[{"publisher":"Elsevier","_id":"12172","doi":"10.1016/j.matpr.2022.11.037","date_created":"2023-01-12T12:11:26Z","author":[{"full_name":"Khatoon, Bushra","last_name":"Khatoon","first_name":"Bushra"},{"first_name":"Shoaib","last_name":"Kamil","full_name":"Kamil, Shoaib","id":"185a19af-dc7d-11ea-9b2f-8eb2201959e9"},{"full_name":"Babu, Hitesh","first_name":"Hitesh","last_name":"Babu"},{"full_name":"Siraj Alam, M.","last_name":"Siraj Alam","first_name":"M."}],"intvolume":"        78","type":"journal_article","day":"20","oa_version":"None","month":"03","year":"2023","volume":78,"date_published":"2023-03-20T00:00:00Z","publication_status":"published","article_type":"original","abstract":[{"text":"In industrial reactors and equipment, non-ideality is quite a common phenomenon rather than an exception. These deviations from ideality impact the process's overall efficiency and the effectiveness of the equipment. To recognize the associated non-ideality, one needs to have enough understanding of the formulation of the equations and in-depth knowledge of the residence time distribution (RTD) data of real reactors. In the current work, step input and pulse input were used to create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the aforementioned configuration, experiments were run at various flow rates to validate the developed characteristic equations. To produce RTD data, distilled water was utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior of tracer concentration exits age distribution, and cumulative fraction for each setup and each input was plotted and experimental results were compared with perfect behavior. Deviation of concentration exit age distribution and cumulative fractional distribution from ideal behavior is more in pulse input as compared to a step input. For ideal cases, the exit age distribution curve and cumulative fraction curves are independent of the type of input. But a significant difference was observed for the two cases, which may be due to non-measurable fluctuations in volumetric flow rate, non-achievement of instant injection of tracer in case of pulse input, and slight variations in the sampling period. Further, with increasing flow rate, concentration, exit age, and cumulative fractional curves shifted upward, and this behavior matches with the actual case.","lang":"eng"}],"quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2214-7853"]},"date_updated":"2023-08-16T09:08:11Z","title":"Experimental analysis of Cascade CSTRs with step and pulse inputs","article_processing_charge":"No","issue":"Part 1","department":[{"_id":"BjHo"}],"keyword":["General Medicine"],"status":"public","scopus_import":"1","publication":"Materials Today: Proceedings","page":"40-47","citation":{"apa":"Khatoon, B., Kamil, S., Babu, H., &#38; Siraj Alam, M. (2023). Experimental analysis of Cascade CSTRs with step and pulse inputs. <i>Materials Today: Proceedings</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpr.2022.11.037\">https://doi.org/10.1016/j.matpr.2022.11.037</a>","ama":"Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade CSTRs with step and pulse inputs. <i>Materials Today: Proceedings</i>. 2023;78(Part 1):40-47. doi:<a href=\"https://doi.org/10.1016/j.matpr.2022.11.037\">10.1016/j.matpr.2022.11.037</a>","ieee":"B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis of Cascade CSTRs with step and pulse inputs,” <i>Materials Today: Proceedings</i>, vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.","short":"B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings 78 (2023) 40–47.","chicago":"Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” <i>Materials Today: Proceedings</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.matpr.2022.11.037\">https://doi.org/10.1016/j.matpr.2022.11.037</a>.","ista":"Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part 1), 40–47.","mla":"Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” <i>Materials Today: Proceedings</i>, vol. 78, no. Part 1, Elsevier, 2023, pp. 40–47, doi:<a href=\"https://doi.org/10.1016/j.matpr.2022.11.037\">10.1016/j.matpr.2022.11.037</a>."}},{"article_processing_charge":"No","date_updated":"2025-04-14T07:26:59Z","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged.","publication_identifier":{"issn":["1424-0637"]},"title":"The Bose Gas in a box with Neumann boundary conditions","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","page":"1505-1560","citation":{"short":"C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.","chicago":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” <i>Annales Henri Poincare</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00023-022-01252-3\">https://doi.org/10.1007/s00023-022-01252-3</a>.","ista":"Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 1505–1560.","mla":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” <i>Annales Henri Poincare</i>, vol. 24, Springer Nature, 2023, pp. 1505–60, doi:<a href=\"https://doi.org/10.1007/s00023-022-01252-3\">10.1007/s00023-022-01252-3</a>.","ama":"Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions. <i>Annales Henri Poincare</i>. 2023;24:1505-1560. doi:<a href=\"https://doi.org/10.1007/s00023-022-01252-3\">10.1007/s00023-022-01252-3</a>","apa":"Boccato, C., &#38; Seiringer, R. (2023). The Bose Gas in a box with Neumann boundary conditions. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-022-01252-3\">https://doi.org/10.1007/s00023-022-01252-3</a>","ieee":"C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary conditions,” <i>Annales Henri Poincare</i>, vol. 24. Springer Nature, pp. 1505–1560, 2023."},"publication":"Annales Henri Poincare","status":"public","department":[{"_id":"RoSe"}],"corr_author":"1","intvolume":"        24","type":"journal_article","doi":"10.1007/s00023-022-01252-3","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"}],"author":[{"full_name":"Boccato, Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","last_name":"Boccato","first_name":"Chiara"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"date_created":"2023-01-15T23:00:52Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.15284"}],"publisher":"Springer Nature","_id":"12183","abstract":[{"lang":"eng","text":"We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii regime, with an optimal bound on the condensate depletion. Moreover, our lower bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann bracketing) a lower bound for the ground state energy of N bosons in a large box [−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit."}],"publication_status":"published","article_type":"original","volume":24,"date_published":"2023-05-01T00:00:00Z","oa":1,"year":"2023","arxiv":1,"month":"05","day":"01","oa_version":"Preprint","external_id":{"arxiv":["2205.15284"],"isi":["000910751800002"]},"ec_funded":1},{"ddc":["610"],"license":"https://creativecommons.org/licenses/by/4.0/","pmid":1,"department":[{"_id":"JoDa"}],"status":"public","keyword":["Oncology","Surgery"],"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":"35-45","citation":{"chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of Surgical Oncology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1245/s10434-022-12459-3\">https://doi.org/10.1245/s10434-022-12459-3</a>.","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.","mla":"Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of Surgical Oncology</i>, vol. 30, Springer Nature, 2023, pp. 35–45, doi:<a href=\"https://doi.org/10.1245/s10434-022-12459-3\">10.1245/s10434-022-12459-3</a>.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 35–45.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. <i>Annals of Surgical Oncology</i>. Springer Nature. <a href=\"https://doi.org/10.1245/s10434-022-12459-3\">https://doi.org/10.1245/s10434-022-12459-3</a>","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. <i>Annals of Surgical Oncology</i>. 2023;30:35-45. doi:<a href=\"https://doi.org/10.1245/s10434-022-12459-3\">10.1245/s10434-022-12459-3</a>","ieee":"J. Glajzer <i>et al.</i>, “Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” <i>Annals of Surgical Oncology</i>, vol. 30. Springer Nature, pp. 35–45, 2023."},"publication":"Annals of Surgical Oncology","isi":1,"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium","date_updated":"2026-06-18T17:21:24Z","acknowledgement":"E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin Berlin and the Berlin Institute of Health. This work was supported by European Commission’s Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen Access funding enabled and organized by Projekt DEAL.","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"article_processing_charge":"No","oa_version":"Published Version","external_id":{"isi":["000852125500006"],"pmid":["36085390"]},"day":"01","has_accepted_license":"1","month":"01","volume":30,"date_published":"2023-01-01T00:00:00Z","oa":1,"year":"2023","related_material":{"record":[{"relation":"other","status":"public","id":"12115"}]},"file_date_updated":"2023-02-02T13:01:20Z","abstract":[{"text":"Background: This study seeks to evaluate the impact of breast cancer (BRCA) gene status on tumor dissemination pattern, surgical outcome and survival in a multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data from 190 patients were gathered retrospectively. All patients had surgery at pOC and at least one further rOC surgery at four European high-volume centers. Patients were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut) and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor presentation, surgical outcome and survival data were analyzed between the two groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years younger and had significantly more tumor involvement upon diagnosis. Patients with BRCAmut disease showed higher debulking rates at all stages. Multivariate analysis showed that only patient age had significant predictive value for complete tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated with optimal debulking. Patients with BRCAmut disease showed significantly prolonged overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged in the BRCAmut group at all stages as well, reaching statistical significance during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a more aggressive course of disease with earlier onset and more extensive tumor dissemination at pOC. However, surgical outcome and OS were significantly better in patients with BRCAmut disease compared with patients with BRCAwt disease. We therefore propose to consider BRCAmut status in regard to patient selection for cytoreductive surgery, especially in rOC.","lang":"eng"}],"article_type":"original","publication_status":"published","file":[{"creator":"dernst","date_created":"2023-02-02T13:01:20Z","file_name":"2023_AnnalsSurgicalOncology_Glajzer.pdf","date_updated":"2023-02-02T13:01:20Z","access_level":"open_access","file_size":365865,"content_type":"application/pdf","file_id":"12490","relation":"main_file","success":1,"checksum":"36a1200e1011f4b2155a8041d0308f34"}],"_id":"12205","publisher":"Springer Nature","author":[{"full_name":"Glajzer, Jacek","last_name":"Glajzer","first_name":"Jacek"},{"last_name":"Castillo-Tong","first_name":"Dan Cacsire","full_name":"Castillo-Tong, Dan Cacsire"},{"last_name":"Richter","first_name":"Rolf","full_name":"Richter, Rolf"},{"full_name":"Vergote, Ignace","last_name":"Vergote","first_name":"Ignace"},{"last_name":"Kulbe","first_name":"Hagen","full_name":"Kulbe, Hagen"},{"last_name":"Vanderstichele","first_name":"Adriaan","full_name":"Vanderstichele, Adriaan"},{"full_name":"Ruscito, Ilary","last_name":"Ruscito","first_name":"Ilary"},{"first_name":"Fabian","last_name":"Trillsch","full_name":"Trillsch, Fabian"},{"full_name":"Mustea, Alexander","first_name":"Alexander","last_name":"Mustea"},{"last_name":"Kreuzinger","first_name":"Caroline","full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gourley, Charlie","last_name":"Gourley","first_name":"Charlie"},{"first_name":"Hani","last_name":"Gabra","full_name":"Gabra, Hani"},{"last_name":"Taube","first_name":"Eliane T.","full_name":"Taube, Eliane T."},{"full_name":"Dorigo, Oliver","first_name":"Oliver","last_name":"Dorigo"},{"last_name":"Horst","first_name":"David","full_name":"Horst, David"},{"first_name":"Carlotta","last_name":"Keunecke","full_name":"Keunecke, Carlotta"},{"last_name":"Baum","first_name":"Joanna","full_name":"Baum, Joanna"},{"last_name":"Angelotti","first_name":"Timothy","full_name":"Angelotti, Timothy"},{"full_name":"Sehouli, Jalid","first_name":"Jalid","last_name":"Sehouli"},{"full_name":"Braicu, Elena Ioana","first_name":"Elena Ioana","last_name":"Braicu"}],"date_created":"2023-01-16T09:44:36Z","doi":"10.1245/s10434-022-12459-3","intvolume":"        30","type":"journal_article"},{"citation":{"short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete &#38; Computational Geometry 69 (2023) 156–191.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete &#38; Computational Geometry. 69, 156–191.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” <i>Discrete &#38; Computational Geometry</i>, vol. 69, Springer Nature, 2023, pp. 156–91, doi:<a href=\"https://doi.org/10.1007/s00454-022-00431-7\">10.1007/s00454-022-00431-7</a>.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-022-00431-7\">https://doi.org/10.1007/s00454-022-00431-7</a>.","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” <i>Discrete &#38; Computational Geometry</i>, vol. 69. Springer Nature, pp. 156–191, 2023.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., &#38; Wintraecken, M. (2023). Local criteria for triangulating general manifolds. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00431-7\">https://doi.org/10.1007/s00454-022-00431-7</a>","ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. <i>Discrete &#38; Computational Geometry</i>. 2023;69:156-191. doi:<a href=\"https://doi.org/10.1007/s00454-022-00431-7\">10.1007/s00454-022-00431-7</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"},"page":"156-191","publication":"Discrete & Computational Geometry","isi":1,"scopus_import":"1","status":"public","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"department":[{"_id":"HeEd"}],"ddc":["510"],"corr_author":"1","article_processing_charge":"No","title":"Local criteria for triangulating general manifolds","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","date_updated":"2025-04-14T07:44:00Z","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2023-02-02T11:01:10Z","abstract":[{"text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use.","lang":"eng"}],"article_type":"original","publication_status":"published","volume":69,"date_published":"2023-01-01T00:00:00Z","year":"2023","oa":1,"has_accepted_license":"1","month":"01","oa_version":"Published Version","external_id":{"isi":["000862193600001"]},"ec_funded":1,"day":"01","intvolume":"        69","type":"journal_article","author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"full_name":"Dyer, Ramsay","last_name":"Dyer","first_name":"Ramsay"},{"full_name":"Ghosh, Arijit","first_name":"Arijit","last_name":"Ghosh"},{"first_name":"Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220"}],"date_created":"2023-01-16T10:04:06Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses","grant_number":"M03073"}],"doi":"10.1007/s00454-022-00431-7","_id":"12287","publisher":"Springer Nature","file":[{"date_updated":"2023-02-02T11:01:10Z","file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","date_created":"2023-02-02T11:01:10Z","creator":"dernst","content_type":"application/pdf","file_size":582850,"access_level":"open_access","relation":"main_file","checksum":"46352e0ee71e460848f88685ca852681","success":1,"file_id":"12488"}]},{"date_published":"2023-01-10T00:00:00Z","volume":13,"year":"2023","oa":1,"file_date_updated":"2023-01-23T07:53:23Z","abstract":[{"lang":"eng","text":"In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection."}],"article_type":"original","publication_status":"published","oa_version":"Published Version","external_id":{"isi":["001003345000051"]},"day":"10","has_accepted_license":"1","month":"01","date_created":"2023-01-22T23:00:55Z","author":[{"first_name":"Arturo","last_name":"Gómez","full_name":"Gómez, Arturo"},{"full_name":"Oliveira, Goncalo","id":"58abbde8-f455-11eb-a497-98c8fd71b905","first_name":"Goncalo","last_name":"Oliveira"}],"doi":"10.1038/s41598-022-19827-9","intvolume":"        13","type":"journal_article","file":[{"file_id":"12336","checksum":"a8b83739f4a951e83e0b2a778f03b327","success":1,"relation":"main_file","file_size":2167792,"access_level":"open_access","content_type":"application/pdf","date_created":"2023-01-23T07:53:23Z","file_name":"2023_ScientificReports_Gomez.pdf","creator":"dernst","date_updated":"2023-01-23T07:53:23Z"}],"_id":"12329","publisher":"Springer Nature","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":{"apa":"Gómez, A., &#38; Oliveira, G. (2023). New approaches to epidemic modeling on networks. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-19827-9\">https://doi.org/10.1038/s41598-022-19827-9</a>","ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. <i>Scientific Reports</i>. 2023;13. doi:<a href=\"https://doi.org/10.1038/s41598-022-19827-9\">10.1038/s41598-022-19827-9</a>","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” <i>Scientific Reports</i>, vol. 13. Springer Nature, 2023.","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-022-19827-9\">https://doi.org/10.1038/s41598-022-19827-9</a>.","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” <i>Scientific Reports</i>, vol. 13, 468, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-022-19827-9\">10.1038/s41598-022-19827-9</a>."},"publication":"Scientific Reports","isi":1,"scopus_import":"1","corr_author":"1","ddc":["510"],"department":[{"_id":"TaHa"}],"title":"New approaches to epidemic modeling on networks","date_updated":"2024-10-09T21:03:29Z","acknowledgement":"Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira 1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.","publication_identifier":{"eissn":["2045-2322"]},"article_processing_charge":"No","article_number":"468","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"quality_controlled":"1"},{"publication_status":"published","article_type":"original","abstract":[{"text":"The design and implementation of efficient concurrent data structures has seen significant attention. However, most of this work has focused on concurrent data structures providing good worst-case guarantees, although, in real workloads, objects are often accessed at different rates. Efficient distribution-adaptive data structures, such as splay-trees, are known in the sequential case; however, they often are hard to translate efficiently to the concurrent case. We investigate distribution-adaptive concurrent data structures, and propose a new design called the splay-list. At a high level, the splay-list is similar to a standard skip-list, with the key distinction that the height of each element adapts dynamically to its access rate: popular elements “move up,” whereas rarely-accessed elements decrease in height. We show that the splay-list provides order-optimal amortized complexity bounds for a subset of operations, while being amenable to efficient concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity for performance, and can outperform the only previously-known distribution-adaptive concurrent design in certain workloads.","lang":"eng"}],"arxiv":1,"year":"2023","oa":1,"volume":36,"date_published":"2023-09-01T00:00:00Z","month":"09","external_id":{"arxiv":["2008.01009"],"isi":["000913424000001"]},"oa_version":"Preprint","day":"01","type":"journal_article","intvolume":"        36","date_created":"2023-01-22T23:00:55Z","author":[{"first_name":"Vitalii","last_name":"Aksenov","full_name":"Aksenov, Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"last_name":"Drozdova","first_name":"Alexandra","full_name":"Drozdova, Alexandra"},{"last_name":"Mohtashami","first_name":"Amirkeivan","full_name":"Mohtashami, Amirkeivan"}],"doi":"10.1007/s00446-022-00441-x","_id":"12330","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2008.01009","open_access":"1"}],"publisher":"Springer Nature","publication":"Distributed Computing","citation":{"chicago":"Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” <i>Distributed Computing</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00446-022-00441-x\">https://doi.org/10.1007/s00446-022-00441-x</a>.","ista":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.","mla":"Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” <i>Distributed Computing</i>, vol. 36, Springer Nature, 2023, pp. 395–418, doi:<a href=\"https://doi.org/10.1007/s00446-022-00441-x\">10.1007/s00446-022-00441-x</a>.","short":"V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing 36 (2023) 395–418.","apa":"Aksenov, V., Alistarh, D.-A., Drozdova, A., &#38; Mohtashami, A. (2023). The splay-list: A distribution-adaptive concurrent skip-list. <i>Distributed Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00446-022-00441-x\">https://doi.org/10.1007/s00446-022-00441-x</a>","ama":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive concurrent skip-list. <i>Distributed Computing</i>. 2023;36:395-418. doi:<a href=\"https://doi.org/10.1007/s00446-022-00441-x\">10.1007/s00446-022-00441-x</a>","ieee":"V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list: A distribution-adaptive concurrent skip-list,” <i>Distributed Computing</i>, vol. 36. Springer Nature, pp. 395–418, 2023."},"page":"395-418","scopus_import":"1","isi":1,"status":"public","department":[{"_id":"DaAl"}],"article_processing_charge":"No","title":"The splay-list: A distribution-adaptive concurrent skip-list","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"date_updated":"2023-08-14T12:54:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1"},{"file":[{"date_updated":"2023-08-14T12:57:25Z","creator":"dernst","file_name":"2023_ChemistryMaterials_Wang.pdf","date_created":"2023-08-14T12:57:25Z","content_type":"application/pdf","access_level":"open_access","file_size":2961043,"success":1,"relation":"main_file","checksum":"b21dca2aa7a80c068bc256bdd1fea9df","file_id":"14055"}],"_id":"12331","publisher":"American Chemical Society","date_created":"2023-01-22T23:00:55Z","author":[{"last_name":"Wang","first_name":"Siqi","full_name":"Wang, Siqi"},{"orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","first_name":"Cheng"},{"full_name":"Bai, Shulin","last_name":"Bai","first_name":"Shulin"},{"first_name":"Bingchao","last_name":"Qin","full_name":"Qin, Bingchao"},{"full_name":"Zhu, Yingcai","last_name":"Zhu","first_name":"Yingcai"},{"full_name":"Zhan, Shaoping","first_name":"Shaoping","last_name":"Zhan"},{"last_name":"Zheng","first_name":"Junqing","full_name":"Zheng, Junqing"},{"last_name":"Tang","first_name":"Shuwei","full_name":"Tang, Shuwei"},{"first_name":"Li Dong","last_name":"Zhao","full_name":"Zhao, Li Dong"}],"project":[{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"}],"doi":"10.1021/acs.chemmater.2c03542","intvolume":"        35","type":"journal_article","external_id":{"pmid":["36711054"],"isi":["000914749700001"]},"oa_version":"Published Version","day":"24","month":"01","has_accepted_license":"1","oa":1,"year":"2023","date_published":"2023-01-24T00:00:00Z","volume":35,"file_date_updated":"2023-08-14T12:57:25Z","article_type":"original","publication_status":"published","abstract":[{"text":"High carrier mobility is critical to improving thermoelectric performance over a broad temperature range. However, traditional doping inevitably deteriorates carrier mobility. Herein, we develop a strategy for fine tuning of defects to improve carrier mobility. To begin, n-type PbTe is created by compensating for the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering, resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is introduced to compensate for the remaining intrinsic Pb vacancies. We find that excess Ag exhibits a dynamic doping process with increasing temperatures, increasing both the carrier concentration and carrier mobility throughout a wide temperature range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier concentration suppresses the bipolar thermal conductivity at high temperatures. The final step is using iodine to optimize the carrier concentration to ∼1019 cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of ∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance carrier mobility and improve thermoelectric performance.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe","publication_identifier":{"eissn":["1520-5002"],"issn":["0897-4756"]},"acknowledgement":"The National Key Research and Development Program of China (2018YFA0702100), the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Natural Science Foundation of China (51571007 and 51772012), the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian Science Fund (FWF).","date_updated":"2025-04-23T08:47:37Z","article_processing_charge":"No","issue":"2","corr_author":"1","ddc":["540"],"department":[{"_id":"MaIb"}],"pmid":1,"status":"public","publication":"Chemistry of Materials","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":"755-763","citation":{"ama":"Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. <i>Chemistry of Materials</i>. 2023;35(2):755-763. doi:<a href=\"https://doi.org/10.1021/acs.chemmater.2c03542\">10.1021/acs.chemmater.2c03542</a>","apa":"Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023). Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. <i>Chemistry of Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.chemmater.2c03542\">https://doi.org/10.1021/acs.chemmater.2c03542</a>","ieee":"S. Wang <i>et al.</i>, “Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe,” <i>Chemistry of Materials</i>, vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.","chicago":"Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” <i>Chemistry of Materials</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.chemmater.2c03542\">https://doi.org/10.1021/acs.chemmater.2c03542</a>.","mla":"Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” <i>Chemistry of Materials</i>, vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:<a href=\"https://doi.org/10.1021/acs.chemmater.2c03542\">10.1021/acs.chemmater.2c03542</a>.","ista":"Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763.","short":"S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D. Zhao, Chemistry of Materials 35 (2023) 755–763."},"scopus_import":"1","isi":1},{"article_type":"original","publication_status":"published","abstract":[{"text":"Let X be a sufficiently large positive integer. We prove that one may choose a subset S of primes with cardinality O(logX) such that a positive proportion of integers less than X can be represented by x2+py2 for at least one p∈S.","lang":"eng"}],"year":"2023","oa":1,"volume":207,"date_published":"2023-01-09T00:00:00Z","arxiv":1,"month":"01","day":"09","external_id":{"arxiv":["2103.08268"],"isi":["000912903000001"]},"oa_version":"Preprint","intvolume":"       207","type":"journal_article","doi":"10.4064/aa210830-24-11","date_created":"2023-01-26T21:17:04Z","author":[{"orcid":"0000-0002-4989-5330","id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b","full_name":"Diao, Yijie","last_name":"Diao","first_name":"Yijie"}],"publisher":"Instytut Matematyczny","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.08268","open_access":"1"}],"_id":"12406","scopus_import":"1","isi":1,"publication":"Acta Arithmetica","page":"1-17","citation":{"apa":"Diao, Y. (2023). Density of the union of positive diagonal binary quadratic forms. <i>Acta Arithmetica</i>. Instytut Matematyczny. <a href=\"https://doi.org/10.4064/aa210830-24-11\">https://doi.org/10.4064/aa210830-24-11</a>","ama":"Diao Y. Density of the union of positive diagonal binary quadratic forms. <i>Acta Arithmetica</i>. 2023;207:1-17. doi:<a href=\"https://doi.org/10.4064/aa210830-24-11\">10.4064/aa210830-24-11</a>","ieee":"Y. Diao, “Density of the union of positive diagonal binary quadratic forms,” <i>Acta Arithmetica</i>, vol. 207. Instytut Matematyczny, pp. 1–17, 2023.","chicago":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” <i>Acta Arithmetica</i>. Instytut Matematyczny, 2023. <a href=\"https://doi.org/10.4064/aa210830-24-11\">https://doi.org/10.4064/aa210830-24-11</a>.","mla":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” <i>Acta Arithmetica</i>, vol. 207, Instytut Matematyczny, 2023, pp. 1–17, doi:<a href=\"https://doi.org/10.4064/aa210830-24-11\">10.4064/aa210830-24-11</a>.","ista":"Diao Y. 2023. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 207, 1–17.","short":"Y. Diao, Acta Arithmetica 207 (2023) 1–17."},"keyword":["Algebra","Number Theory"],"status":"public","department":[{"_id":"GradSch"}],"corr_author":"1","article_processing_charge":"No","publication_identifier":{"issn":["0065-1036"],"eissn":["1730-6264"]},"acknowledgement":"This article is a version the author’s master thesis at the University of Bonn. The author would like to thank his advisor Valentin Blomer for introducing the problem, and giving generous feedback and encouragement along the way, especially during the global pandemic.\r\nThe author thanks Edgar Assing for his lectures on analytic number theory. Finally, the author is grateful to the anonymous referees for their valuable time and comments.\r\n","date_updated":"2024-10-21T06:01:30Z","title":"Density of the union of positive diagonal binary quadratic forms","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","keyword":["runtime monitoring","best effort","third party"],"citation":{"ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria, 2023.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria; 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12407\">10.15479/AT:ISTA:12407</a>","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., &#38; Henzinger, T. A. (2023). <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12407\">https://doi.org/10.15479/AT:ISTA:12407</a>","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 38p.","mla":"Chalupa, Marek, et al. <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12407\">10.15479/AT:ISTA:12407</a>.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. <i>VAMOS: Middleware for Best-Effort Third-Party Monitoring</i>. Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12407\">https://doi.org/10.15479/AT:ISTA:12407</a>.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 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"},"page":"38","corr_author":"1","ddc":["005"],"department":[{"_id":"ToHe"}],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","date_updated":"2025-09-09T12:25:29Z","publication_identifier":{"eissn":["2664-1690"]},"title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-01-27T00:00:00Z","oa":1,"year":"2023","alternative_title":["IST Austria Technical Report"],"abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\n\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"12856","relation":"later_version"}]},"file_date_updated":"2023-01-27T03:18:34Z","day":"27","oa_version":"Published Version","ec_funded":1,"has_accepted_license":"1","month":"01","doi":"10.15479/AT:ISTA:12407","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"date_created":"2023-01-27T03:18:08Z","author":[{"full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","last_name":"Chalupa"},{"first_name":"Fabian","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177"},{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei","first_name":"Stefanie"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"}],"type":"technical_report","file":[{"creator":"fmuehlbo","file_name":"main.pdf","date_created":"2023-01-27T03:18:34Z","date_updated":"2023-01-27T03:18:34Z","file_id":"12408","checksum":"55426e463fdeafe9777fc3ff635154c7","relation":"main_file","success":1,"file_size":662409,"access_level":"open_access","content_type":"application/pdf"}],"publisher":"Institute of Science and Technology Austria","_id":"12407"},{"year":"2023","oa":1,"date_published":"2023-01-19T00:00:00Z","volume":2608,"alternative_title":["Methods in Molecular Biology"],"publication_status":"published","abstract":[{"lang":"eng","text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis."}],"file_date_updated":"2023-02-03T10:56:39Z","day":"19","external_id":{"pmid":["36653709"]},"oa_version":"Published Version","month":"01","series_title":"MIMB","has_accepted_license":"1","doi":"10.1007/978-1-0716-2887-4_12","author":[{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"last_name":"Scheele","first_name":"Colinda L.G.J.","full_name":"Scheele, Colinda L.G.J."}],"date_created":"2023-01-29T23:00:58Z","editor":[{"full_name":"Margadant, Coert","first_name":"Coert","last_name":"Margadant"}],"type":"book_chapter","intvolume":"      2608","file":[{"file_id":"12500","success":1,"checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","relation":"main_file","file_size":826598,"access_level":"open_access","content_type":"application/pdf","creator":"dernst","date_created":"2023-02-03T10:56:39Z","file_name":"2023_MIMB_Hannezo.pdf","date_updated":"2023-02-03T10:56:39Z"}],"publisher":"Springer Nature","_id":"12428","status":"public","scopus_import":"1","publication":"Cell Migration in Three Dimensions","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":"183-205","citation":{"ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in <i>Cell Migration in Three Dimensions</i>, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. <i>Cell Migration in Three Dimensions</i>. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>","apa":"Hannezo, E. B., &#38; Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), <i>Cell Migration in Three Dimensions</i> (Vol. 2608, pp. 183–205). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">10.1007/978-1-0716-2887-4_12</a>.","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In <i>Cell Migration in Three Dimensions</i>, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-2887-4_12\">https://doi.org/10.1007/978-1-0716-2887-4_12</a>."},"corr_author":"1","ddc":["570"],"pmid":1,"department":[{"_id":"EdHa"}],"publication_identifier":{"eissn":["1940-6029"],"isbn":["9781071628867"],"eisbn":["9781071628874"]},"date_updated":"2024-10-09T21:04:04Z","title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"doi":"10.1002/mana.202100192","date_created":"2023-01-29T23:00:59Z","author":[{"first_name":"Antonio","last_name":"Agresti","full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962"},{"last_name":"Lindemulder","first_name":"Nick","full_name":"Lindemulder, Nick"},{"last_name":"Veraar","first_name":"Mark","full_name":"Veraar, Mark"}],"intvolume":"       296","type":"journal_article","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":449280,"success":1,"checksum":"6f099f1d064173784d1a27716a2cc795","relation":"main_file","file_id":"14067","date_updated":"2023-08-16T11:40:02Z","creator":"dernst","date_created":"2023-08-16T11:40:02Z","file_name":"2023_MathNachrichten_Agresti.pdf"}],"publisher":"Wiley","_id":"12429","date_published":"2023-04-01T00:00:00Z","volume":296,"oa":1,"year":"2023","arxiv":1,"abstract":[{"lang":"eng","text":"In this paper, we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement is that we can allow general interpolation couples. The abstract results are applied to regularity problems for fractional evolution equations and stochastic evolution equations, where uniform trace estimates on the half-line are shown."}],"article_type":"original","publication_status":"published","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","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).","date_updated":"2023-08-16T11:41:42Z","publication_identifier":{"issn":["0025-584X"],"eissn":["1522-2616"]},"title":"On the trace embedding and its applications to evolution equations","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","isi":1,"scopus_import":"1","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":{"ieee":"A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its applications to evolution equations,” <i>Mathematische Nachrichten</i>, vol. 296, no. 4. Wiley, pp. 1319–1350, 2023.","ama":"Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications to evolution equations. <i>Mathematische Nachrichten</i>. 2023;296(4):1319-1350. doi:<a href=\"https://doi.org/10.1002/mana.202100192\">10.1002/mana.202100192</a>","apa":"Agresti, A., Lindemulder, N., &#38; Veraar, M. (2023). On the trace embedding and its applications to evolution equations. <i>Mathematische Nachrichten</i>. Wiley. <a href=\"https://doi.org/10.1002/mana.202100192\">https://doi.org/10.1002/mana.202100192</a>","mla":"Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution Equations.” <i>Mathematische Nachrichten</i>, vol. 296, no. 4, Wiley, 2023, pp. 1319–50, doi:<a href=\"https://doi.org/10.1002/mana.202100192\">10.1002/mana.202100192</a>.","ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 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>.","short":"A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023) 1319–1350."},"page":"1319-1350","publication":"Mathematische Nachrichten","ddc":["510"],"issue":"4","license":"https://creativecommons.org/licenses/by-nc/4.0/","department":[{"_id":"JuFi"}]},{"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_number":"2350006","article_processing_charge":"No","date_updated":"2023-08-16T11:47:27Z","publication_identifier":{"issn":["0129-055X"]},"title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","department":[{"_id":"RoSe"}],"issue":"4","isi":1,"scopus_import":"1","citation":{"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>","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>","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.","short":"M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical Physics 35 (2023).","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>.","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."},"publication":"Reviews in Mathematical Physics","status":"public","publisher":"World Scientific Publishing","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2110.00458"}],"_id":"12430","type":"journal_article","intvolume":"        35","doi":"10.1142/S0129055X2350006X","author":[{"first_name":"Marco","last_name":"Falconi","full_name":"Falconi, Marco"},{"full_name":"Leopold, Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","last_name":"Leopold"},{"full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","last_name":"Mitrouskas"},{"full_name":"Petrat, Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889","first_name":"Sören P","last_name":"Petrat"}],"date_created":"2023-01-29T23:00:59Z","month":"01","day":"09","oa_version":"Preprint","external_id":{"arxiv":["2110.00458"],"isi":["000909760300001"]},"abstract":[{"text":"We study the time evolution of the Nelson model in a mean-field limit in which N nonrelativistic bosons weakly couple (with respect to the particle number) to a positive or zero mass quantized scalar field. Our main result is the derivation of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove the convergence of the approximate wave function to the many-body wave function in norm, with a convergence rate proportional to the number of corrections taken into account in the approximation. We prove an analogous result for the unitary propagator. As an application, we derive a simple system of partial differential equations describing the time evolution of the first- and second-order approximations to the one-particle reduced density matrices of the particles and the quantum field, respectively.","lang":"eng"}],"publication_status":"published","article_type":"original","volume":35,"date_published":"2023-01-09T00:00:00Z","oa":1,"year":"2023","arxiv":1},{"quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"location":"Paris, France","end_date":"2023-04-27","name":"FOSSACS: Foundations of Software Science and Computation Structures","start_date":"2023-04-22"},"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"]},"title":"Quantitative safety and liveness","article_processing_charge":"No","ddc":["000"],"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"status":"public","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"},"page":"349-370","citation":{"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.","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>","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.","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>.","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>."},"publication":"26th International Conference Foundations of Software Science and Computation Structures","file":[{"date_updated":"2023-01-31T07:22:21Z","creator":"esarac","file_name":"qsl.pdf","date_created":"2023-01-31T07:22:21Z","checksum":"981025aed580b6b27c426cb8856cf63e","relation":"main_file","success":1,"file_id":"12468","content_type":"application/pdf","access_level":"open_access","file_size":449027},{"success":1,"relation":"main_file","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","file_id":"13153","content_type":"application/pdf","access_level":"open_access","file_size":1048171,"date_updated":"2023-06-19T10:28:09Z","creator":"dernst","file_name":"2023_LNCS_HenzingerT.pdf","date_created":"2023-06-19T10:28:09Z"}],"publisher":"Springer Nature","_id":"12467","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"doi":"10.1007/978-3-031-30829-1_17","author":[{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","last_name":"Mazzocchi"},{"first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"date_created":"2023-01-31T07:23:56Z","intvolume":"     13992","type":"conference","day":"21","oa_version":"Published Version","external_id":{"arxiv":["2301.11175"],"isi":["001288609300017"]},"ec_funded":1,"has_accepted_license":"1","month":"04","volume":13992,"date_published":"2023-04-21T00:00:00Z","oa":1,"year":"2023","alternative_title":["LNCS"],"arxiv":1,"abstract":[{"text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.","lang":"eng"}],"publication_status":"published","file_date_updated":"2023-06-19T10:28:09Z"},{"file":[{"success":1,"relation":"main_file","checksum":"cd52292963acce1111634d9fac08c699","file_id":"12843","content_type":"application/pdf","file_size":4866332,"access_level":"open_access","date_updated":"2023-04-17T07:49:09Z","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","date_created":"2023-04-17T07:49:09Z","creator":"dernst"}],"_id":"12469","publisher":"Frontiers","author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias","last_name":"Fürst","first_name":"Matthias"},{"first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"first_name":"Jaana","last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana"},{"last_name":"Oh","first_name":"Jinook","orcid":"0000-0001-7425-2372","full_name":"Oh, Jinook","id":"403169A4-080F-11EA-9993-BF3F3DDC885E"},{"first_name":"Lassi","last_name":"Tolonen","full_name":"Tolonen, Lassi"},{"last_name":"Eder","first_name":"Thomas","full_name":"Eder, Thomas"},{"full_name":"Rattei, Thomas","first_name":"Thomas","last_name":"Rattei"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"date_created":"2023-01-31T08:13:40Z","doi":"10.3389/fmicb.2023.1119002","project":[{"_id":"25DF61D8-B435-11E9-9278-68D0E5697425","name":"Viral pathogens and social immunity in ants","call_identifier":"FWF","grant_number":"M02076"}],"intvolume":"        14","type":"journal_article","oa_version":"Published Version","external_id":{"isi":["000961542100001"],"pmid":["37007485"]},"day":"16","has_accepted_license":"1","month":"03","date_published":"2023-03-16T00:00:00Z","volume":14,"oa":1,"year":"2023","file_date_updated":"2023-04-17T07:49:09Z","abstract":[{"text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.","lang":"eng"}],"article_type":"original","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","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","ddc":["570"],"corr_author":"1","pmid":1,"department":[{"_id":"SyCr"}],"status":"public","citation":{"ieee":"L. Viljakainen <i>et al.</i>, “Antiviral immune response reveals host-specific virus infections in natural ant populations,” <i>Frontiers in Microbiology</i>, vol. 14. Frontiers, 2023.","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>","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>","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.","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>.","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)."},"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"},{"volume":14,"date_published":"2023-06-20T00:00:00Z","oa":1,"year":"2023","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"}],"article_type":"original","publication_status":"published","file_date_updated":"2023-07-31T07:16:34Z","day":"20","oa_version":"Published Version","external_id":{"isi":["001030002600001"],"pmid":["37485524"]},"has_accepted_license":"1","month":"06","doi":"10.3389/fmicb.2023.1049255","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","last_name":"Bruneaux","first_name":"L"},{"first_name":"P","last_name":"Oikonomou","full_name":"Oikonomou, P"},{"first_name":"M","last_name":"Aldana","full_name":"Aldana, M"},{"full_name":"Cluzel, P","first_name":"P","last_name":"Cluzel"}],"date_created":"2023-02-02T08:13:28Z","intvolume":"        14","type":"journal_article","file":[{"access_level":"open_access","file_size":6452841,"content_type":"application/pdf","file_id":"13322","checksum":"7dd322347512afaa5daf72a0154f2f07","relation":"main_file","success":1,"date_created":"2023-07-31T07:16:34Z","file_name":"2023_FrontiersMicrobiology_Guet.pdf","creator":"dernst","date_updated":"2023-07-31T07:16:34Z"}],"publisher":"Frontiers","_id":"12478","status":"public","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":{"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.","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>","short":"C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in Microbiology 14 (2023).","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.","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>."},"publication":"Frontiers in Microbiology","corr_author":"1","ddc":["570"],"pmid":1,"department":[{"_id":"CaGu"}],"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.","publication_identifier":{"eissn":["1664-302X"]},"title":"Monitoring lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon expression","article_number":"1049255","article_processing_charge":"Yes","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"year":"2023","oa":1,"date_published":"2023-10-20T00:00:00Z","volume":26,"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"}],"file_date_updated":"2023-10-09T07:23:46Z","day":"20","external_id":{"pmid":["37766992"],"isi":["001082331200001"]},"ec_funded":1,"oa_version":"Published Version","month":"10","has_accepted_license":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318"}],"doi":"10.1016/j.isci.2023.107840","author":[{"last_name":"Scarpetta","first_name":"Silvia","full_name":"Scarpetta, Silvia"},{"last_name":"Morrisi","first_name":"Niccolò","full_name":"Morrisi, Niccolò"},{"full_name":"Mutti, Carlotta","last_name":"Mutti","first_name":"Carlotta"},{"full_name":"Azzi, Nicoletta","first_name":"Nicoletta","last_name":"Azzi"},{"last_name":"Trippi","first_name":"Irene","full_name":"Trippi, Irene"},{"first_name":"Rosario","last_name":"Ciliento","full_name":"Ciliento, Rosario"},{"full_name":"Apicella, Ilenia","first_name":"Ilenia","last_name":"Apicella"},{"full_name":"Messuti, Giovanni","first_name":"Giovanni","last_name":"Messuti"},{"full_name":"Angiolelli, Marianna","last_name":"Angiolelli","first_name":"Marianna"},{"orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio","last_name":"Lombardi","first_name":"Fabrizio"},{"full_name":"Parrino, Liborio","last_name":"Parrino","first_name":"Liborio"},{"full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano","first_name":"Anna Elisabetta"}],"date_created":"2023-02-02T10:50:17Z","type":"journal_article","intvolume":"        26","file":[{"access_level":"open_access","file_size":4872708,"content_type":"application/pdf","file_id":"14412","relation":"main_file","success":1,"checksum":"f499836af172ecc9865de4bb41fa99d1","creator":"dernst","date_created":"2023-10-09T07:23:46Z","file_name":"2023_iScience_Scarpetta.pdf","date_updated":"2023-10-09T07:23:46Z"}],"publisher":"Elsevier","_id":"12487","status":"public","scopus_import":"1","isi":1,"publication":"iScience","citation":{"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>.","short":"S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.","ieee":"S. Scarpetta <i>et al.</i>, “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” <i>iScience</i>, vol. 26, no. 10. Elsevier, p. 107840, 2023.","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>"},"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","issue":"10","ddc":["570"],"department":[{"_id":"GaTk"}],"pmid":1,"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.","title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","article_processing_charge":"Yes","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"23","ddc":["572"],"corr_author":"1","oa_version":"Published Version","month":"03","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"oa":1,"year":"2023","date_published":"2023-03-23T00:00:00Z","status":"public","abstract":[{"text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and  HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture.","lang":"eng"}],"file_date_updated":"2023-03-24T09:42:03Z","citation":{"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>","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>.","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>.","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>.","short":"L.M. Becker, P. Schanda, (2023)."},"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":[{"relation":"used_in_publication","status":"public","id":"12675"}]},"contributor":[{"last_name":"Berbon","contributor_type":"researcher","first_name":"Mélanie"},{"first_name":"Alicia","last_name":"Vallet","contributor_type":"researcher"},{"first_name":"Axelle","last_name":"Grelard","contributor_type":"researcher"},{"last_name":"Morvan","contributor_type":"researcher","first_name":"Estelle"},{"contributor_type":"researcher","last_name":"Bardiaux","first_name":"Benjamin"},{"last_name":"Lichtenecker","contributor_type":"researcher","first_name":"Roman"},{"first_name":"Matthias","last_name":"Ernst","contributor_type":"researcher"},{"first_name":"Antoine","last_name":"Loquet","contributor_type":"researcher"},{"first_name":"Paul","last_name":"Schanda","contributor_type":"contact_person","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"first_name":"Lea Marie","contributor_type":"researcher","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_size":87018103,"content_type":"application/zip","file_id":"12743","checksum":"fd9a28620a81a82991fb70f4fd6591d9","relation":"main_file","file_name":"Research_Data.zip","date_created":"2023-03-23T10:03:16Z","creator":"lbecker","date_updated":"2023-03-24T09:34:20Z"},{"file_size":747,"access_level":"open_access","content_type":"text/plain","file_id":"12755","relation":"main_file","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","creator":"dernst","date_created":"2023-03-24T07:13:55Z","file_name":"README.txt","date_updated":"2023-03-24T09:42:03Z"}],"publisher":"Institute of Science and Technology Austria","_id":"12497","doi":"10.15479/AT:ISTA:12497","date_updated":"2024-10-21T06:01:38Z","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"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"}],"title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","type":"research_data","article_processing_charge":"No"},{"publisher":"Oxford University Press","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/evolut/qpac004"}],"_id":"12514","intvolume":"        77","type":"journal_article","doi":"10.1093/evolut/qpac004","author":[{"first_name":"Daniel I.","last_name":"Bolnick","full_name":"Bolnick, Daniel I."},{"full_name":"Hund, Amanda K.","first_name":"Amanda K.","last_name":"Hund"},{"first_name":"Patrik","last_name":"Nosil","full_name":"Nosil, Patrik"},{"full_name":"Peng, Foen","first_name":"Foen","last_name":"Peng"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski"},{"last_name":"Subramanian","first_name":"Swapna","full_name":"Subramanian, Swapna"},{"last_name":"Wolf","first_name":"Jochen B.W.","full_name":"Wolf, Jochen B.W."},{"last_name":"Yukilevich","first_name":"Roman","full_name":"Yukilevich, Roman"}],"date_created":"2023-02-05T23:00:59Z","month":"01","day":"01","external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"oa_version":"Published Version","publication_status":"published","article_type":"original","abstract":[{"text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.","lang":"eng"}],"oa":1,"year":"2023","volume":77,"date_published":"2023-01-01T00:00:00Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_processing_charge":"No","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","department":[{"_id":"NiBa"}],"pmid":1,"issue":"1","ddc":["570"],"scopus_import":"1","isi":1,"publication":"Evolution: International journal of organic evolution","citation":{"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>","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>","ieee":"D. I. Bolnick <i>et al.</i>, “A multivariate view of the speciation continuum,” <i>Evolution: International journal of organic evolution</i>, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","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>."},"page":"318-328","status":"public"},{"article_processing_charge":"No","article_number":"1097467","title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","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","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication":"Frontiers in Neuroanatomy","citation":{"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>","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).","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.","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>.","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>."},"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"},"scopus_import":"1","isi":1,"status":"public","department":[{"_id":"PeJo"}],"pmid":1,"ddc":["570"],"type":"journal_article","intvolume":"        16","author":[{"full_name":"Ortiz-Leal, Irene","first_name":"Irene","last_name":"Ortiz-Leal"},{"last_name":"Torres","first_name":"Mateo V.","full_name":"Torres, Mateo V."},{"last_name":"Vargas Barroso","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M"},{"full_name":"Fidalgo, Luis Eusebio","first_name":"Luis Eusebio","last_name":"Fidalgo"},{"full_name":"López-Beceiro, Ana María","last_name":"López-Beceiro","first_name":"Ana María"},{"first_name":"Jorge A.","last_name":"Larriva-Sahd","full_name":"Larriva-Sahd, Jorge A."},{"first_name":"Pablo","last_name":"Sánchez-Quinteiro","full_name":"Sánchez-Quinteiro, Pablo"}],"date_created":"2023-02-05T23:01:00Z","doi":"10.3389/fnana.2022.1097467","_id":"12515","publisher":"Frontiers","file":[{"file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf","date_created":"2023-02-06T07:56:14Z","creator":"dernst","date_updated":"2023-02-06T07:56:14Z","file_id":"12518","checksum":"49cd40f3bda6f267079427042e7d15e3","relation":"main_file","success":1,"file_size":21943473,"access_level":"open_access","content_type":"application/pdf"}],"file_date_updated":"2023-02-06T07:56:14Z","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"}],"oa":1,"year":"2023","volume":16,"date_published":"2023-01-10T00:00:00Z","month":"01","has_accepted_license":"1","external_id":{"pmid":["36704406"],"isi":["000919786900001"]},"oa_version":"Published Version","day":"10"},{"ec_funded":1,"oa_version":"Published Version","day":"20","month":"01","has_accepted_license":"1","year":"2023","oa":1,"date_published":"2023-01-20T00:00:00Z","volume":5,"file_date_updated":"2023-02-13T10:38:10Z","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","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."}],"file":[{"file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","date_created":"2023-02-13T10:38:10Z","creator":"dernst","date_updated":"2023-02-13T10:38:10Z","file_size":865150,"access_level":"open_access","content_type":"application/pdf","file_id":"12546","relation":"main_file","checksum":"6068b62874c0099628a108bb9c5c6bd2","success":1}],"_id":"12534","publisher":"American Physical Society","date_created":"2023-02-10T09:02:26Z","author":[{"first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543"},{"full_name":"Cappellaro, Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359","first_name":"Alberto","last_name":"Cappellaro"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"project":[{"grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"doi":"10.1103/physrevresearch.5.013029","intvolume":"         5","type":"journal_article","issue":"1","ddc":["530"],"corr_author":"1","department":[{"_id":"MiLe"}],"status":"public","publication":"Physical Review Research","citation":{"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>","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>","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.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","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>."},"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"},"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","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","article_processing_charge":"No","article_number":"013029"}]