","creator":"dernst","date_created":"2025-02-04T08:30:05Z","file_name":"2023_TMLR_Scott.pdf","date_updated":"2025-02-04T08:30:05Z"}],"_id":"12660","publisher":"Curran Associates","author":[{"full_name":"Scott, Jonathan A","id":"e499926b-f6e0-11ea-865d-9c63db0031e8","first_name":"Jonathan A","last_name":"Scott"},{"orcid":"0009-0001-3676-4809","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo","first_name":"Michelle X"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph"}],"date_created":"2023-02-20T08:21:50Z","type":"conference","oa_version":"Preprint","external_id":{"arxiv":["2210.06434"]},"day":"27","OA_place":"repository","has_accepted_license":"1","month":"11","alternative_title":["TMLR"],"arxiv":1,"date_published":"2023-11-27T00:00:00Z","year":"2023","oa":1,"related_material":{"link":[{"url":"https://github.com/jonnyascott/xclp","relation":"software"}]},"file_date_updated":"2025-02-04T08:30:05Z","abstract":[{"text":"We present Cross-Client Label Propagation(XCLP), a new method for transductive federated learning. XCLP estimates a data graph jointly from the data of multiple clients and computes labels for the unlabeled data by propagating label information across the graph. To avoid clients having to share their data with anyone, XCLP employs two cryptographically secure protocols: secure Hamming distance computation and secure summation. We demonstrate two distinct applications of XCLP within federated learning. In the first, we use it in a one-shot way to predict labels for unseen test points. In the second, we use it to repeatedly pseudo-label unlabeled training data in a federated semi-supervised setting. Experiments on both real federated and standard benchmark datasets show that in both applications XCLP achieves higher classification accuracy than alternative approaches.","lang":"eng"}],"publication_status":"published"},{"month":"01","extern":"1","external_id":{"pmid":["36639687"]},"oa_version":"Published Version","day":"13","publication_status":"published","article_type":"original","abstract":[{"text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.","lang":"eng"}],"oa":1,"year":"2023","volume":24,"date_published":"2023-01-13T00:00:00Z","_id":"12668","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"publisher":"Springer Nature","type":"journal_article","intvolume":"        24","date_created":"2023-02-23T09:13:49Z","author":[{"full_name":"Zhao, Long","last_name":"Zhao","first_name":"Long"},{"full_name":"Yang, Yiman","last_name":"Yang","first_name":"Yiman"},{"first_name":"Jinchao","last_name":"Chen","full_name":"Chen, Jinchao"},{"last_name":"Lin","first_name":"Xuelei","full_name":"Lin, Xuelei"},{"first_name":"Hao","last_name":"Zhang","full_name":"Zhang, Hao"},{"full_name":"Wang, Hao","last_name":"Wang","first_name":"Hao"},{"last_name":"Wang","first_name":"Hongzhe","full_name":"Wang, Hongzhe"},{"full_name":"Bie, Xiaomin","first_name":"Xiaomin","last_name":"Bie"},{"full_name":"Jiang, Jiafu","first_name":"Jiafu","last_name":"Jiang"},{"first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234"},{"last_name":"Fu","first_name":"Xiangdong","full_name":"Fu, Xiangdong"},{"full_name":"Zhang, Xiansheng","first_name":"Xiansheng","last_name":"Zhang"},{"full_name":"Du, Zhuo","first_name":"Zhuo","last_name":"Du"},{"last_name":"Xiao","first_name":"Jun","full_name":"Xiao, Jun"}],"doi":"10.1186/s13059-022-02844-2","department":[{"_id":"XiFe"}],"pmid":1,"publication":"Genome Biology","citation":{"ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. 2023;24. doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>","ieee":"L. Zhao <i>et al.</i>, “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” <i>Genome Biology</i>, vol. 24. Springer Nature, 2023.","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>.","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>, vol. 24, 7, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>.","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7."},"scopus_import":"1","status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","article_number":"7","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","publication_identifier":{"issn":["1474-760X"]},"date_updated":"2023-05-08T10:52:49Z"}]