[{"ddc":["510"],"quality_controlled":"1","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00028-022-00859-7","type":"journal_article","_id":"12104","date_updated":"2023-06-28T11:54:35Z","publication":"Journal of Evolution Equations","status":"public","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"},{"_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","name":"Gradient flow techniques for quantum Markov semigroups","grant_number":"ESP156_N"}],"date_published":"2023-01-01T00:00:00Z","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","ec_funded":1,"external_id":{"isi":["000906214600004"]},"isi":1,"year":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.","lang":"eng"}],"intvolume":" 23","has_accepted_license":"1","file_date_updated":"2023-01-20T10:45:06Z","publication_identifier":{"issn":["1424-3199"],"eissn":["1424-3202"]},"publication_status":"published","title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","oa_version":"Published Version","day":"01","scopus_import":"1","author":[{"first_name":"Lorenzo","orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo"},{"orcid":"0000-0002-0519-4241","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","full_name":"Wirth, Melchior","last_name":"Wirth"}],"date_created":"2023-01-08T23:00:53Z","article_type":"original","volume":23,"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023.","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7.","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7.","apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7"},"issue":"1","month":"01","article_number":"9","file":[{"file_id":"12325","creator":"dernst","date_updated":"2023-01-20T10:45:06Z","date_created":"2023-01-20T10:45:06Z","file_size":422612,"checksum":"1f34f3e2cb521033de6154f274ea3a4e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf"}],"department":[{"_id":"JaMa"}]},{"has_accepted_license":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion."}],"intvolume":" 954","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"publication_status":"published","file_date_updated":"2023-02-02T12:34:54Z","author":[{"last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","full_name":"Marensi, Elena","first_name":"Elena"},{"first_name":"Gökhan","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","last_name":"Yalniz"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010"}],"day":"10","scopus_import":"1","oa_version":"Published Version","title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","volume":954,"article_type":"original","date_created":"2023-01-08T23:00:53Z","oa":1,"language":[{"iso":"eng"}],"citation":{"chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001.","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University Press, 2023, doi:10.1017/jfm.2022.1001.","apa":"Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001","ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023).","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics, vol. 954. Cambridge University Press, 2023."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","arxiv":1,"month":"01","department":[{"_id":"BjHo"}],"file":[{"checksum":"9224f987caefe5dd85a70814d3cce65c","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_JourFluidMechanics_Marensi.pdf","file_id":"12489","creator":"dernst","date_updated":"2023-02-02T12:34:54Z","date_created":"2023-02-02T12:34:54Z","file_size":1931647}],"article_number":"A10","ddc":["530"],"quality_controlled":"1","doi":"10.1017/jfm.2022.1001","article_processing_charge":"Yes (via OA deal)","publisher":"Cambridge University Press","date_updated":"2023-08-01T12:53:23Z","_id":"12105","type":"journal_article","project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"status":"public","publication":"Journal of Fluid Mechanics","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","date_published":"2023-01-10T00:00:00Z","year":"2023","isi":1,"external_id":{"arxiv":["2101.07516"],"isi":["000903336600001"]}},{"publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"publication_status":"published","file_date_updated":"2023-08-16T11:30:45Z","abstract":[{"lang":"eng","text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells."}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 41","has_accepted_license":"1","article_type":"original","date_created":"2023-01-08T23:00:53Z","volume":41,"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","oa_version":"Published Version","author":[{"first_name":"Jake","orcid":"0000-0003-1732-1559","last_name":"Yeung","id":"123012b2-db30-11eb-b4d8-a35840c0551b","full_name":"Yeung, Jake"},{"first_name":"Maria","last_name":"Florescu","full_name":"Florescu, Maria"},{"first_name":"Peter","last_name":"Zeller","full_name":"Zeller, Peter"},{"last_name":"De Barbanson","full_name":"De Barbanson, Buys Anton","first_name":"Buys Anton"},{"first_name":"Max D.","full_name":"Wellenstein, Max D.","last_name":"Wellenstein"},{"first_name":"Alexander","full_name":"Van Oudenaarden, Alexander","last_name":"Van Oudenaarden"}],"day":"01","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823, 2023.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., & Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-022-01560-3","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3."},"language":[{"iso":"eng"}],"oa":1,"file":[{"relation":"main_file","checksum":"668447a1c8d360b68f8aaf9e08ed644f","success":1,"file_name":"2023_NatureBioTech_Yeung.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"14066","file_size":12040976,"date_created":"2023-08-16T11:30:45Z","date_updated":"2023-08-16T11:30:45Z","creator":"dernst"}],"department":[{"_id":"ScienComp"}],"month":"06","quality_controlled":"1","ddc":["570"],"page":"813–823","type":"journal_article","date_updated":"2023-08-16T11:32:33Z","_id":"12106","publisher":"Springer Nature","doi":"10.1038/s41587-022-01560-3","article_processing_charge":"No","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","date_published":"2023-06-01T00:00:00Z","publication":"Nature Biotechnology","status":"public","external_id":{"isi":["000909067600003"]},"isi":1,"year":"2023"},{"publication_status":"epub_ahead","publication_identifier":{"issn":["0169-4332"]},"abstract":[{"lang":"eng","text":"The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices."}],"intvolume":" 613","date_created":"2023-01-12T11:55:02Z","article_type":"original","volume":613,"title":"Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient","oa_version":"None","scopus_import":"1","day":"15","author":[{"first_name":"Li","full_name":"Zhang, Li","last_name":"Zhang"},{"last_name":"Liu","full_name":"Liu, Xingyu","first_name":"Xingyu"},{"full_name":"Wu, Ting","last_name":"Wu","first_name":"Ting"},{"first_name":"Shengduo","id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f","full_name":"Xu, Shengduo","last_name":"Xu"},{"first_name":"Guoquan","last_name":"Suo","full_name":"Suo, Guoquan"},{"first_name":"Xiaohui","full_name":"Ye, Xiaohui","last_name":"Ye"},{"first_name":"Xiaojiang","full_name":"Hou, Xiaojiang","last_name":"Hou"},{"first_name":"Yanling","full_name":"Yang, Yanling","last_name":"Yang"},{"first_name":"Qingfeng","last_name":"Liu","full_name":"Liu, Qingfeng"},{"first_name":"Hongqiang","full_name":"Wang, Hongqiang","last_name":"Wang"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H. Wang, Applied Surface Science 613 (2023).","ieee":"L. Zhang et al., “Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient,” Applied Surface Science, vol. 613. Elsevier, 2023.","ama":"Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 2023;613. doi:10.1016/j.apsusc.2022.156101","mla":"Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science, vol. 613, 156101, Elsevier, 2023, doi:10.1016/j.apsusc.2022.156101.","apa":"Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. Elsevier. https://doi.org/10.1016/j.apsusc.2022.156101","chicago":"Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science. Elsevier, 2023. https://doi.org/10.1016/j.apsusc.2022.156101.","ista":"Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 613, 156101."},"language":[{"iso":"eng"}],"article_number":"156101","department":[{"_id":"MaIb"}],"month":"03","quality_controlled":"1","type":"journal_article","_id":"12113","date_updated":"2023-08-14T11:47:06Z","publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.apsusc.2022.156101","acknowledgement":"Scientific Research Program Funded by Shaanxi Provincial Education Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi (Grant No.2022JZ-31), Young Talent fund of University Association for Science and Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation (Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology (Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry and Technology for Chemical Industry, Ministry of Education, Shaanxi University of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology, Shaanxi University of Science and Technology (Grant No. KFKT2022-15).","date_published":"2023-03-15T00:00:00Z","publication":"Applied Surface Science","status":"public","keyword":["Surfaces","Coatings and Films","Condensed Matter Physics","Surfaces and Interfaces","General Physics and Astronomy","General Chemistry"],"external_id":{"isi":["000911497000001"]},"isi":1,"year":"2023"},{"year":"2023","external_id":{"pmid":["36578472"]},"keyword":["Structural Biology"],"publication":"Journal of Structural Biology: X","status":"public","pmid":1,"date_published":"2023-01-01T00:00:00Z","acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","doi":"10.1016/j.yjsbx.2022.100079","article_processing_charge":"No","publisher":"Elsevier","date_updated":"2023-08-16T09:37:25Z","_id":"12114","type":"journal_article","ddc":["570"],"quality_controlled":"1","month":"01","department":[{"_id":"PaSc"}],"article_number":"100079","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_JourStrucBiologyX_Gauto.pdf","checksum":"b4b1c10a31018aafe053b7d55a470e54","relation":"main_file","date_updated":"2023-08-16T09:36:28Z","creator":"dernst","date_created":"2023-08-16T09:36:28Z","file_size":5132322,"file_id":"14064"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).","ieee":"D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” Journal of Structural Biology: X, vol. 7. Elsevier, 2023.","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X, vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"last_name":"Lebedenko","full_name":"Lebedenko, Olga O.","first_name":"Olga O."},{"orcid":"0000-0002-6401-5151","first_name":"Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie"},{"first_name":"Isabel","full_name":"Ayala, Isabel","last_name":"Ayala"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"full_name":"Skrynnikov, Nikolai R.","last_name":"Skrynnikov","first_name":"Nikolai R."},{"orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda"}],"scopus_import":"1","day":"01","oa_version":"Published Version","title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","volume":7,"article_type":"original","date_created":"2023-01-12T11:55:38Z","has_accepted_license":"1","abstract":[{"text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.","lang":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":" 7","publication_status":"published","publication_identifier":{"issn":["2590-1524"]},"file_date_updated":"2023-08-16T09:36:28Z"},{"keyword":["Oncology","Surgery"],"isi":1,"year":"2023","related_material":{"record":[{"relation":"other","status":"public","id":"12205"}]},"external_id":{"isi":["000879151800001"]},"acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","date_published":"2023-01-01T00:00:00Z","status":"public","publication":"Annals of Surgical Oncology","_id":"12115","date_updated":"2023-09-05T15:18:36Z","type":"journal_article","article_processing_charge":"No","doi":"10.1245/s10434-022-12681-z","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1245/s10434-022-12681-z"}],"quality_controlled":"1","page":"46-47","department":[{"_id":"JoDa"}],"month":"01","citation":{"ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z.","mla":"Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 46–47, doi:10.1245/s10434-022-12681-z.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47. doi:10.1245/s10434-022-12681-z","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","ieee":"J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 46–47, 2023."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"volume":30,"date_created":"2023-01-12T11:56:22Z","article_type":"original","day":"01","scopus_import":"1","author":[{"last_name":"Glajzer","full_name":"Glajzer, Jacek","first_name":"Jacek"},{"first_name":"Dan Cacsire","last_name":"Castillo-Tong","full_name":"Castillo-Tong, Dan Cacsire"},{"first_name":"Rolf","last_name":"Richter","full_name":"Richter, Rolf"},{"first_name":"Ignace","full_name":"Vergote, Ignace","last_name":"Vergote"},{"first_name":"Hagen","full_name":"Kulbe, Hagen","last_name":"Kulbe"},{"last_name":"Vanderstichele","full_name":"Vanderstichele, Adriaan","first_name":"Adriaan"},{"first_name":"Ilary","last_name":"Ruscito","full_name":"Ruscito, Ilary"},{"first_name":"Fabian","last_name":"Trillsch","full_name":"Trillsch, Fabian"},{"first_name":"Alexander","full_name":"Mustea, Alexander","last_name":"Mustea"},{"first_name":"Caroline","full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger"},{"first_name":"Charlie","full_name":"Gourley, Charlie","last_name":"Gourley"},{"last_name":"Gabra","full_name":"Gabra, Hani","first_name":"Hani"},{"first_name":"Eliane T.","full_name":"Taube, Eliane T.","last_name":"Taube"},{"first_name":"Oliver","last_name":"Dorigo","full_name":"Dorigo, Oliver"},{"last_name":"Horst","full_name":"Horst, David","first_name":"David"},{"first_name":"Carlotta","last_name":"Keunecke","full_name":"Keunecke, Carlotta"},{"last_name":"Baum","full_name":"Baum, Joanna","first_name":"Joanna"},{"first_name":"Timothy","last_name":"Angelotti","full_name":"Angelotti, Timothy"},{"first_name":"Jalid","full_name":"Sehouli, Jalid","last_name":"Sehouli"},{"first_name":"Elena Ioana","full_name":"Braicu, Elena Ioana","last_name":"Braicu"}],"oa_version":"Published Version","title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","publication_status":"published","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"intvolume":" 30"},{"year":"2023","keyword":["Genetics"],"status":"public","publication":"Nature Genetics","date_published":"2023-02-01T00:00:00Z","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1038/s41588-022-01260-3","type":"journal_article","_id":"12158","date_updated":"2023-02-27T07:48:24Z","ddc":["570","000"],"page":"333-345","quality_controlled":"1","month":"02","file":[{"file_size":21484855,"date_created":"2023-02-27T07:46:45Z","creator":"dernst","date_updated":"2023-02-27T07:46:45Z","file_id":"12688","success":1,"file_name":"2023_NatureGenetics_Zeller.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e"}],"department":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3"},"title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","oa_version":"Published Version","day":"01","scopus_import":"1","author":[{"last_name":"Zeller","full_name":"Zeller, Peter","first_name":"Peter"},{"first_name":"Jake","orcid":"0000-0003-1732-1559","id":"123012b2-db30-11eb-b4d8-a35840c0551b","full_name":"Yeung, Jake","last_name":"Yeung"},{"full_name":"Viñas Gaza, Helena","last_name":"Viñas Gaza","first_name":"Helena"},{"last_name":"de Barbanson","full_name":"de Barbanson, Buys Anton","first_name":"Buys Anton"},{"full_name":"Bhardwaj, Vivek","last_name":"Bhardwaj","first_name":"Vivek"},{"first_name":"Maria","full_name":"Florescu, Maria","last_name":"Florescu"},{"first_name":"Reinier","last_name":"van der Linden","full_name":"van der Linden, Reinier"},{"first_name":"Alexander","full_name":"van Oudenaarden, Alexander","last_name":"van Oudenaarden"}],"date_created":"2023-01-12T12:09:09Z","article_type":"review","volume":55,"intvolume":" 55","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.","lang":"eng"}],"has_accepted_license":"1","file_date_updated":"2023-02-27T07:46:45Z","publication_status":"published","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]}},{"type":"journal_article","date_updated":"2023-08-16T08:18:47Z","_id":"12159","publisher":"Wiley","doi":"10.1111/mec.16793","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","ddc":["570"],"page":"1441-1457","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"year":"2023","isi":1,"date_published":"2023-03-01T00:00:00Z","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","pmid":1,"project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"status":"public","publication":"Molecular Ecology","article_type":"original","date_created":"2023-01-12T12:09:17Z","volume":32,"title":"On the origin and structure of haplotype blocks","oa_version":"Published Version","author":[{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","full_name":"Shipilina, Daria","last_name":"Shipilina","first_name":"Daria","orcid":"0000-0002-1145-9226"},{"orcid":"0000-0002-4530-8469","first_name":"Arka","full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal"},{"first_name":"Sean","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank","last_name":"Chan"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"day":"01","scopus_import":"1","publication_status":"published","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"file_date_updated":"2023-08-16T08:15:41Z","abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 32","has_accepted_license":"1","file":[{"success":1,"file_name":"2023_MolecularEcology_Shipilina.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_size":7144607,"date_created":"2023-08-16T08:15:41Z","creator":"dernst","date_updated":"2023-08-16T08:15:41Z","file_id":"14062"}],"department":[{"_id":"NiBa"}],"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","citation":{"chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023."},"language":[{"iso":"eng"}],"oa":1},{"title":"Modelling the dynamics of mammalian gut homeostasis","oa_version":"Published Version","scopus_import":"1","day":"02","author":[{"full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"}],"date_created":"2023-01-12T12:09:47Z","article_type":"review","volume":"150-151","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues."}],"has_accepted_license":"1","file_date_updated":"2024-01-08T10:16:04Z","publication_status":"published","publication_identifier":{"issn":["1084-9521"]},"month":"12","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","checksum":"c619887cf130f4649bf3035417186004","relation":"main_file","creator":"dernst","date_updated":"2024-01-08T10:16:04Z","file_size":1343750,"date_created":"2024-01-08T10:16:04Z","file_id":"14741"}],"department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” Seminars in Cell & Developmental Biology, vol. 150–151. Elsevier, pp. 58–65, 2023.","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology 150–151 (2023) 58–65.","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 2023;150-151:58-65. doi:10.1016/j.semcdb.2022.11.005","apa":"Corominas-Murtra, B., & Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. Elsevier. https://doi.org/10.1016/j.semcdb.2022.11.005","mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:10.1016/j.semcdb.2022.11.005.","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65.","chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology. Elsevier, 2023. https://doi.org/10.1016/j.semcdb.2022.11.005."},"publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.semcdb.2022.11.005","type":"journal_article","_id":"12162","date_updated":"2024-01-16T13:22:32Z","ddc":["570"],"page":"58-65","quality_controlled":"1","external_id":{"isi":["001053522200001"],"pmid":["36470715"]},"year":"2023","isi":1,"keyword":["Cell Biology","Developmental Biology"],"status":"public","publication":"Seminars in Cell & Developmental Biology","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"acknowledgement":"This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB. C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","date_published":"2023-12-02T00:00:00Z","ec_funded":1,"pmid":1},{"volume":597,"article_type":"review","date_created":"2023-01-12T12:09:58Z","author":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"last_name":"Auer","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","first_name":"Albert"},{"first_name":"Gabriel","full_name":"Brognara, Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","last_name":"Brognara"},{"last_name":"Budiman","full_name":"Budiman, Hanifatul R","id":"55380f95-15b2-11ec-abd3-aff8e230696b","first_name":"Hanifatul R"},{"first_name":"Lukasz M","last_name":"Kowalski","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","full_name":"Kowalski, Lukasz M"},{"last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana","first_name":"Ivana"}],"scopus_import":"1","day":"01","oa_version":"Published Version","title":"In vitro reconstitution of small GTPase regulation","publication_identifier":{"eissn":["1873-3468"],"issn":["0014-5793"]},"publication_status":"published","file_date_updated":"2023-08-16T08:31:04Z","has_accepted_license":"1","intvolume":" 597","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"abstract":[{"lang":"eng","text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time."}],"department":[{"_id":"MaLo"}],"file":[{"relation":"main_file","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","success":1,"file_name":"2023_FEBSLetters_Loose.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"14063","file_size":3148143,"date_created":"2023-08-16T08:31:04Z","creator":"dernst","date_updated":"2023-08-16T08:31:04Z"}],"month":"03","issue":"6","citation":{"ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters. Wiley. https://doi.org/10.1002/1873-3468.14540","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777. doi:10.1002/1873-3468.14540","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"date_updated":"2023-08-16T08:32:29Z","_id":"12163","type":"journal_article","doi":"10.1002/1873-3468.14540","article_processing_charge":"Yes (via OA deal)","publisher":"Wiley","quality_controlled":"1","page":"762-777","ddc":["570"],"keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"year":"2023","isi":1,"external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"pmid":1,"date_published":"2023-03-01T00:00:00Z","acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","publication":"FEBS Letters","status":"public"},{"acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","date_published":"2023-03-01T00:00:00Z","publication":"Distributed Computing","status":"public","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"external_id":{"isi":["000890138700001"]},"year":"2023","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/"}],"page":"29-43","type":"journal_article","date_updated":"2023-08-16T08:39:36Z","_id":"12164","publisher":"Springer Nature","doi":"10.1007/s00446-022-00439-5","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” Distributed Computing, vol. 36. Springer Nature, pp. 29–43, 2023.","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5.","mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 29–43, doi:10.1007/s00446-022-00439-5.","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00439-5"},"language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"KrPi"}],"month":"03","publication_status":"published","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"intvolume":" 36","abstract":[{"text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity.","lang":"eng"}],"article_type":"original","date_created":"2023-01-12T12:10:08Z","volume":36,"title":"Long-lived counters with polylogarithmic amortized step complexity","oa_version":"Preprint","author":[{"last_name":"Baig","full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad"},{"last_name":"Hendler","full_name":"Hendler, Danny","first_name":"Danny"},{"last_name":"Milani","full_name":"Milani, Alessia","first_name":"Alessia"},{"last_name":"Travers","full_name":"Travers, Corentin","first_name":"Corentin"}],"scopus_import":"1","day":"01"},{"date_published":"2023-01-01T00:00:00Z","status":"public","publication":"Nature Reviews Physics","keyword":["General Physics and Astronomy"],"year":"2023","isi":1,"external_id":{"isi":["000890148700002"]},"quality_controlled":"1","page":"62-72","_id":"12165","date_updated":"2023-08-01T12:50:48Z","type":"journal_article","article_processing_charge":"No","doi":"10.1038/s42254-022-00539-y","publisher":"Springer Nature","citation":{"ama":"Hof B. Directed percolation and the transition to turbulence. Nature Reviews Physics. 2023;5:62-72. doi:10.1038/s42254-022-00539-y","ieee":"B. Hof, “Directed percolation and the transition to turbulence,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 62–72, 2023.","short":"B. Hof, Nature Reviews Physics 5 (2023) 62–72.","ista":"Hof B. 2023. Directed percolation and the transition to turbulence. Nature Reviews Physics. 5, 62–72.","chicago":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-022-00539-y.","apa":"Hof, B. (2023). Directed percolation and the transition to turbulence. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-022-00539-y","mla":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 62–72, doi:10.1038/s42254-022-00539-y."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"month":"01","publication_identifier":{"eissn":["2522-5820"]},"publication_status":"published","intvolume":" 5","abstract":[{"text":"It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective.","lang":"eng"}],"volume":5,"date_created":"2023-01-12T12:10:18Z","article_type":"original","scopus_import":"1","day":"01","author":[{"last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"oa_version":"None","title":"Directed percolation and the transition to turbulence"},{"publication_identifier":{"issn":["2214-7853"]},"publication_status":"published","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"}],"intvolume":" 78","article_type":"original","date_created":"2023-01-12T12:11:26Z","volume":78,"title":"Experimental analysis of Cascade CSTRs with step and pulse inputs","oa_version":"None","author":[{"full_name":"Khatoon, Bushra","last_name":"Khatoon","first_name":"Bushra"},{"last_name":"Kamil","full_name":"Kamil, Shoaib","id":"185a19af-dc7d-11ea-9b2f-8eb2201959e9","first_name":"Shoaib"},{"first_name":"Hitesh","last_name":"Babu","full_name":"Babu, Hitesh"},{"last_name":"Siraj Alam","full_name":"Siraj Alam, M.","first_name":"M."}],"day":"20","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"Part 1","citation":{"short":"B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings 78 (2023) 40–47.","ieee":"B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings, vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.","ama":"Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part 1):40-47. doi:10.1016/j.matpr.2022.11.037","mla":"Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier, 2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.","apa":"Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037","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.","chicago":"Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings. Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037."},"language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"month":"03","quality_controlled":"1","page":"40-47","type":"journal_article","date_updated":"2023-08-16T09:08:11Z","_id":"12172","publisher":"Elsevier","doi":"10.1016/j.matpr.2022.11.037","article_processing_charge":"No","date_published":"2023-03-20T00:00:00Z","publication":"Materials Today: Proceedings","status":"public","keyword":["General Medicine"],"year":"2023"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.","apa":"Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3","ista":"Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 1505–1560.","chicago":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.","short":"C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.","ieee":"C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560, 2023.","ama":"Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3"},"arxiv":1,"month":"05","department":[{"_id":"RoSe"}],"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."}],"intvolume":" 24","publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"title":"The Bose Gas in a box with Neumann boundary conditions","oa_version":"Preprint","author":[{"last_name":"Boccato","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","full_name":"Boccato, Chiara","first_name":"Chiara"},{"orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"scopus_import":"1","day":"01","article_type":"original","date_created":"2023-01-15T23:00:52Z","volume":24,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020"}],"publication":"Annales Henri Poincare","status":"public","date_published":"2023-05-01T00:00:00Z","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged.","ec_funded":1,"external_id":{"isi":["000910751800002"],"arxiv":["2205.15284"]},"isi":1,"year":"2023","page":"1505-1560","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2205.15284","open_access":"1"}],"publisher":"Springer Nature","doi":"10.1007/s00023-022-01252-3","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-16T11:34:03Z","_id":"12183"},{"keyword":["Oncology","Surgery"],"external_id":{"isi":["000852125500006"]},"related_material":{"record":[{"status":"public","relation":"other","id":"12115"}]},"year":"2023","isi":1,"date_published":"2023-01-01T00:00:00Z","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":"Annals of Surgical Oncology","status":"public","type":"journal_article","date_updated":"2023-09-05T15:18:37Z","_id":"12205","publisher":"Springer Nature","doi":"10.1245/s10434-022-12459-3","article_processing_charge":"No","quality_controlled":"1","ddc":["610"],"page":"35-45","file":[{"success":1,"file_name":"2023_AnnalsSurgicalOncology_Glajzer.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"36a1200e1011f4b2155a8041d0308f34","file_size":365865,"date_created":"2023-02-02T13:01:20Z","date_updated":"2023-02-02T13:01:20Z","creator":"dernst","file_id":"12490"}],"department":[{"_id":"JoDa"}],"month":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. 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.","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3.","mla":"Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3","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.","ieee":"J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023."},"language":[{"iso":"eng"}],"oa":1,"article_type":"original","date_created":"2023-01-16T09:44:36Z","volume":30,"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","oa_version":"Published Version","author":[{"last_name":"Glajzer","full_name":"Glajzer, Jacek","first_name":"Jacek"},{"full_name":"Castillo-Tong, Dan Cacsire","last_name":"Castillo-Tong","first_name":"Dan Cacsire"},{"first_name":"Rolf","last_name":"Richter","full_name":"Richter, Rolf"},{"last_name":"Vergote","full_name":"Vergote, Ignace","first_name":"Ignace"},{"full_name":"Kulbe, Hagen","last_name":"Kulbe","first_name":"Hagen"},{"full_name":"Vanderstichele, Adriaan","last_name":"Vanderstichele","first_name":"Adriaan"},{"full_name":"Ruscito, Ilary","last_name":"Ruscito","first_name":"Ilary"},{"first_name":"Fabian","full_name":"Trillsch, Fabian","last_name":"Trillsch"},{"first_name":"Alexander","last_name":"Mustea","full_name":"Mustea, Alexander"},{"last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","first_name":"Caroline"},{"first_name":"Charlie","last_name":"Gourley","full_name":"Gourley, Charlie"},{"last_name":"Gabra","full_name":"Gabra, Hani","first_name":"Hani"},{"full_name":"Taube, Eliane T.","last_name":"Taube","first_name":"Eliane T."},{"first_name":"Oliver","last_name":"Dorigo","full_name":"Dorigo, Oliver"},{"last_name":"Horst","full_name":"Horst, David","first_name":"David"},{"last_name":"Keunecke","full_name":"Keunecke, Carlotta","first_name":"Carlotta"},{"first_name":"Joanna","full_name":"Baum, Joanna","last_name":"Baum"},{"last_name":"Angelotti","full_name":"Angelotti, Timothy","first_name":"Timothy"},{"full_name":"Sehouli, Jalid","last_name":"Sehouli","first_name":"Jalid"},{"first_name":"Elena Ioana","full_name":"Braicu, Elena Ioana","last_name":"Braicu"}],"scopus_import":"1","day":"01","publication_status":"published","publication_identifier":{"eissn":["1534-4681"],"issn":["1068-9265"]},"file_date_updated":"2023-02-02T13:01:20Z","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Background: This study seeks to evaluate the impact of breast cancer (BRCA) gene status on tumor dissemination pattern, surgical outcome and survival in a multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data from 190 patients were gathered retrospectively. All patients had surgery at pOC and at least one further rOC surgery at four European high-volume centers. Patients were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut) and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor presentation, surgical outcome and survival data were analyzed between the two groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years younger and had significantly more tumor involvement upon diagnosis. Patients with BRCAmut disease showed higher debulking rates at all stages. Multivariate analysis showed that only patient age had significant predictive value for complete tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated with optimal debulking. Patients with BRCAmut disease showed significantly prolonged overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged in the BRCAmut group at all stages as well, reaching statistical significance during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a more aggressive course of disease with earlier onset and more extensive tumor dissemination at pOC. However, surgical outcome and OS were significantly better in patients with BRCAmut disease compared with patients with BRCAwt disease. We therefore propose to consider BRCAmut status in regard to patient selection for cytoreductive surgery, especially in rOC."}],"intvolume":" 30","has_accepted_license":"1"},{"intvolume":" 69","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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"}],"has_accepted_license":"1","file_date_updated":"2023-02-02T11:01:10Z","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"publication_status":"published","oa_version":"Published Version","title":"Local criteria for triangulating general manifolds","scopus_import":"1","day":"01","author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"first_name":"Ramsay","full_name":"Dyer, Ramsay","last_name":"Dyer"},{"first_name":"Arijit","full_name":"Ghosh, Arijit","last_name":"Ghosh"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220"}],"date_created":"2023-01-16T10:04:06Z","article_type":"original","volume":69,"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7."},"month":"01","file":[{"checksum":"46352e0ee71e460848f88685ca852681","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","file_id":"12488","creator":"dernst","date_updated":"2023-02-02T11:01:10Z","date_created":"2023-02-02T11:01:10Z","file_size":582850}],"department":[{"_id":"HeEd"}],"ddc":["510"],"page":"156-191","quality_controlled":"1","publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1007/s00454-022-00431-7","type":"journal_article","_id":"12287","date_updated":"2023-08-01T12:47:32Z","status":"public","publication":"Discrete & Computational Geometry","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses","grant_number":"M03073"}],"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_published":"2023-01-01T00:00:00Z","ec_funded":1,"external_id":{"isi":["000862193600001"]},"isi":1,"year":"2023","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"]},{"title":"Some effectivity results for primitive divisors of elliptic divisibility sequences","oa_version":"Published Version","scopus_import":"1","day":"03","author":[{"orcid":"0000-0002-0854-0306","first_name":"Matteo","last_name":"Verzobio","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","full_name":"Verzobio, Matteo"}],"date_created":"2023-01-16T11:46:19Z","article_type":"original","volume":325,"intvolume":" 325","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Let P be a nontorsion point on an elliptic curve defined over a number field K and consider the sequence {Bn}n∈N of the denominators of x(nP). We prove that every term of the sequence of the Bn has a primitive divisor for n greater than an effectively computable constant that we will explicitly compute. This constant will depend only on the model defining the curve.","lang":"eng"}],"has_accepted_license":"1","file_date_updated":"2023-11-13T09:50:41Z","publication_status":"published","publication_identifier":{"eissn":["0030-8730"]},"month":"11","arxiv":1,"file":[{"checksum":"b6218d16a72742d8bb38d6fc3c9bb8c6","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_PacificJourMaths_Verzobio.pdf","file_id":"14525","creator":"dernst","date_updated":"2023-11-13T09:50:41Z","file_size":389897,"date_created":"2023-11-13T09:50:41Z"}],"department":[{"_id":"TiBr"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Verzobio M. Some effectivity results for primitive divisors of elliptic divisibility sequences. Pacific Journal of Mathematics. 2023;325(2):331-351. doi:10.2140/pjm.2023.325.331","ieee":"M. Verzobio, “Some effectivity results for primitive divisors of elliptic divisibility sequences,” Pacific Journal of Mathematics, vol. 325, no. 2. Mathematical Sciences Publishers, pp. 331–351, 2023.","short":"M. Verzobio, Pacific Journal of Mathematics 325 (2023) 331–351.","ista":"Verzobio M. 2023. Some effectivity results for primitive divisors of elliptic divisibility sequences. Pacific Journal of Mathematics. 325(2), 331–351.","chicago":"Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic Divisibility Sequences.” Pacific Journal of Mathematics. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.325.331.","apa":"Verzobio, M. (2023). Some effectivity results for primitive divisors of elliptic divisibility sequences. Pacific Journal of Mathematics. Mathematical Sciences Publishers. https://doi.org/10.2140/pjm.2023.325.331","mla":"Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic Divisibility Sequences.” Pacific Journal of Mathematics, vol. 325, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–51, doi:10.2140/pjm.2023.325.331."},"issue":"2","publisher":"Mathematical Sciences Publishers","article_processing_charge":"Yes (in subscription journal)","doi":"10.2140/pjm.2023.325.331","type":"journal_article","_id":"12313","date_updated":"2023-12-13T11:18:14Z","ddc":["510"],"page":"331-351","quality_controlled":"1","external_id":{"arxiv":["2001.02987"],"isi":["001104766900001"]},"isi":1,"year":"2023","publication":"Pacific Journal of Mathematics","status":"public","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"acknowledgement":"This paper is part of the author’s PhD thesis at Università of Pisa. Moreover, this\r\nproject has received funding from the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement\r\nNo. 101034413. I thank the referee for many helpful comments.","date_published":"2023-11-03T00:00:00Z","ec_funded":1},{"date_published":"2023-01-10T00:00:00Z","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.","status":"public","publication":"Scientific Reports","year":"2023","isi":1,"external_id":{"isi":["001003345000051"]},"quality_controlled":"1","ddc":["510"],"_id":"12329","date_updated":"2023-08-01T12:31:40Z","type":"journal_article","article_processing_charge":"No","doi":"10.1038/s41598-022-19827-9","publisher":"Springer Nature","citation":{"apa":"Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9.","chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9.","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” Scientific Reports, vol. 13. Springer Nature, 2023.","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific Reports. 2023;13. doi:10.1038/s41598-022-19827-9"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"TaHa"}],"article_number":"468","file":[{"file_name":"2023_ScientificReports_Gomez.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"a8b83739f4a951e83e0b2a778f03b327","date_created":"2023-01-23T07:53:23Z","file_size":2167792,"creator":"dernst","date_updated":"2023-01-23T07:53:23Z","file_id":"12336"}],"month":"01","file_date_updated":"2023-01-23T07:53:23Z","publication_identifier":{"eissn":["2045-2322"]},"publication_status":"published","has_accepted_license":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 13","abstract":[{"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.","lang":"eng"}],"volume":13,"date_created":"2023-01-22T23:00:55Z","article_type":"original","scopus_import":"1","day":"10","author":[{"first_name":"Arturo","full_name":"Gómez, Arturo","last_name":"Gómez"},{"full_name":"Oliveira, Goncalo","id":"58abbde8-f455-11eb-a497-98c8fd71b905","last_name":"Oliveira","first_name":"Goncalo"}],"title":"New approaches to epidemic modeling on networks","oa_version":"Published Version"},{"department":[{"_id":"DaAl"}],"arxiv":1,"month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.","ista":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.","apa":"Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00441-x","mla":"Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 395–418, doi:10.1007/s00446-022-00441-x.","ama":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x","ieee":"V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list: A distribution-adaptive concurrent skip-list,” Distributed Computing, vol. 36. Springer Nature, pp. 395–418, 2023.","short":"V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing 36 (2023) 395–418."},"language":[{"iso":"eng"}],"oa":1,"date_created":"2023-01-22T23:00:55Z","article_type":"original","volume":36,"oa_version":"Preprint","title":"The splay-list: A distribution-adaptive concurrent skip-list","oaworkID":1,"day":"01","scopus_import":"1","author":[{"id":"2980135A-F248-11E8-B48F-1D18A9856A87","full_name":"Aksenov, Vitalii","last_name":"Aksenov","first_name":"Vitalii"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"Alexandra","last_name":"Drozdova","full_name":"Drozdova, Alexandra"},{"first_name":"Amirkeivan","last_name":"Mohtashami","full_name":"Mohtashami, Amirkeivan"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"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"}],"intvolume":" 36","external_id":{"isi":["000913424000001"],"oaworkID":["w4390499170"],"arxiv":["2008.01009"]},"year":"2023","isi":1,"date_published":"2023-09-01T00:00:00Z","status":"public","publication":"Distributed Computing","type":"journal_article","_id":"12330","date_updated":"2025-07-22T14:06:00Z","publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1007/s00446-022-00441-x","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2008.01009","open_access":"1"}],"page":"395-418"},{"author":[{"first_name":"Siqi","last_name":"Wang","full_name":"Wang, Siqi"},{"first_name":"Cheng","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang"},{"first_name":"Shulin","full_name":"Bai, Shulin","last_name":"Bai"},{"first_name":"Bingchao","last_name":"Qin","full_name":"Qin, Bingchao"},{"first_name":"Yingcai","last_name":"Zhu","full_name":"Zhu, Yingcai"},{"first_name":"Shaoping","full_name":"Zhan, Shaoping","last_name":"Zhan"},{"first_name":"Junqing","full_name":"Zheng, Junqing","last_name":"Zheng"},{"first_name":"Shuwei","full_name":"Tang, Shuwei","last_name":"Tang"},{"last_name":"Zhao","full_name":"Zhao, Li Dong","first_name":"Li Dong"}],"day":"24","scopus_import":"1","title":"Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe","oa_version":"Published Version","volume":35,"article_type":"original","date_created":"2023-01-22T23:00:55Z","has_accepted_license":"1","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"}],"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 35","publication_identifier":{"eissn":["1520-5002"],"issn":["0897-4756"]},"publication_status":"published","file_date_updated":"2023-08-14T12:57:25Z","month":"01","department":[{"_id":"MaIb"}],"file":[{"checksum":"b21dca2aa7a80c068bc256bdd1fea9df","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2023_ChemistryMaterials_Wang.pdf","success":1,"file_id":"14055","date_updated":"2023-08-14T12:57:25Z","creator":"dernst","date_created":"2023-08-14T12:57:25Z","file_size":2961043}],"oa":1,"language":[{"iso":"eng"}],"issue":"2","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. Chemistry of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542","short":"S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D. Zhao, Chemistry of Materials 35 (2023) 755–763.","ieee":"S. Wang et al., “Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials, vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.","chicago":"Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542.","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.","mla":"Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials, vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542.","apa":"Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023). Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.2c03542"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1021/acs.chemmater.2c03542","article_processing_charge":"No","publisher":"American Chemical Society","date_updated":"2023-08-14T12:57:44Z","_id":"12331","type":"journal_article","page":"755-763","ddc":["540"],"quality_controlled":"1","year":"2023","isi":1,"external_id":{"isi":["000914749700001"]},"project":[{"grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"}],"publication":"Chemistry of Materials","status":"public","date_published":"2023-01-24T00:00:00Z","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)."}]