[{"author":[{"full_name":"Nies, Fabian","first_name":"Fabian","last_name":"Nies"},{"first_name":"Tanita","full_name":"Wein, Tanita","last_name":"Wein"},{"last_name":"Hanke","full_name":"Hanke, Dustin M.","first_name":"Dustin M."},{"full_name":"Springstein, Benjamin L","first_name":"Benjamin L","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","last_name":"Springstein","orcid":"0000-0002-3461-5391"},{"last_name":"Alcorta","full_name":"Alcorta, Jaime","first_name":"Jaime"},{"last_name":"Taubenheim","full_name":"Taubenheim, Claudia","first_name":"Claudia"},{"first_name":"Tal","full_name":"Dagan, Tal","last_name":"Dagan"}],"_id":"14785","oa":1,"date_published":"2023-12-01T00:00:00Z","doi":"10.1111/1758-2229.13203","language":[{"iso":"eng"}],"year":"2023","publisher":"Wiley","type":"journal_article","month":"12","publication_identifier":{"eissn":["1758-2229"]},"quality_controlled":"1","isi":1,"volume":15,"article_type":"original","date_created":"2024-01-10T10:41:07Z","department":[{"_id":"MaLo"}],"acknowledgement":"We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla, Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann, FennaStücker,  and  Lidusha  Manivannan  for  technicalsupport.\r\nChilean National Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft, Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber: 101043835","pmid":1,"file_date_updated":"2024-01-16T09:42:10Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","intvolume":"        15","keyword":["Agricultural and Biological Sciences (miscellaneous)","Ecology","Evolution","Behavior and Systematics"],"day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","publication_status":"published","page":"656-668","abstract":[{"lang":"eng","text":"Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid‐encoded genes is similar to that of chromosome‐encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two <jats:italic>Synechocystis</jats:italic> sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited."}],"date_updated":"2024-01-16T09:46:12Z","status":"public","license":"https://creativecommons.org/licenses/by/4.0/","publication":"Environmental Microbiology Reports","title":"Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2024-01-16T09:42:10Z","success":1,"file_id":"14810","date_created":"2024-01-16T09:42:10Z","checksum":"d09ebb68fee61f4e2e09ec286c9cf1d3","file_size":1518350,"file_name":"2023_EnvirMicroBiolReports_Nies.pdf"}],"external_id":{"pmid":["37794696"],"isi":["001080203100001"]},"citation":{"chicago":"Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” <i>Environmental Microbiology Reports</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/1758-2229.13203\">https://doi.org/10.1111/1758-2229.13203</a>.","ieee":"F. Nies <i>et al.</i>, “Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803,” <i>Environmental Microbiology Reports</i>, vol. 15, no. 6. Wiley, pp. 656–668, 2023.","mla":"Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” <i>Environmental Microbiology Reports</i>, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:<a href=\"https://doi.org/10.1111/1758-2229.13203\">10.1111/1758-2229.13203</a>.","ista":"Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. 2023. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.","short":"F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim, T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.","apa":"Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim, C., &#38; Dagan, T. (2023). Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. <i>Environmental Microbiology Reports</i>. Wiley. <a href=\"https://doi.org/10.1111/1758-2229.13203\">https://doi.org/10.1111/1758-2229.13203</a>","ama":"Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. <i>Environmental Microbiology Reports</i>. 2023;15(6):656-668. doi:<a href=\"https://doi.org/10.1111/1758-2229.13203\">10.1111/1758-2229.13203</a>"},"issue":"6","has_accepted_license":"1"},{"isi":1,"volume":887,"article_type":"original","month":"08","quality_controlled":"1","publication_identifier":{"issn":["0048-9697"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"intvolume":"       887","article_number":"164010","date_created":"2024-01-10T10:43:08Z","pmid":1,"department":[{"_id":"LifeSc"}],"acknowledgement":"The authors thank the Czech Science Foundation (project No. 19-28399X) and the Czech Academy of Sciences (RVO: 60077344) and are sincerely grateful to the Bordeaux Imaging Centre (member of the France BioImaging national infrastructure, ANR-10-INBS-04) for help with TEM and to members of the Laboratory of Biological Effects of Metals and Laboratory of Aquaculture and Pathology of Aquatic Organisms (Ruđer Bošković Institute, Croatia) for the assistance with fieldwork.","date_published":"2023-08-20T00:00:00Z","author":[{"last_name":"Filipović Marijić","first_name":"Vlatka","full_name":"Filipović Marijić, Vlatka"},{"last_name":"Subirana","full_name":"Subirana, Maria Angels","first_name":"Maria Angels"},{"last_name":"Schaumlöffel","first_name":"Dirk","full_name":"Schaumlöffel, Dirk"},{"last_name":"Barišić","first_name":"Josip","full_name":"Barišić, Josip"},{"last_name":"Gontier","full_name":"Gontier, Etienne","first_name":"Etienne"},{"first_name":"Nesrete","full_name":"Krasnici, Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","last_name":"Krasnici"},{"last_name":"Mijošek","first_name":"Tatjana","full_name":"Mijošek, Tatjana"},{"full_name":"Hernández-Orts, Jesús S.","first_name":"Jesús S.","last_name":"Hernández-Orts"},{"last_name":"Scholz","first_name":"Tomáš","full_name":"Scholz, Tomáš"},{"last_name":"Erk","first_name":"Marijana","full_name":"Erk, Marijana"}],"_id":"14786","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.scitotenv.2023.164010","publisher":"Elsevier","year":"2023","publication":"Science of The Total Environment","external_id":{"isi":["001002645100001"],"pmid":["37169189"]},"title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","citation":{"ieee":"V. Filipović Marijić <i>et al.</i>, “First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS,” <i>Science of The Total Environment</i>, vol. 887. Elsevier, 2023.","chicago":"Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts, Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” <i>Science of The Total Environment</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>.","ama":"Filipović Marijić V, Subirana MA, Schaumlöffel D, et al. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. <i>Science of The Total Environment</i>. 2023;887. doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>","ista":"Filipović Marijić V, Subirana MA, Schaumlöffel D, Barišić J, Gontier E, Krasnici N, Mijošek T, Hernández-Orts JS, Scholz T, Erk M. 2023. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 887, 164010.","apa":"Filipović Marijić, V., Subirana, M. A., Schaumlöffel, D., Barišić, J., Gontier, E., Krasnici, N., … Erk, M. (2023). First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. <i>Science of The Total Environment</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>","mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” <i>Science of The Total Environment</i>, vol. 887, 164010, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>.","short":"V. Filipović Marijić, M.A. Subirana, D. Schaumlöffel, J. Barišić, E. Gontier, N. Krasnici, T. Mijošek, J.S. Hernández-Orts, T. Scholz, M. Erk, Science of The Total Environment 887 (2023)."},"oa_version":"None","publication_status":"published","day":"20","abstract":[{"text":"Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species.","lang":"eng"}],"status":"public","date_updated":"2024-01-16T10:04:57Z"},{"author":[{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"full_name":"Chase, Madeline A.","first_name":"Madeline A.","last_name":"Chase"},{"last_name":"McIntosh","full_name":"McIntosh, Hanna","first_name":"Hanna"},{"last_name":"Streisfeld","full_name":"Streisfeld, Matthew A.","first_name":"Matthew A."}],"_id":"14787","oa":1,"date_published":"2023-04-01T00:00:00Z","doi":"10.1111/mec.16849","language":[{"iso":"eng"}],"year":"2023","publisher":"Wiley","type":"journal_article","month":"04","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"quality_controlled":"1","isi":1,"article_type":"original","volume":32,"date_created":"2024-01-10T10:44:45Z","acknowledgement":"We thank Julian Catchen for making modifications to Stacks to aid this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and Nicholas H. Barton provided advice, stimulating discussion and critical feedback. The project was supported by National Science Foundation grant DEB-1258199.","department":[{"_id":"NiBa"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","intvolume":"        32","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"day":"01","publication_status":"published","oa_version":"Preprint","page":"2041-2054","abstract":[{"text":"Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes of<jats:italic>Mimulus aurantiacus</jats:italic>. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system.","lang":"eng"}],"date_updated":"2024-01-16T10:10:00Z","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.01.28.478139"}],"publication":"Molecular Ecology","title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","external_id":{"isi":["000919244600001"],"pmid":["36651268"]},"citation":{"apa":"Stankowski, S., Chase, M. A., McIntosh, H., &#38; Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>","ista":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054.","mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>.","ama":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. 2023;32(8):2041-2054. doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>","chicago":"Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>.","ieee":"S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone,” <i>Molecular Ecology</i>, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023."},"issue":"8"},{"title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"date_updated":"2024-01-16T10:15:09Z","file_id":"14811","checksum":"505d5cac36c14b073b68c7fed1a92bd3","date_created":"2024-01-16T10:15:09Z","file_size":5678069,"file_name":"2023_JCB_Mund.pdf"}],"external_id":{"isi":["000978065000001"],"pmid":["36734980"]},"publication":"Journal of Cell Biology","has_accepted_license":"1","issue":"3","citation":{"ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. 2023;222(3). doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>","short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>","mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>.","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038.","ieee":"M. Mund <i>et al.</i>, “Clathrin coats partially preassemble and subsequently bend during endocytosis,” <i>Journal of Cell Biology</i>, vol. 222, no. 3. Rockefeller University Press, 2023.","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2023. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>."},"abstract":[{"lang":"eng","text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"03","publication_status":"published","oa_version":"Published Version","status":"public","date_updated":"2024-01-16T10:17:05Z","volume":222,"article_type":"original","isi":1,"publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"quality_controlled":"1","month":"02","intvolume":"       222","keyword":["Cell Biology"],"file_date_updated":"2024-01-16T10:15:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","ddc":["570"],"acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair.","department":[{"_id":"AnSa"}],"pmid":1,"article_number":"e202206038","date_created":"2024-01-10T10:45:55Z","date_published":"2023-02-03T00:00:00Z","_id":"14788","oa":1,"author":[{"full_name":"Mund, Markus","first_name":"Markus","last_name":"Mund"},{"last_name":"Tschanz","first_name":"Aline","full_name":"Tschanz, Aline"},{"last_name":"Wu","first_name":"Yu-Le","full_name":"Wu, Yu-Le"},{"orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","last_name":"Frey","full_name":"Frey, Felix F","first_name":"Felix F"},{"first_name":"Johanna L.","full_name":"Mehl, Johanna L.","last_name":"Mehl"},{"first_name":"Marko","full_name":"Kaksonen, Marko","last_name":"Kaksonen"},{"last_name":"Avinoam","full_name":"Avinoam, Ori","first_name":"Ori"},{"last_name":"Schwarz","full_name":"Schwarz, Ulrich S.","first_name":"Ulrich S."},{"last_name":"Ries","first_name":"Jonas","full_name":"Ries, Jonas"}],"type":"journal_article","year":"2023","publisher":"Rockefeller University Press","doi":"10.1083/jcb.202206038","language":[{"iso":"eng"}]},{"day":"10","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","oa_version":"Published Version","abstract":[{"text":"A faithful reproduction of gloss is inherently difficult because of the limited dynamic range, peak luminance, and 3D capabilities of display devices. This work investigates how the display capabilities affect gloss appearance with respect to a real-world reference object. To this end, we employ an accurate imaging pipeline to achieve a perceptual gloss match between a virtual and real object presented side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display, which has not been previously attained to this extent. Based on this precise gloss reproduction, we conduct a series of gloss matching experiments to study how gloss perception degrades based on individual factors: object albedo, display luminance, dynamic range, stereopsis, and tone mapping. We support the study with a detailed analysis of individual factors, followed by an in-depth discussion on the observed perceptual effects. Our experiments demonstrate that stereoscopic presentation has a limited effect on the gloss matching task on our HDR display. However, both reduced luminance and dynamic range of the display reduce the perceived gloss. This means that the visual system cannot compensate for the changes in gloss appearance across luminance (lack of gloss constancy), and the tone mapping operator should be carefully selected when reproducing gloss on a low dynamic range (LDR) display.","lang":"eng"}],"date_updated":"2024-01-17T08:38:35Z","status":"public","publication":"Proceedings of the SIGGRAPH Asia 2023 Conference","title":"The effect of display capabilities on the gloss consistency between real and virtual objects","file":[{"date_updated":"2024-01-17T08:33:06Z","success":1,"date_created":"2024-01-17T08:33:06Z","file_id":"14823","checksum":"8abe27432ed222b50d1af9b3388db1b0","file_size":95967451,"file_name":"2023_SA_Chen.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"citation":{"ama":"Chen B, Jindal A, Piovarci M, et al. The effect of display capabilities on the gloss consistency between real and virtual objects. In: <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>. Association for Computing Machinery; 2023. doi:<a href=\"https://doi.org/10.1145/3610548.3618226\">10.1145/3610548.3618226</a>","apa":"Chen, B., Jindal, A., Piovarci, M., Wang, C., Seidel, H. P., Didyk, P., … Mantiuk, R. K. (2023). The effect of display capabilities on the gloss consistency between real and virtual objects. In <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>. Sydney, Australia: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3610548.3618226\">https://doi.org/10.1145/3610548.3618226</a>","ista":"Chen B, Jindal A, Piovarci M, Wang C, Seidel HP, Didyk P, Myszkowski K, Serrano A, Mantiuk RK. 2023. The effect of display capabilities on the gloss consistency between real and virtual objects. Proceedings of the SIGGRAPH Asia 2023 Conference. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 90.","mla":"Chen, Bin, et al. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>, 90, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3610548.3618226\">10.1145/3610548.3618226</a>.","short":"B. Chen, A. Jindal, M. Piovarci, C. Wang, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, R.K. Mantiuk, in:, Proceedings of the SIGGRAPH Asia 2023 Conference, Association for Computing Machinery, 2023.","ieee":"B. Chen <i>et al.</i>, “The effect of display capabilities on the gloss consistency between real and virtual objects,” in <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>, Sydney, Australia, 2023.","chicago":"Chen, Bin, Akshay Jindal, Michael Piovarci, Chao Wang, Hans Peter Seidel, Piotr Didyk, Karol Myszkowski, Ana Serrano, and Rafał K. Mantiuk. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” In <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3610548.3618226\">https://doi.org/10.1145/3610548.3618226</a>."},"project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication","grant_number":"M03319"}],"scopus_import":"1","has_accepted_license":"1","author":[{"last_name":"Chen","first_name":"Bin","full_name":"Chen, Bin"},{"full_name":"Jindal, Akshay","first_name":"Akshay","last_name":"Jindal"},{"orcid":"0000-0002-5062-4474","last_name":"Piovarci","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael","full_name":"Piovarci, Michael"},{"last_name":"Wang","full_name":"Wang, Chao","first_name":"Chao"},{"last_name":"Seidel","first_name":"Hans Peter","full_name":"Seidel, Hans Peter"},{"last_name":"Didyk","full_name":"Didyk, Piotr","first_name":"Piotr"},{"last_name":"Myszkowski","full_name":"Myszkowski, Karol","first_name":"Karol"},{"first_name":"Ana","full_name":"Serrano, Ana","last_name":"Serrano"},{"last_name":"Mantiuk","first_name":"Rafał K.","full_name":"Mantiuk, Rafał K."}],"_id":"14798","oa":1,"date_published":"2023-12-10T00:00:00Z","doi":"10.1145/3610548.3618226","language":[{"iso":"eng"}],"year":"2023","publisher":"Association for Computing Machinery","type":"conference","month":"12","publication_identifier":{"isbn":["9798400703157"]},"quality_controlled":"1","date_created":"2024-01-14T23:00:57Z","article_number":"90","department":[{"_id":"BeBi"}],"acknowledgement":"This work is supported by FWF Lise Meitner (Grant M 3319), Spanish Agencia Estatal de Investigación (project PID2022-141539NBI00), European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement\r\nN◦ 725253–EyeCode), Swiss National Science Foundation (Grant no. 200502), and academic gifts from Meta. We thank Dmitry Lubyako and Ali Özgür Yöntem for building the turntable for our experiment.","file_date_updated":"2024-01-17T08:33:06Z","conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","end_date":"2023-12-15","start_date":"2023-12-12","location":"Sydney, Australia"},"ddc":["000"],"article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","date_updated":"2024-01-17T07:49:52Z","abstract":[{"lang":"eng","text":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population\r\nmean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","publication_status":"published","oa_version":"Published Version","page":"1618-1629","has_accepted_license":"1","scopus_import":"1","issue":"6","arxiv":1,"citation":{"ieee":"B. R. Pauw <i>et al.</i>, “The human factor: Results of a small-angle scattering data analysis round robin,” <i>Journal of Applied Crystallography</i>, vol. 56, no. 6. pp. 1618–1629, 2023.","chicago":"Pauw, Brian R., Glen J. Smales, Andy S. Anker, Venkatasamy Annadurai, Daniel Balazs, Ralf Bienert, Wim G. Bouwman, et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” <i>Journal of Applied Crystallography</i>, 2023. <a href=\"https://doi.org/10.1107/S1600576723008324\">https://doi.org/10.1107/S1600576723008324</a>.","ama":"Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle scattering data analysis round robin. <i>Journal of Applied Crystallography</i>. 2023;56(6):1618-1629. doi:<a href=\"https://doi.org/10.1107/S1600576723008324\">10.1107/S1600576723008324</a>","apa":"Pauw, B. R., Smales, G. J., Anker, A. S., Annadurai, V., Balazs, D., Bienert, R., … Wuttke, J. (2023). The human factor: Results of a small-angle scattering data analysis round robin. <i>Journal of Applied Crystallography</i>. <a href=\"https://doi.org/10.1107/S1600576723008324\">https://doi.org/10.1107/S1600576723008324</a>","mla":"Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” <i>Journal of Applied Crystallography</i>, vol. 56, no. 6, 2023, pp. 1618–29, doi:<a href=\"https://doi.org/10.1107/S1600576723008324\">10.1107/S1600576723008324</a>.","short":"B.R. Pauw, G.J. Smales, A.S. Anker, V. Annadurai, D. Balazs, R. Bienert, W.G. Bouwman, I. Breßler, J. Breternitz, E.S. Brok, G. Bryant, A.J. Clulow, E.R. Crater, F. De Geuser, A.D. Giudice, J. Deumer, S. Disch, S. Dutt, K. Frank, E. Fratini, P.R.A.F. Garcia, E.P. Gilbert, M.B. Hahn, J. Hallett, M. Hohenschutz, M. Hollamby, S. Huband, J. Ilavsky, J.K. Jochum, M. Juelsholt, B.W. Mansel, P. Penttilä, R.K. Pittkowski, G. Portale, L.D. Pozzo, L. Rochels, J.M. Rosalie, P.E.J. Saloga, S. Seibt, A.J. Smith, G.N. Smith, G.A. Spiering, T.M. Stawski, O. Taché, A.F. Thünemann, K. Toth, A.E. Whitten, J. Wuttke, Journal of Applied Crystallography 56 (2023) 1618–1629.","ista":"Pauw BR, Smales GJ, Anker AS, Annadurai V, Balazs D, Bienert R, Bouwman WG, Breßler I, Breternitz J, Brok ES, Bryant G, Clulow AJ, Crater ER, De Geuser F, Giudice AD, Deumer J, Disch S, Dutt S, Frank K, Fratini E, Garcia PRAF, Gilbert EP, Hahn MB, Hallett J, Hohenschutz M, Hollamby M, Huband S, Ilavsky J, Jochum JK, Juelsholt M, Mansel BW, Penttilä P, Pittkowski RK, Portale G, Pozzo LD, Rochels L, Rosalie JM, Saloga PEJ, Seibt S, Smith AJ, Smith GN, Spiering GA, Stawski TM, Taché O, Thünemann AF, Toth K, Whitten AE, Wuttke J. 2023. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 56(6), 1618–1629."},"file":[{"creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":2165864,"file_name":"2023_JourApplCrystallography_Pauw.pdf","date_updated":"2024-01-17T07:47:35Z","success":1,"date_created":"2024-01-17T07:47:35Z","file_id":"14822","checksum":"dab30d4556360f2cecf99f4b7efb0ee9"}],"title":"The human factor: Results of a small-angle scattering data analysis round robin","external_id":{"arxiv":["2303.03772"]},"publication":"Journal of Applied Crystallography","type":"journal_article","year":"2023","doi":"10.1107/S1600576723008324","language":[{"iso":"eng"}],"date_published":"2023-12-01T00:00:00Z","_id":"14799","oa":1,"author":[{"full_name":"Pauw, Brian R.","first_name":"Brian R.","last_name":"Pauw"},{"last_name":"Smales","first_name":"Glen J.","full_name":"Smales, Glen J."},{"first_name":"Andy S.","full_name":"Anker, Andy S.","last_name":"Anker"},{"first_name":"Venkatasamy","full_name":"Annadurai, Venkatasamy","last_name":"Annadurai"},{"last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","first_name":"Daniel"},{"full_name":"Bienert, Ralf","first_name":"Ralf","last_name":"Bienert"},{"last_name":"Bouwman","full_name":"Bouwman, Wim G.","first_name":"Wim G."},{"last_name":"Breßler","full_name":"Breßler, Ingo","first_name":"Ingo"},{"first_name":"Joachim","full_name":"Breternitz, Joachim","last_name":"Breternitz"},{"last_name":"Brok","full_name":"Brok, Erik S.","first_name":"Erik S."},{"last_name":"Bryant","first_name":"Gary","full_name":"Bryant, Gary"},{"last_name":"Clulow","first_name":"Andrew J.","full_name":"Clulow, Andrew J."},{"first_name":"Erin R.","full_name":"Crater, Erin R.","last_name":"Crater"},{"last_name":"De Geuser","first_name":"Frédéric","full_name":"De Geuser, Frédéric"},{"full_name":"Giudice, Alessandra Del","first_name":"Alessandra Del","last_name":"Giudice"},{"full_name":"Deumer, Jérôme","first_name":"Jérôme","last_name":"Deumer"},{"last_name":"Disch","full_name":"Disch, Sabrina","first_name":"Sabrina"},{"last_name":"Dutt","first_name":"Shankar","full_name":"Dutt, Shankar"},{"first_name":"Kilian","full_name":"Frank, Kilian","last_name":"Frank"},{"last_name":"Fratini","first_name":"Emiliano","full_name":"Fratini, Emiliano"},{"first_name":"Paulo R.A.F.","full_name":"Garcia, Paulo R.A.F.","last_name":"Garcia"},{"full_name":"Gilbert, Elliot P.","first_name":"Elliot P.","last_name":"Gilbert"},{"last_name":"Hahn","first_name":"Marc B.","full_name":"Hahn, Marc B."},{"last_name":"Hallett","first_name":"James","full_name":"Hallett, James"},{"first_name":"Max","full_name":"Hohenschutz, Max","last_name":"Hohenschutz"},{"last_name":"Hollamby","first_name":"Martin","full_name":"Hollamby, Martin"},{"last_name":"Huband","full_name":"Huband, Steven","first_name":"Steven"},{"last_name":"Ilavsky","full_name":"Ilavsky, Jan","first_name":"Jan"},{"first_name":"Johanna K.","full_name":"Jochum, Johanna K.","last_name":"Jochum"},{"first_name":"Mikkel","full_name":"Juelsholt, Mikkel","last_name":"Juelsholt"},{"first_name":"Bradley W.","full_name":"Mansel, Bradley W.","last_name":"Mansel"},{"last_name":"Penttilä","first_name":"Paavo","full_name":"Penttilä, Paavo"},{"full_name":"Pittkowski, Rebecca K.","first_name":"Rebecca K.","last_name":"Pittkowski"},{"last_name":"Portale","first_name":"Giuseppe","full_name":"Portale, Giuseppe"},{"last_name":"Pozzo","full_name":"Pozzo, Lilo D.","first_name":"Lilo D."},{"full_name":"Rochels, Leonhard","first_name":"Leonhard","last_name":"Rochels"},{"last_name":"Rosalie","first_name":"Julian M.","full_name":"Rosalie, Julian M."},{"first_name":"Patrick E.J.","full_name":"Saloga, Patrick E.J.","last_name":"Saloga"},{"full_name":"Seibt, Susanne","first_name":"Susanne","last_name":"Seibt"},{"last_name":"Smith","first_name":"Andrew J.","full_name":"Smith, Andrew J."},{"last_name":"Smith","full_name":"Smith, Gregory N.","first_name":"Gregory N."},{"last_name":"Spiering","full_name":"Spiering, Glenn A.","first_name":"Glenn A."},{"full_name":"Stawski, Tomasz M.","first_name":"Tomasz M.","last_name":"Stawski"},{"first_name":"Olivier","full_name":"Taché, Olivier","last_name":"Taché"},{"last_name":"Thünemann","full_name":"Thünemann, Andreas F.","first_name":"Andreas F."},{"last_name":"Toth","first_name":"Kristof","full_name":"Toth, Kristof"},{"last_name":"Whitten","first_name":"Andrew E.","full_name":"Whitten, Andrew E."},{"last_name":"Wuttke","full_name":"Wuttke, Joachim","first_name":"Joachim"}],"intvolume":"        56","file_date_updated":"2024-01-17T07:47:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","ddc":["540"],"department":[{"_id":"LifeSc"}],"acknowledgement":"KT acknowledges the NIST–NRC postdoctoral fellowship program for support. This work was partially funded through the European Metrology Programme for Innovation and Research (EMPIR) project No. 17NRM04.\r\nCertain commercial equipment, instruments, materials or software are identified in this article in order to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement by NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. Open access funding enabled and organized by Projekt DEAL.","date_created":"2024-01-14T23:00:57Z","volume":56,"article_type":"original","publication_identifier":{"eissn":["1600-5767"],"issn":["0021-8898"]},"quality_controlled":"1","month":"12"},{"has_accepted_license":"1","ddc":["570"],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"citation":{"ama":"Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8318995\">10.5281/ZENODO.8318995</a>","apa":"Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8318995\">https://doi.org/10.5281/ZENODO.8318995</a>","ista":"Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8318995\">10.5281/ZENODO.8318995</a>.","mla":"Stankowski, Sean. <i>Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8318995\">10.5281/ZENODO.8318995</a>.","short":"S. Stankowski, (2023).","ieee":"S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.","chicago":"Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8318995\">https://doi.org/10.5281/ZENODO.8318995</a>."},"date_created":"2024-01-16T10:23:01Z","title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","related_material":{"record":[{"relation":"used_in_publication","id":"14796","status":"for_moderation"}]},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8318995","open_access":"1"}],"month":"09","type":"research_data_reference","status":"public","year":"2023","publisher":"Zenodo","date_updated":"2025-08-12T09:04:30Z","doi":"10.5281/ZENODO.8318995","abstract":[{"text":"This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode","lang":"eng"}],"day":"05","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","date_published":"2023-09-05T00:00:00Z","_id":"14812","oa":1,"contributor":[{"first_name":"Zusanna","last_name":"Zagrodzka"},{"last_name":"Garlovsky","first_name":"Martin"},{"orcid":"0000-0002-4530-8469","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka"},{"orcid":"0000-0002-1145-9226","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria"},{"first_name":"Diego Fernando","last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","last_name":"Lifchitz"},{"first_name":"Alan","last_name":"Le Moan"},{"first_name":"Erica","last_name":"Leder"},{"last_name":"Reeve","first_name":"James"},{"first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"first_name":"Roger","last_name":"Butlin"}],"author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean"}]},{"quality_controlled":"1","publication_identifier":{"eissn":["1533-7928"]},"month":"10","volume":24,"article_type":"original","isi":1,"department":[{"_id":"DaAl"}],"acknowledgement":"The work in Sections 1-5 was conducted while A. Beznosikov was a research intern in the Optimizationand Machine Learning Lab of Peter Richtárik at KAUST; this visit was funded by the KAUST Baseline Research Funding Scheme. The work of A. Beznosikov in Section 6 was conducted in Skoltech and was supported by Ministry of Science and Higher Education grant No. 075-10-2021-068. ","date_created":"2024-01-16T12:13:36Z","intvolume":"        24","article_processing_charge":"Yes (in subscription journal)","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T12:13:27Z","oa":1,"_id":"14815","author":[{"full_name":"Beznosikov, Aleksandr","first_name":"Aleksandr","last_name":"Beznosikov"},{"full_name":"Horvath, Samuel","first_name":"Samuel","last_name":"Horvath"},{"first_name":"Peter","full_name":"Richtarik, Peter","last_name":"Richtarik"},{"full_name":"Safaryan, Mher","first_name":"Mher","id":"dd546b39-0804-11ed-9c55-ef075c39778d","last_name":"Safaryan"}],"date_published":"2023-10-01T00:00:00Z","publisher":"Journal of Machine Learning Research","year":"2023","language":[{"iso":"eng"}],"type":"journal_article","external_id":{"arxiv":["2002.12410"],"isi":["001111578500001"]},"file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"14816","date_created":"2024-01-16T12:13:27Z","checksum":"c50f2b9db53938b755e30a085f464059","success":1,"date_updated":"2024-01-16T12:13:27Z","file_name":"2023_JMLR_Beznosikov.pdf","file_size":1510993}],"title":"On biased compression for distributed learning","publication":"Journal of Machine Learning Research","citation":{"chicago":"Beznosikov, Aleksandr, Samuel Horvath, Peter Richtarik, and Mher Safaryan. “On Biased Compression for Distributed Learning.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2023.","ieee":"A. Beznosikov, S. Horvath, P. Richtarik, and M. Safaryan, “On biased compression for distributed learning,” <i>Journal of Machine Learning Research</i>, vol. 24. Journal of Machine Learning Research, pp. 1–50, 2023.","short":"A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine Learning Research 24 (2023) 1–50.","apa":"Beznosikov, A., Horvath, S., Richtarik, P., &#38; Safaryan, M. (2023). On biased compression for distributed learning. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","mla":"Beznosikov, Aleksandr, et al. “On Biased Compression for Distributed Learning.” <i>Journal of Machine Learning Research</i>, vol. 24, Journal of Machine Learning Research, 2023, pp. 1–50.","ista":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. 2023. On biased compression for distributed learning. Journal of Machine Learning Research. 24, 1–50.","ama":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. On biased compression for distributed learning. <i>Journal of Machine Learning Research</i>. 2023;24:1-50."},"arxiv":1,"has_accepted_license":"1","abstract":[{"text":"In the last few years, various communication compression techniques have emerged as an indispensable tool helping to alleviate the communication bottleneck in distributed learning. However, despite the fact biased compressors often show superior performance in practice when compared to the much more studied and understood unbiased compressors, very little is known about them. In this work we study three classes of biased compression operators, two of which are new, and their performance when applied to (stochastic) gradient descent and distributed (stochastic) gradient descent. We show for the first time that biased compressors can lead to linear convergence rates both in the single node and distributed settings. We prove that distributed compressed SGD method, employed with error feedback mechanism, enjoys the ergodic rate O(δLexp[−μKδL]+(C+δD)Kμ), where δ≥1 is a compression parameter which grows when more compression is applied, L and μ are the smoothness and strong convexity constants, C captures stochastic gradient noise (C=0 if full gradients are computed on each node) and D captures the variance of the gradients at the optimum (D=0 for over-parameterized models). Further, via a theoretical study of several synthetic and empirical distributions of communicated gradients, we shed light on why and by how much biased compressors outperform their unbiased variants. Finally, we propose several new biased compressors with promising theoretical guarantees and practical performance.","lang":"eng"}],"oa_version":"Published Version","page":"1-50","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","date_updated":"2024-01-17T09:14:13Z","status":"public"},{"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"quality_controlled":"1","month":"12","article_type":"original","volume":136,"department":[{"_id":"EdHa"},{"_id":"CaHe"}],"acknowledgement":"We thank Prisca Liberali and Edouard Hannezo for many inspiring discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3. We would also like to thank The Company of Biologists for the opportunity to attend the 2023 workshop on Collective Cell Migration, and all workshop participants for discussions.\r\nC.S. was supported by a European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program (HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","pmid":1,"date_created":"2024-01-17T12:46:55Z","article_number":"jcs.261515","intvolume":"       136","keyword":["Cell Biology"],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14827","author":[{"orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","full_name":"Schwayer, Cornelia","first_name":"Cornelia"},{"full_name":"Brückner, David","first_name":"David","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"}],"date_published":"2023-12-27T00:00:00Z","year":"2023","publisher":"The Company of Biologists","doi":"10.1242/jcs.261515","language":[{"iso":"eng"}],"type":"journal_article","title":"Connecting theory and experiment in cell and tissue mechanics","external_id":{"pmid":["38149871"]},"publication":"Journal of Cell Science","citation":{"ama":"Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. 2023;136(24). doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).","mla":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>, vol. 136, no. 24, jcs. 261515, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>.","apa":"Schwayer, C., &#38; Brückner, D. (2023). Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>","ieee":"C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and tissue mechanics,” <i>Journal of Cell Science</i>, vol. 136, no. 24. The Company of Biologists, 2023.","chicago":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>."},"project":[{"grant_number":"343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"scopus_import":"1","issue":"24","abstract":[{"lang":"eng","text":"Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems."}],"day":"27","publication_status":"published","oa_version":"None","date_updated":"2024-01-22T13:35:48Z","status":"public"},{"publisher":"Springer Nature","year":"2023","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-47751-5_3","type":"conference","oa":1,"_id":"14829","author":[{"last_name":"Cohen","full_name":"Cohen, Shir","first_name":"Shir"},{"first_name":"Guy","full_name":"Goren, Guy","last_name":"Goren"},{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios"},{"first_name":"Alberto","full_name":"Sonnino, Alberto","last_name":"Sonnino"},{"last_name":"Spiegelman","first_name":"Alexander","full_name":"Spiegelman, Alexander"}],"date_published":"2023-12-01T00:00:00Z","acknowledgement":"This work is partially supported by Meta. Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N. Shir Cohen is supported by the Adams Fellowship Program of the Israel Academy of Sciences and Humanities.","department":[{"_id":"ElKo"}],"date_created":"2024-01-18T07:41:12Z","intvolume":"     13951","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","conference":{"name":"FC: Financial Cryptography and Data Security","end_date":"2023-05-05","start_date":"2023-05-01","location":"Bol, Brac, Croatia"},"quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031477508"],"eisbn":["9783031477515"],"eissn":["1611-3349"]},"month":"12","volume":13951,"date_updated":"2024-01-22T13:58:07Z","status":"public","abstract":[{"lang":"eng","text":"This paper explores a modular design architecture aimed at helping blockchains (and other SMR implementation) to scale to a very large number of processes. This comes in contrast to existing monolithic architectures that interleave transaction dissemination, ordering, and execution in a single functionality. To achieve this we first split the monolith to multiple layers which can use existing distributed computing primitives. The exact specifications of the data dissemination part are formally defined by the Proof of Availability & Retrieval (PoA &R) abstraction. Solutions to the PoA &R problem contain two related sub-protocols: one that “pushes” information into the network and another that “pulls” this information. Regarding the latter, there is a dearth of research literature which is rectified in this paper. We present a family of pulling sub-protocols and rigorously analyze them. Extensive simulations support the theoretical claims of efficiency and robustness in case of a very large number of players. Finally, actual implementation and deployment on a small number of machines (roughly the size of several industrial systems) demonstrates the viability of the architecture’s paradigm."}],"oa_version":"Submitted Version","page":"36-53","publication_status":"published","day":"01","project":[{"name":"Secure Network and Hardware for Efficient Blockchains","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","grant_number":"F8512"}],"citation":{"ieee":"S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Proof of availability and retrieval in a modular blockchain architecture,” in <i>27th International Conference on Financial Cryptography and Data Security</i>, Bol, Brac, Croatia, 2023, vol. 13951, pp. 36–53.","chicago":"Cohen, Shir, Guy Goren, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander Spiegelman. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” In <i>27th International Conference on Financial Cryptography and Data Security</i>, 13951:36–53. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">https://doi.org/10.1007/978-3-031-47751-5_3</a>.","ama":"Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. Proof of availability and retrieval in a modular blockchain architecture. In: <i>27th International Conference on Financial Cryptography and Data Security</i>. Vol 13951. Springer Nature; 2023:36-53. doi:<a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">10.1007/978-3-031-47751-5_3</a>","apa":"Cohen, S., Goren, G., Kokoris Kogias, E., Sonnino, A., &#38; Spiegelman, A. (2023). Proof of availability and retrieval in a modular blockchain architecture. In <i>27th International Conference on Financial Cryptography and Data Security</i> (Vol. 13951, pp. 36–53). Bol, Brac, Croatia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">https://doi.org/10.1007/978-3-031-47751-5_3</a>","short":"S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 36–53.","ista":"Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2023. Proof of availability and retrieval in a modular blockchain architecture. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13951, 36–53.","mla":"Cohen, Shir, et al. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” <i>27th International Conference on Financial Cryptography and Data Security</i>, vol. 13951, Springer Nature, 2023, pp. 36–53, doi:<a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">10.1007/978-3-031-47751-5_3</a>."},"alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://fc23.ifca.ai/preproceedings/150.pdf"}],"title":"Proof of availability and retrieval in a modular blockchain architecture","publication":"27th International Conference on Financial Cryptography and Data Security"},{"date_updated":"2025-07-14T09:10:02Z","status":"public","abstract":[{"text":"We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold p in [0,1] over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on 3 stochastic non-linear reinforcement learning tasks.","lang":"eng"}],"ec_funded":1,"day":"26","oa_version":"Preprint","publication_status":"published","page":"11926-11935","citation":{"ieee":"D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control policies for stochastic systems with reach-avoid guarantees,” in <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, Washington, DC, United States, 2023, vol. 37, no. 10, pp. 11926–11935.","chicago":"Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, 37:11926–35. Association for the Advancement of Artificial Intelligence, 2023. <a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">https://doi.org/10.1609/aaai.v37i10.26407</a>.","ama":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. In: <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>. Vol 37. Association for the Advancement of Artificial Intelligence; 2023:11926-11935. doi:<a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">10.1609/aaai.v37i10.26407</a>","apa":"Zikelic, D., Lechner, M., Henzinger, T. A., &#38; Chatterjee, K. (2023). Learning control policies for stochastic systems with reach-avoid guarantees. In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i> (Vol. 37, pp. 11926–11935). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">https://doi.org/10.1609/aaai.v37i10.26407</a>","mla":"Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, vol. 37, no. 10, Association for the Advancement of Artificial Intelligence, 2023, pp. 11926–35, doi:<a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">10.1609/aaai.v37i10.26407</a>.","ista":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. 2023. Learning control policies for stochastic systems with reach-avoid guarantees. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 11926–11935.","short":"D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2023, pp. 11926–11935."},"arxiv":1,"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093"},{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"issue":"10","title":"Learning control policies for stochastic systems with reach-avoid guarantees","related_material":{"record":[{"id":"14600","status":"public","relation":"earlier_version"}]},"external_id":{"arxiv":["2210.05308"]},"publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","year":"2023","publisher":"Association for the Advancement of Artificial Intelligence","doi":"10.1609/aaai.v37i10.26407","language":[{"iso":"eng"}],"type":"conference","_id":"14830","author":[{"orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","full_name":"Zikelic, Dorde","first_name":"Dorde"},{"full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"date_published":"2023-06-26T00:00:00Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","date_created":"2024-01-18T07:44:31Z","intvolume":"        37","keyword":["General Medicine"],"conference":{"location":"Washington, DC, United States","name":"AAAI: Conference on Artificial Intelligence","start_date":"2023-02-07","end_date":"2023-02-14"},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"]},"quality_controlled":"1","month":"06","volume":37},{"month":"12","quality_controlled":"1","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"isi":1,"volume":127,"article_type":"original","date_created":"2024-01-18T07:47:11Z","acknowledgement":"We acknowledge funding from ANR-22-CE06-0037-02. This work has received funding from the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754387.","department":[{"_id":"AnSa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"intvolume":"       127","author":[{"first_name":"Yann","full_name":"Sakref, Yann","last_name":"Sakref"},{"first_name":"Maitane","full_name":"Muñoz Basagoiti, Maitane","last_name":"Muñoz Basagoiti","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","orcid":"0000-0003-1483-1457"},{"first_name":"Zorana","full_name":"Zeravcic, Zorana","last_name":"Zeravcic"},{"last_name":"Rivoire","full_name":"Rivoire, Olivier","first_name":"Olivier"}],"oa":1,"_id":"14831","date_published":"2023-12-13T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1021/acs.jpcb.3c04627","publisher":"American Chemical Society","year":"2023","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2312.15940"}],"publication":"The Journal of Physical Chemistry B","external_id":{"arxiv":["2312.15940"],"isi":["001134068000001"]},"title":"On kinetic constraints that catalysis imposes on elementary processes","citation":{"ista":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 127(51), 10950–10959.","apa":"Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., &#38; Rivoire, O. (2023). On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>","short":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical Chemistry B 127 (2023) 10950–10959.","mla":"Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51, American Chemical Society, 2023, pp. 10950–59, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>.","ama":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. 2023;127(51):10950-10959. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>","chicago":"Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>.","ieee":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints that catalysis imposes on elementary processes,” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023."},"arxiv":1,"issue":"51","oa_version":"Preprint","publication_status":"published","page":"10950-10959","day":"13","abstract":[{"lang":"eng","text":"Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis."}],"date_updated":"2024-01-23T07:58:27Z","status":"public"},{"abstract":[{"text":"Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.","lang":"eng"}],"publication_status":"published","oa_version":"Published Version","day":"17","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","status":"public","date_updated":"2024-01-23T08:13:43Z","title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","file":[{"creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":3408944,"file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf","date_updated":"2024-01-23T08:10:00Z","success":1,"file_id":"14875","date_created":"2024-01-23T08:10:00Z","checksum":"ba6f9102d3a9fe6631c4fa398c5e4313"}],"publication":"Evolutionary Journal of the Linnean Society","has_accepted_license":"1","issue":"1","citation":{"ama":"Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. <i>Evolutionary Journal of the Linnean Society</i>. 2023;2(1). doi:<a href=\"https://doi.org/10.1093/evolinnean/kzad002\">10.1093/evolinnean/kzad002</a>","apa":"Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolinnean/kzad002\">https://doi.org/10.1093/evolinnean/kzad002</a>","mla":"Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” <i>Evolutionary Journal of the Linnean Society</i>, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evolinnean/kzad002\">10.1093/evolinnean/kzad002</a>.","ista":"Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.","short":"S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023).","ieee":"S. Stankowski <i>et al.</i>, “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” <i>Evolutionary Journal of the Linnean Society</i>, vol. 2, no. 1. Oxford University Press, 2023.","chicago":"Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolinnean/kzad002\">https://doi.org/10.1093/evolinnean/kzad002</a>."},"date_published":"2023-08-17T00:00:00Z","oa":1,"_id":"14833","author":[{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"last_name":"Zagrodzka","first_name":"Zuzanna B","full_name":"Zagrodzka, Zuzanna B"},{"last_name":"Galindo","first_name":"Juan","full_name":"Galindo, Juan"},{"last_name":"Montaño-Rendón","first_name":"Mauricio","full_name":"Montaño-Rendón, Mauricio"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Natalia","full_name":"Mikhailova, Natalia","last_name":"Mikhailova"},{"last_name":"Blakeslee","full_name":"Blakeslee, April M H","first_name":"April M H"},{"first_name":"Einar","full_name":"Arnason, Einar","last_name":"Arnason"},{"first_name":"Thomas","full_name":"Broquet, Thomas","last_name":"Broquet"},{"full_name":"Morales, Hernán E","first_name":"Hernán E","last_name":"Morales"},{"last_name":"Grahame","full_name":"Grahame, John W","first_name":"John W"},{"orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","first_name":"Roger K","full_name":"Butlin, Roger K"}],"type":"journal_article","publisher":"Oxford University Press","year":"2023","language":[{"iso":"eng"}],"doi":"10.1093/evolinnean/kzad002","article_type":"original","volume":2,"quality_controlled":"1","publication_identifier":{"eissn":["2752-938X"]},"month":"08","intvolume":"         2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","ddc":["570"],"file_date_updated":"2024-01-23T08:10:00Z","department":[{"_id":"NiBa"}],"acknowledgement":"Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).","article_number":"kzad002","date_created":"2024-01-18T07:54:10Z"},{"date_updated":"2024-01-23T12:23:35Z","status":"public","day":"02","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"oa_version":"Published Version","publication_status":"published","abstract":[{"text":"Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht.","lang":"ger"}],"citation":{"ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. 135(19), e202219314.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie 135 (2023).","mla":"Becker, Lea Marie, et al. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” <i>Angewandte Chemie</i>, vol. 135, no. 19, e202219314, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/ange.202219314\">10.1002/ange.202219314</a>.","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. <i>Angewandte Chemie</i>. Wiley. <a href=\"https://doi.org/10.1002/ange.202219314\">https://doi.org/10.1002/ange.202219314</a>","ama":"Becker LM, Berbon M, Vallet A, et al. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. <i>Angewandte Chemie</i>. 2023;135(19). doi:<a href=\"https://doi.org/10.1002/ange.202219314\">10.1002/ange.202219314</a>","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” <i>Angewandte Chemie</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/ange.202219314\">https://doi.org/10.1002/ange.202219314</a>.","ieee":"L. M. Becker <i>et al.</i>, “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten,” <i>Angewandte Chemie</i>, vol. 135, no. 19. Wiley, 2023."},"issue":"19","has_accepted_license":"1","publication":"Angewandte Chemie","title":"Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"dernst","checksum":"98e68d370159f7be52a3d7c8a8ee1198","file_id":"14876","date_created":"2024-01-23T08:57:01Z","date_updated":"2024-01-23T08:57:01Z","success":1,"file_name":"2023_AngewChem_Becker.pdf","file_size":1004676}],"doi":"10.1002/ange.202219314","language":[{"iso":"ger"}],"year":"2023","publisher":"Wiley","type":"journal_article","author":[{"full_name":"Becker, Lea Marie","first_name":"Lea Marie","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker"},{"last_name":"Berbon","first_name":"Mélanie","full_name":"Berbon, Mélanie"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"last_name":"Grelard","first_name":"Axelle","full_name":"Grelard, Axelle"},{"full_name":"Morvan, Estelle","first_name":"Estelle","last_name":"Morvan"},{"full_name":"Bardiaux, Benjamin","first_name":"Benjamin","last_name":"Bardiaux"},{"full_name":"Lichtenecker, Roman","first_name":"Roman","last_name":"Lichtenecker"},{"full_name":"Ernst, Matthias","first_name":"Matthias","last_name":"Ernst"},{"last_name":"Loquet","first_name":"Antoine","full_name":"Loquet, Antoine"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul"}],"_id":"14835","oa":1,"date_published":"2023-05-02T00:00:00Z","date_created":"2024-01-18T10:01:01Z","article_number":"e202219314","department":[{"_id":"PaSc"}],"acknowledgement":"Wir danken Albert A. Smith (Leipzig) für aufschlussreiche Diskussionen. Diese Arbeit wurde mit Mitteln des Europäischen Forschungsrats (StG-2012-311318 an P.S.) unterstützt und nutzte die Plattformen des Grenoble Instruct-ERIC Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) im Rahmen der Grenoble Partnership for Structural Biology (PSB) sowie die Einrichtungen und das Fachwissen der Biophysical and Structural Chemistry Platform (BPCS) am IECB, CNRS UAR3033, INSERM US001 und der Universität Bordeaux.","file_date_updated":"2024-01-23T08:57:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","ddc":["540"],"intvolume":"       135","keyword":["General Medicine"],"month":"05","publication_identifier":{"eissn":["1521-3757"],"issn":["0044-8249"]},"quality_controlled":"1","volume":135,"article_type":"original"},{"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2023.12.020","publisher":"Elsevier","year":"2023","date_published":"2023-12-29T00:00:00Z","author":[{"last_name":"Azadbakht","full_name":"Azadbakht, Ali","first_name":"Ali"},{"orcid":"0000-0003-3441-1337","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft","first_name":"Billie","full_name":"Meadowcroft, Billie"},{"full_name":"Majek, Juraj","first_name":"Juraj","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","last_name":"Majek"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela"},{"last_name":"Kraft","first_name":"Daniela J.","full_name":"Kraft, Daniela J."}],"oa":1,"_id":"14844","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_created":"2024-01-21T23:00:56Z","acknowledgement":"We gratefully acknowledge useful discussions with Casper van der Wel, help by Yogesh Shelke with PAA coverslip preparation, and support by Rachel Doherty with particle functionalization. A.A. and D.J.K. would like to thank Timon Idema and George Dadunashvili for initial attempts to simulate the experimental system. D.J.K. would like to thank the physics department at Leiden University for funding the PhD position of A.A. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC starting grant no. 802960).","department":[{"_id":"AnSa"}],"article_type":"original","month":"12","quality_controlled":"1","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"status":"public","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2024-01-23T09:26:35Z","publication_status":"inpress","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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"},"day":"29","ec_funded":1,"abstract":[{"lang":"eng","text":"Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules."}],"scopus_import":"1","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960"}],"citation":{"chicago":"Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>. Elsevier, n.d. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>.","ieee":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity in interactions between three membrane-wrapped colloidal spheres,” <i>Biophysical Journal</i>. Elsevier.","apa":"Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., &#38; Kraft, D. J. (n.d.). Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>","short":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal (n.d.).","mla":"Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>.","ista":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal.","ama":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>"},"publication":"Biophysical Journal","title":"Nonadditivity in interactions between three membrane-wrapped colloidal spheres","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.bpj.2023.12.020"}]},{"status":"public","date_updated":"2024-01-23T11:50:10Z","page":"136-161","oa_version":"Preprint","publication_status":"published","day":"01","abstract":[{"text":"Understanding the mechanisms of chaperones at the atomic level generally requires producing chaperone–client complexes in vitro. This task comes with significant challenges, because one needs to find conditions in which the client protein is presented to the chaperone in a state that binds and at the same time avoid the pitfalls of protein aggregation that are often inherent to such states. The strategy differs significantly for different client proteins and chaperones, but there are common underlying principles. Here, we discuss these principles and deduce the strategies that can be successfully applied for different chaperone–client complexes. We review successful biochemical strategies applied to making the client protein “binding competent” and illustrate the different strategies with examples of recent biophysical and biochemical studies.","lang":"eng"}],"editor":[{"last_name":"Hiller","first_name":"Sebastian","full_name":"Hiller, Sebastian"},{"last_name":"Liu","first_name":"Maili","full_name":"Liu, Maili"},{"full_name":"He, Lichun","first_name":"Lichun","last_name":"He"}],"alternative_title":["New Developments in NMR"],"citation":{"ieee":"I. Sučec and P. Schanda, “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies,” in <i>Biophysics of Molecular Chaperones</i>, vol. 29, S. Hiller, M. Liu, and L. He, Eds. Royal Society of Chemistry, 2023, pp. 136–161.","chicago":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” In <i>Biophysics of Molecular Chaperones</i>, edited by Sebastian Hiller, Maili Liu, and Lichun He, 29:136–61. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/bk9781839165986-00136\">https://doi.org/10.1039/bk9781839165986-00136</a>.","ama":"Sučec I, Schanda P. Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Hiller S, Liu M, He L, eds. <i>Biophysics of Molecular Chaperones</i>. Vol 29. Royal Society of Chemistry; 2023:136-161. doi:<a href=\"https://doi.org/10.1039/bk9781839165986-00136\">10.1039/bk9781839165986-00136</a>","short":"I. Sučec, P. Schanda, in:, S. Hiller, M. Liu, L. He (Eds.), Biophysics of Molecular Chaperones, Royal Society of Chemistry, 2023, pp. 136–161.","apa":"Sučec, I., &#38; Schanda, P. (2023). Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In S. Hiller, M. Liu, &#38; L. He (Eds.), <i>Biophysics of Molecular Chaperones</i> (Vol. 29, pp. 136–161). Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/bk9781839165986-00136\">https://doi.org/10.1039/bk9781839165986-00136</a>","ista":"Sučec I, Schanda P. 2023.Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Biophysics of Molecular Chaperones. New Developments in NMR, vol. 29, 136–161.","mla":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” <i>Biophysics of Molecular Chaperones</i>, edited by Sebastian Hiller et al., vol. 29, Royal Society of Chemistry, 2023, pp. 136–61, doi:<a href=\"https://doi.org/10.1039/bk9781839165986-00136\">10.1039/bk9781839165986-00136</a>."},"publication":"Biophysics of Molecular Chaperones","title":"Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2023-rpn28"}],"type":"book_chapter","language":[{"iso":"eng"}],"doi":"10.1039/bk9781839165986-00136","publisher":"Royal Society of Chemistry","year":"2023","date_published":"2023-11-01T00:00:00Z","author":[{"first_name":"I.","full_name":"Sučec, I.","last_name":"Sučec"},{"full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"oa":1,"_id":"14847","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","intvolume":"        29","date_created":"2024-01-22T08:04:57Z","department":[{"_id":"PaSc"}],"volume":29,"month":"11","quality_controlled":"1","publication_identifier":{"isbn":["9781839162824"],"eisbn":["9781839165993"]}},{"abstract":[{"lang":"eng","text":"Regulating protein states is considered the core function of chaperones. However, despite their importance to all major cellular processes, the conformational changes that chaperones impart on polypeptide chains are difficult to study directly due to their heterogeneous, dynamic, and multi-step nature. Here, we review recent advances towards this aim using single-molecule manipulation methods, which are rapidly revealing new mechanisms of conformational control and helping to define a different perspective on the chaperone function."}],"publication_status":"published","date_published":"2023-11-01T00:00:00Z","oa_version":"None","page":"278-318","day":"01","_id":"14848","author":[{"first_name":"F.","full_name":"Wruck, F.","last_name":"Wruck"},{"full_name":"Avellaneda Sarrió, Mario","first_name":"Mario","last_name":"Avellaneda Sarrió","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","orcid":"0000-0001-6406-524X"},{"last_name":"Naqvi","first_name":"M. M.","full_name":"Naqvi, M. M."},{"last_name":"Koers","full_name":"Koers, E. J.","first_name":"E. J."},{"last_name":"Till","full_name":"Till, K.","first_name":"K."},{"full_name":"Gross, L.","first_name":"L.","last_name":"Gross"},{"first_name":"F.","full_name":"Moayed, F.","last_name":"Moayed"},{"last_name":"Roland","full_name":"Roland, A.","first_name":"A."},{"full_name":"Heling, L. W. H. J.","first_name":"L. W. H. J.","last_name":"Heling"},{"first_name":"A.","full_name":"Mashaghi, A.","last_name":"Mashaghi"},{"full_name":"Tans, S. J.","first_name":"S. J.","last_name":"Tans"}],"type":"book_chapter","status":"public","publisher":"Royal Society of Chemistry","date_updated":"2024-01-23T12:01:53Z","year":"2023","language":[{"iso":"eng"}],"doi":"10.1039/bk9781839165986-00278","volume":29,"title":"Probing Single Chaperone Substrates","publication":"Biophysics of Molecular Chaperones","quality_controlled":"1","publication_identifier":{"eisbn":["9781839165993"],"isbn":["9781839162824"]},"month":"11","alternative_title":["New Developments in NMR"],"intvolume":"        29","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","editor":[{"first_name":"Sebastian","full_name":"Hiller, Sebastian","last_name":"Hiller"},{"last_name":"Liu","first_name":"Maili","full_name":"Liu, Maili"},{"last_name":"He","full_name":"He, Lichun","first_name":"Lichun"}],"citation":{"ieee":"F. Wruck <i>et al.</i>, “Probing Single Chaperone Substrates,” in <i>Biophysics of Molecular Chaperones</i>, vol. 29, S. Hiller, M. Liu, and L. He, Eds. Royal Society of Chemistry, 2023, pp. 278–318.","chicago":"Wruck, F., Mario Avellaneda Sarrió, M. M. Naqvi, E. J. Koers, K. Till, L. Gross, F. Moayed, et al. “Probing Single Chaperone Substrates.” In <i>Biophysics of Molecular Chaperones</i>, edited by Sebastian Hiller, Maili Liu, and Lichun He, 29:278–318. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/bk9781839165986-00278\">https://doi.org/10.1039/bk9781839165986-00278</a>.","ama":"Wruck F, Avellaneda Sarrió M, Naqvi MM, et al. Probing Single Chaperone Substrates. In: Hiller S, Liu M, He L, eds. <i>Biophysics of Molecular Chaperones</i>. Vol 29. Royal Society of Chemistry; 2023:278-318. doi:<a href=\"https://doi.org/10.1039/bk9781839165986-00278\">10.1039/bk9781839165986-00278</a>","apa":"Wruck, F., Avellaneda Sarrió, M., Naqvi, M. M., Koers, E. J., Till, K., Gross, L., … Tans, S. J. (2023). Probing Single Chaperone Substrates. In S. Hiller, M. Liu, &#38; L. He (Eds.), <i>Biophysics of Molecular Chaperones</i> (Vol. 29, pp. 278–318). Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/bk9781839165986-00278\">https://doi.org/10.1039/bk9781839165986-00278</a>","ista":"Wruck F, Avellaneda Sarrió M, Naqvi MM, Koers EJ, Till K, Gross L, Moayed F, Roland A, Heling LWHJ, Mashaghi A, Tans SJ. 2023.Probing Single Chaperone Substrates. In: Biophysics of Molecular Chaperones. New Developments in NMR, vol. 29, 278–318.","short":"F. Wruck, M. Avellaneda Sarrió, M.M. Naqvi, E.J. Koers, K. Till, L. Gross, F. Moayed, A. Roland, L.W.H.J. Heling, A. Mashaghi, S.J. Tans, in:, S. Hiller, M. Liu, L. He (Eds.), Biophysics of Molecular Chaperones, Royal Society of Chemistry, 2023, pp. 278–318.","mla":"Wruck, F., et al. “Probing Single Chaperone Substrates.” <i>Biophysics of Molecular Chaperones</i>, edited by Sebastian Hiller et al., vol. 29, Royal Society of Chemistry, 2023, pp. 278–318, doi:<a href=\"https://doi.org/10.1039/bk9781839165986-00278\">10.1039/bk9781839165986-00278</a>."},"department":[{"_id":"MiSi"}],"date_created":"2024-01-22T08:07:02Z"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.04448","open_access":"1"}],"publication":"The Annals of Probability","external_id":{"arxiv":["2206.04448"]},"title":"On the rightmost eigenvalue of non-Hermitian random matrices","project":[{"grant_number":"101020331","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"arxiv":1,"citation":{"chicago":"Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” <i>The Annals of Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/23-aop1643\">https://doi.org/10.1214/23-aop1643</a>.","ieee":"G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “On the rightmost eigenvalue of non-Hermitian random matrices,” <i>The Annals of Probability</i>, vol. 51, no. 6. Institute of Mathematical Statistics, pp. 2192–2242, 2023.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, The Annals of Probability 51 (2023) 2192–2242.","mla":"Cipolloni, Giorgio, et al. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” <i>The Annals of Probability</i>, vol. 51, no. 6, Institute of Mathematical Statistics, 2023, pp. 2192–242, doi:<a href=\"https://doi.org/10.1214/23-aop1643\">10.1214/23-aop1643</a>.","apa":"Cipolloni, G., Erdös, L., Schröder, D. J., &#38; Xu, Y. (2023). On the rightmost eigenvalue of non-Hermitian random matrices. <i>The Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-aop1643\">https://doi.org/10.1214/23-aop1643</a>","ista":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2023. On the rightmost eigenvalue of non-Hermitian random matrices. The Annals of Probability. 51(6), 2192–2242.","ama":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. On the rightmost eigenvalue of non-Hermitian random matrices. <i>The Annals of Probability</i>. 2023;51(6):2192-2242. doi:<a href=\"https://doi.org/10.1214/23-aop1643\">10.1214/23-aop1643</a>"},"issue":"6","page":"2192-2242","publication_status":"published","oa_version":"Preprint","day":"01","ec_funded":1,"abstract":[{"text":"We establish a precise three-term asymptotic expansion, with an optimal estimate of the error term, for the rightmost eigenvalue of an n×n random matrix with independent identically distributed complex entries as n tends to infinity. All terms in the expansion are universal.","lang":"eng"}],"date_updated":"2024-01-23T10:56:30Z","status":"public","month":"11","quality_controlled":"1","publication_identifier":{"issn":["0091-1798"]},"article_type":"original","volume":51,"date_created":"2024-01-22T08:08:41Z","acknowledgement":"The second and the fourth author were supported by the ERC Advanced Grant\r\n“RMTBeyond” No. 101020331. The third author was supported by Dr. Max Rössler, the\r\nWalter Haefner Foundation and the ETH Zürich Foundation.","department":[{"_id":"LaEr"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"intvolume":"        51","author":[{"first_name":"Giorgio","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992"},{"first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik J","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xu","full_name":"Xu, Yuanyuan","first_name":"Yuanyuan"}],"oa":1,"_id":"14849","date_published":"2023-11-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1214/23-aop1643","publisher":"Institute of Mathematical Statistics","year":"2023","type":"journal_article"},{"abstract":[{"lang":"eng","text":"Organization – or departure from a random pattern – in tropical deep convection is heavily studied due to its immediate relevance to climate sensitivity and extremes. Low-latitude convection has motivated numerical model idealizations, where the Coriolis force is removed and boundary conditions are simplified spatially and temporally. One of the most stunning aspects of such idealized simulated cloud organization is the spontaneous clumping of convection that can occur without any predetermining external perturbation, such as inhomogeneous surface boundary conditions or large-scale waves. Whereas individual convective rain cells measure only few kilometers in horizontal diameter, the clusters they form can often span hundreds or even thousands of kilometers. Hence, organization may emerge from the very small scales but can show effects at the synoptic scale. We refer to such emergent organization as convective self-organization. Convective self-organization thus features characteristics of emergence, such as non-trivial system-scale pattern formation or hysteresis. We summarize observational evidence for large-scale organization and briefly recap classical idealized modeling studies that yield convective self-aggregation – emergent organization under strongly idealized boundary conditions. We then focus on developing research, where temporal variation, such as the diurnal cycle, or two-way interactive surface properties yield distinct organizational modes. Convectively generated cold pools and mesoscale convective systems, both ubiquitous in nature, are thereby found to potentially play key roles in promoting – rather than suppressing – sustained system-scale organization."}],"page":"179-193","date_published":"2023-12-15T00:00:00Z","oa_version":"None","publication_status":"published","day":"15","_id":"14853","author":[{"full_name":"Haerter, Jan O.","first_name":"Jan O.","last_name":"Haerter"},{"first_name":"Caroline J","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"type":"book_chapter","status":"public","publisher":"Wiley","date_updated":"2024-01-23T12:40:36Z","year":"2023","language":[{"iso":"eng"}],"doi":"10.1002/9781119700357.ch8","title":"Mechanisms for the Self‐Organization of Tropical Deep Convection","publication":"Clouds and Their Climatic Impacts","quality_controlled":"1","publication_identifier":{"eisbn":["9781119700357"],"isbn":["9781119700319"],"issn":["2328-8779"]},"month":"12","alternative_title":["Geophysical Monograph Series"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","editor":[{"last_name":"Sullivan","full_name":"Sullivan, Sylvia","first_name":"Sylvia"},{"last_name":"Hoose","full_name":"Hoose, Corinna","first_name":"Corinna"}],"department":[{"_id":"CaMu"}],"citation":{"ama":"Haerter JO, Muller CJ. Mechanisms for the Self‐Organization of Tropical Deep Convection. In: Sullivan S, Hoose C, eds. <i>Clouds and Their Climatic Impacts</i>. Wiley; 2023:179-193. doi:<a href=\"https://doi.org/10.1002/9781119700357.ch8\">10.1002/9781119700357.ch8</a>","apa":"Haerter, J. O., &#38; Muller, C. J. (2023). Mechanisms for the Self‐Organization of Tropical Deep Convection. In S. Sullivan &#38; C. Hoose (Eds.), <i>Clouds and Their Climatic Impacts</i> (pp. 179–193). Wiley. <a href=\"https://doi.org/10.1002/9781119700357.ch8\">https://doi.org/10.1002/9781119700357.ch8</a>","mla":"Haerter, Jan O., and Caroline J. Muller. “Mechanisms for the Self‐Organization of Tropical Deep Convection.” <i>Clouds and Their Climatic Impacts</i>, edited by Sylvia Sullivan and Corinna Hoose, Wiley, 2023, pp. 179–93, doi:<a href=\"https://doi.org/10.1002/9781119700357.ch8\">10.1002/9781119700357.ch8</a>.","ista":"Haerter JO, Muller CJ. 2023.Mechanisms for the Self‐Organization of Tropical Deep Convection. In: Clouds and Their Climatic Impacts. Geophysical Monograph Series, , 179–193.","short":"J.O. Haerter, C.J. Muller, in:, S. Sullivan, C. Hoose (Eds.), Clouds and Their Climatic Impacts, Wiley, 2023, pp. 179–193.","ieee":"J. O. Haerter and C. J. Muller, “Mechanisms for the Self‐Organization of Tropical Deep Convection,” in <i>Clouds and Their Climatic Impacts</i>, S. Sullivan and C. Hoose, Eds. Wiley, 2023, pp. 179–193.","chicago":"Haerter, Jan O., and Caroline J Muller. “Mechanisms for the Self‐Organization of Tropical Deep Convection.” In <i>Clouds and Their Climatic Impacts</i>, edited by Sylvia Sullivan and Corinna Hoose, 179–93. Wiley, 2023. <a href=\"https://doi.org/10.1002/9781119700357.ch8\">https://doi.org/10.1002/9781119700357.ch8</a>."},"date_created":"2024-01-22T08:23:16Z"},{"month":"12","publication_identifier":{"issn":["2578-5885","2578-5893"]},"quality_controlled":"1","publication":"Pure and Applied Analysis","title":"Ubiquity of bound states for the strongly coupled polaron","article_type":"original","volume":5,"date_created":"2024-01-22T08:24:23Z","citation":{"ieee":"D. J. Mitrouskas and R. Seiringer, “Ubiquity of bound states for the strongly coupled polaron,” <i>Pure and Applied Analysis</i>, vol. 5, no. 4. Mathematical Sciences Publishers, pp. 973–1008, 2023.","chicago":"Mitrouskas, David Johannes, and Robert Seiringer. “Ubiquity of Bound States for the Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2023. <a href=\"https://doi.org/10.2140/paa.2023.5.973\">https://doi.org/10.2140/paa.2023.5.973</a>.","ama":"Mitrouskas DJ, Seiringer R. Ubiquity of bound states for the strongly coupled polaron. <i>Pure and Applied Analysis</i>. 2023;5(4):973-1008. doi:<a href=\"https://doi.org/10.2140/paa.2023.5.973\">10.2140/paa.2023.5.973</a>","mla":"Mitrouskas, David Johannes, and Robert Seiringer. “Ubiquity of Bound States for the Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>, vol. 5, no. 4, Mathematical Sciences Publishers, 2023, pp. 973–1008, doi:<a href=\"https://doi.org/10.2140/paa.2023.5.973\">10.2140/paa.2023.5.973</a>.","ista":"Mitrouskas DJ, Seiringer R. 2023. Ubiquity of bound states for the strongly coupled polaron. Pure and Applied Analysis. 5(4), 973–1008.","apa":"Mitrouskas, D. J., &#38; Seiringer, R. (2023). Ubiquity of bound states for the strongly coupled polaron. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2023.5.973\">https://doi.org/10.2140/paa.2023.5.973</a>","short":"D.J. Mitrouskas, R. Seiringer, Pure and Applied Analysis 5 (2023) 973–1008."},"department":[{"_id":"RoSe"}],"article_processing_charge":"No","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         5","keyword":["General Medicine"],"author":[{"full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"_id":"14854","day":"15","oa_version":"None","page":"973-1008","date_published":"2023-12-15T00:00:00Z","publication_status":"published","abstract":[{"text":"\r\nAbstract\r\nWe study the spectrum of the Fröhlich Hamiltonian for the polaron at fixed total momentum. We prove the existence of excited eigenvalues between the ground state energy and the essential spectrum at strong coupling. In fact, our main result shows that the number of excited energy bands diverges in the strong coupling limit. To prove this we derive upper bounds for the min-max values of the corresponding fiber Hamiltonians and compare them with the bottom of the essential spectrum, a lower bound on which was recently obtained by Brooks and Seiringer (Comm. Math. Phys. 404:1 (2023), 287–337). The upper bounds are given in terms of the ground state energy band shifted by momentum-independent excitation energies determined by an effective Hamiltonian of Bogoliubov type.","lang":"eng"}],"doi":"10.2140/paa.2023.5.973","language":[{"iso":"eng"}],"year":"2023","date_updated":"2024-01-23T12:55:12Z","publisher":"Mathematical Sciences Publishers","status":"public","type":"journal_article"}]