[{"external_id":{"isi":["000999436400001"]},"year":"2023","intvolume":"        50","month":"06","date_published":"2023-06-16T00:00:00Z","article_number":"e2023GL103043","acknowledgement":"This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie Actions Grant 101026058. The authors acknowl-edge the dedicated collection of field data by many parties since 2001, including those acknowledged for the cited works on Arolla Glacier. The authors would like to thank Fabienne Meier, Alice Zaugg, Raphael Willi, Maria Grundmann, and Marta Corrà for assistance in the field for the summers of 2021 and 2022. Off-glacier data provided by Grand Dixence SA (Arolla) and MeteoSwiss are kindly acknowledged. Simone Fatichi is thanked for the provision and support in the use of the Tethys-Chloris model. We thank Editor Mathieu Morlighem and two anonymous reviewers whose comments have helped to improve the quality of the manuscript.","date_updated":"2024-01-16T08:42:36Z","keyword":["General Earth and Planetary Sciences","Geophysics"],"issue":"11","oa":1,"doi":"10.1029/2023gl103043","publication":"Geophysical Research Letters","isi":1,"oa_version":"Published Version","volume":50,"ddc":["550"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2024-01-10T09:28:34Z","day":"16","status":"public","article_processing_charge":"No","department":[{"_id":"FrPe"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"American Geophysical Union","file":[{"checksum":"391a3005c95340a0ae129ce4fbdf2bae","access_level":"open_access","relation":"main_file","file_size":2529327,"creator":"dernst","content_type":"application/pdf","file_id":"14805","date_created":"2024-01-16T08:35:02Z","date_updated":"2024-01-16T08:35:02Z","file_name":"2023_GeophysicalResearchLetter_Shaw.pdf","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The decaying near‐surface boundary layer of a retreating alpine glacier","author":[{"full_name":"Shaw, Thomas E.","first_name":"Thomas E.","last_name":"Shaw"},{"first_name":"Pascal","last_name":"Buri","full_name":"Buri, Pascal"},{"last_name":"McCarthy","first_name":"Michael","full_name":"McCarthy, Michael"},{"full_name":"Miles, Evan S.","first_name":"Evan S.","last_name":"Miles"},{"full_name":"Ayala, Álvaro","first_name":"Álvaro","last_name":"Ayala"},{"orcid":"0000-0002-5554-8087","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca"}],"publication_status":"published","publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"citation":{"ama":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. The decaying near‐surface boundary layer of a retreating alpine glacier. <i>Geophysical Research Letters</i>. 2023;50(11). doi:<a href=\"https://doi.org/10.1029/2023gl103043\">10.1029/2023gl103043</a>","short":"T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical Research Letters 50 (2023).","ieee":"T. E. Shaw, P. Buri, M. McCarthy, E. S. Miles, Á. Ayala, and F. Pellicciotti, “The decaying near‐surface boundary layer of a retreating alpine glacier,” <i>Geophysical Research Letters</i>, vol. 50, no. 11. American Geophysical Union, 2023.","ista":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. 2023. The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. 50(11), e2023GL103043.","chicago":"Shaw, Thomas E., Pascal Buri, Michael McCarthy, Evan S. Miles, Álvaro Ayala, and Francesca Pellicciotti. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” <i>Geophysical Research Letters</i>. American Geophysical Union, 2023. <a href=\"https://doi.org/10.1029/2023gl103043\">https://doi.org/10.1029/2023gl103043</a>.","apa":"Shaw, T. E., Buri, P., McCarthy, M., Miles, E. S., Ayala, Á., &#38; Pellicciotti, F. (2023). The decaying near‐surface boundary layer of a retreating alpine glacier. <i>Geophysical Research Letters</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2023gl103043\">https://doi.org/10.1029/2023gl103043</a>","mla":"Shaw, Thomas E., et al. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” <i>Geophysical Research Letters</i>, vol. 50, no. 11, e2023GL103043, American Geophysical Union, 2023, doi:<a href=\"https://doi.org/10.1029/2023gl103043\">10.1029/2023gl103043</a>."},"file_date_updated":"2024-01-16T08:35:02Z","type":"journal_article","abstract":[{"lang":"eng","text":"The presence of a developed boundary layer decouples a glacier's response from ambient conditions, suggesting that sensitivity to climate change is increased by glacier retreat. To test this hypothesis, we explore six years of distributed meteorological data on a small Swiss glacier in the period 2001–2022. Large glacier fragmentation has occurred since 2001 (−35% area change up to 2022) coinciding with notable frontal retreat, an observed switch from down‐glacier katabatic to up‐glacier valley winds and an increased sensitivity (ratio) of on‐glacier to off‐glacier temperature. As the glacier ceases to develop density‐driven katabatic winds, sensible heat fluxes on the glacier are increasingly determined by the conditions occurring outside the boundary layer of the glacier, sealing the glacier's demise as the climate continues to warm and experience an increased frequency of extreme summers."}],"_id":"14779","quality_controlled":"1"},{"keyword":["Applied Mathematics","Modeling and Simulation","Statistics and Probability"],"date_updated":"2024-01-16T08:49:51Z","oa":1,"date_published":"2023-09-01T00:00:00Z","intvolume":"       163","month":"09","acknowledgement":"The authors would like to thank the editor, the associated editor and two anonymous referees for their many critical suggestions which have significantly improved the paper. The authors are also grateful to Zhigang Bao and Ji Oon Lee for many helpful discussions. The first author also wants to thank Hari Bercovici for many useful comments. The first author is partially supported by National Science Foundation DMS-2113489 and the second author is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","year":"2023","external_id":{"isi":["001113615900001"],"arxiv":["2302.13502"]},"page":"25-60","date_created":"2024-01-10T09:29:25Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"day":"01","status":"public","volume":163,"ec_funded":1,"oa_version":"Published Version","isi":1,"publication":"Stochastic Processes and their Applications","doi":"10.1016/j.spa.2023.05.009","title":"Spiked multiplicative random matrices and principal components","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ding, Xiucai","first_name":"Xiucai","last_name":"Ding"},{"id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d","first_name":"Hong Chang","last_name":"Ji","full_name":"Ji, Hong Chang"}],"file":[{"access_level":"open_access","relation":"main_file","checksum":"46a708b0cd5569a73d0f3d6c3e0a44dc","creator":"dernst","file_size":1870349,"content_type":"application/pdf","file_id":"14806","date_updated":"2024-01-16T08:47:31Z","date_created":"2024-01-16T08:47:31Z","file_name":"2023_StochasticProcAppl_Ding.pdf","success":1}],"has_accepted_license":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"LaEr"}],"_id":"14780","quality_controlled":"1","publication_identifier":{"eissn":["1879-209X"],"issn":["0304-4149"]},"citation":{"chicago":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” <i>Stochastic Processes and Their Applications</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">https://doi.org/10.1016/j.spa.2023.05.009</a>.","ista":"Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 163, 25–60.","short":"X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023) 25–60.","ieee":"X. Ding and H. C. Ji, “Spiked multiplicative random matrices and principal components,” <i>Stochastic Processes and their Applications</i>, vol. 163. Elsevier, pp. 25–60, 2023.","ama":"Ding X, Ji HC. Spiked multiplicative random matrices and principal components. <i>Stochastic Processes and their Applications</i>. 2023;163:25-60. doi:<a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">10.1016/j.spa.2023.05.009</a>","mla":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” <i>Stochastic Processes and Their Applications</i>, vol. 163, Elsevier, 2023, pp. 25–60, doi:<a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">10.1016/j.spa.2023.05.009</a>.","apa":"Ding, X., &#38; Ji, H. C. (2023). Spiked multiplicative random matrices and principal components. <i>Stochastic Processes and Their Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">https://doi.org/10.1016/j.spa.2023.05.009</a>"},"arxiv":1,"abstract":[{"lang":"eng","text":"In this paper, we study the eigenvalues and eigenvectors of the spiked invariant multiplicative models when the randomness is from Haar matrices. We establish the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩ for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence rates. Moreover, we prove that the non-outlier eigenvalues stick with those of the unspiked matrices and the non-outlier eigenvectors are delocalized. The results also hold near the so-called BBP transition and for degenerate spikes. On one hand, our results can be regarded as a refinement of the counterparts of [12] under additional regularity conditions. On the other hand, they can be viewed as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar random matrix."}],"file_date_updated":"2024-01-16T08:47:31Z","type":"journal_article","project":[{"call_identifier":"H2020","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"publication_status":"published"},{"date_created":"2024-01-10T09:41:21Z","status":"public","day":"11","pmid":1,"volume":58,"oa_version":"Preprint","doi":"10.1016/j.devcel.2023.06.009","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"publication":"Developmental Cell","date_updated":"2024-01-16T08:56:36Z","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"issue":"17","oa":1,"month":"09","intvolume":"        58","date_published":"2023-09-11T00:00:00Z","acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","year":"2023","page":"1578-1592.e5","external_id":{"pmid":["37463577"]},"_id":"14781","quality_controlled":"1","citation":{"ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. 2023;58(17):1578-1592.e5. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>","ieee":"K. J. Westerich <i>et al.</i>, “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” <i>Developmental Cell</i>, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>.","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>."},"publication_identifier":{"issn":["1534-5807"]},"type":"journal_article","abstract":[{"text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","author":[{"last_name":"Westerich","first_name":"Kim Joana","full_name":"Westerich, Kim Joana"},{"last_name":"Tarbashevich","first_name":"Katsiaryna","full_name":"Tarbashevich, Katsiaryna"},{"full_name":"Schick, Jan","last_name":"Schick","first_name":"Jan"},{"full_name":"Gupta, Antra","last_name":"Gupta","first_name":"Antra"},{"last_name":"Zhu","first_name":"Mingzhao","full_name":"Zhu, Mingzhao"},{"first_name":"Kenneth","last_name":"Hull","full_name":"Hull, Kenneth"},{"full_name":"Romo, Daniel","last_name":"Romo","first_name":"Daniel"},{"first_name":"Dagmar","last_name":"Zeuschner","full_name":"Zeuschner, Dagmar"},{"full_name":"Goudarzi, Mohammad","first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi"},{"full_name":"Gross-Thebing, Theresa","last_name":"Gross-Thebing","first_name":"Theresa"},{"full_name":"Raz, Erez","first_name":"Erez","last_name":"Raz"}],"publisher":"Elsevier","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"Bio"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Baldauf, Lucia","last_name":"Baldauf","first_name":"Lucia"},{"last_name":"Frey","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F"},{"first_name":"Marcos","last_name":"Arribas Perez","full_name":"Arribas Perez, Marcos"},{"last_name":"Idema","first_name":"Timon","full_name":"Idema, Timon"},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."}],"title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","file":[{"creator":"dernst","file_size":3285810,"file_id":"14807","content_type":"application/pdf","checksum":"70566e54cd95ea6df340909ad44c5cd5","access_level":"open_access","relation":"main_file","file_name":"2023_BiophysicalJournal_Baldauf.pdf","success":1,"date_created":"2024-01-16T09:09:29Z","date_updated":"2024-01-16T09:09:29Z"}],"publisher":"Elsevier","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","_id":"14782","abstract":[{"lang":"eng","text":"The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration."}],"type":"journal_article","file_date_updated":"2024-01-16T09:09:29Z","citation":{"ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. 2023;122(11):2311-2324. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324.","ista":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 122(11), 2311–2324.","ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” <i>Biophysical Journal</i>, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>.","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., &#38; Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>","mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>."},"publication_identifier":{"issn":["0006-3495"]},"publication_status":"published","oa":1,"issue":"11","keyword":["Biophysics"],"date_updated":"2024-01-16T09:20:03Z","acknowledgement":"We thank Jeffrey den Haan for protein purification, Kristina Ganzinger (AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago) for the CP constructs, and Michael Way (Crick Institute) for providing purified human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation experiments that formed the basis for establishing the eDICE method, to Federico Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE, and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling. Lennard van Buren is thanked for his help with image analysis to quantify actin concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher for insightful and inspiring discussions. We acknowledge financial support from The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.","date_published":"2023-06-06T00:00:00Z","month":"06","intvolume":"       122","year":"2023","external_id":{"isi":["001016792600001"],"pmid":["36806830"]},"page":"2311-2324","day":"06","status":"public","ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2024-01-10T09:45:48Z","volume":122,"pmid":1,"oa_version":"Published Version","isi":1,"related_material":{"link":[{"url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing","relation":"software"}]},"publication":"Biophysical Journal","doi":"10.1016/j.bpj.2023.02.018"},{"volume":12,"pmid":1,"day":"11","status":"public","date_created":"2024-01-10T09:46:35Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"publication":"Cells","doi":"10.3390/cells12081133","oa_version":"Published Version","isi":1,"article_number":"1133","acknowledgement":"This research was funded by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie Teillon for support with setting up the MEA system for the two-photon microscope. We would also like to thank Tayfun Palaz for their technical assistance with the EM preparations.","date_published":"2023-04-11T00:00:00Z","month":"04","intvolume":"        12","oa":1,"issue":"8","keyword":["General Medicine"],"date_updated":"2024-01-16T09:29:35Z","external_id":{"isi":["000977445700001"],"pmid":["37190042"]},"year":"2023","abstract":[{"text":"Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy.","lang":"eng"}],"file_date_updated":"2024-01-16T09:26:52Z","type":"journal_article","publication_identifier":{"issn":["2073-4409"]},"citation":{"apa":"Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke, J. H. R., &#38; Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells12081133\">https://doi.org/10.3390/cells12081133</a>","mla":"Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” <i>Cells</i>, vol. 12, no. 8, 1133, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/cells12081133\">10.3390/cells12081133</a>.","ista":"Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 12(8), 1133.","ieee":"G. T. Cheung <i>et al.</i>, “Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses,” <i>Cells</i>, vol. 12, no. 8. MDPI, 2023.","short":"G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke, N. Rouach, Cells 12 (2023).","ama":"Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. <i>Cells</i>. 2023;12(8). doi:<a href=\"https://doi.org/10.3390/cells12081133\">10.3390/cells12081133</a>","chicago":"Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du, Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” <i>Cells</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/cells12081133\">https://doi.org/10.3390/cells12081133</a>."},"quality_controlled":"1","_id":"14783","publication_status":"published","publisher":"MDPI","has_accepted_license":"1","author":[{"full_name":"Cheung, Giselle T","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","last_name":"Cheung"},{"last_name":"Chever","first_name":"Oana","full_name":"Chever, Oana"},{"full_name":"Rollenhagen, Astrid","first_name":"Astrid","last_name":"Rollenhagen"},{"first_name":"Nicole","last_name":"Quenech’du","full_name":"Quenech’du, Nicole"},{"full_name":"Ezan, Pascal","last_name":"Ezan","first_name":"Pascal"},{"first_name":"Joachim H. R.","last_name":"Lübke","full_name":"Lübke, Joachim H. R."},{"full_name":"Rouach, Nathalie","first_name":"Nathalie","last_name":"Rouach"}],"title":"Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"6798cd75d8857976fbc58a43fd173d68","access_level":"open_access","relation":"main_file","file_size":7931643,"creator":"dernst","file_id":"14808","content_type":"application/pdf","date_updated":"2024-01-16T09:26:52Z","date_created":"2024-01-16T09:26:52Z","file_name":"2023_Cells_Cheung.pdf","success":1}],"department":[{"_id":"SiHi"}],"article_processing_charge":"Yes","article_type":"original","language":[{"iso":"eng"}]},{"year":"2023","external_id":{"pmid":["37624890"],"isi":["001054596800007"]},"keyword":["Multidisciplinary"],"date_updated":"2024-01-16T09:38:58Z","oa":1,"issue":"34","date_published":"2023-08-25T00:00:00Z","month":"08","intvolume":"         9","article_number":"adg1610","acknowledgement":"This work was supported by a postdoctoral fellowship from the Swedish Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W., a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the program of fundamental research (theme 65.1) of the Institute for Biomedical Problems of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K., D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation, and Karolinska Institutet to L.S.W.","oa_version":"Published Version","isi":1,"publication":"Science Advances","doi":"10.1126/sciadv.adg1610","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2024-01-10T09:48:01Z","ddc":["570"],"status":"public","day":"25","volume":9,"pmid":1,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes","department":[{"_id":"FlSc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells","author":[{"full_name":"Gallardo-Dodd, Carlos J.","last_name":"Gallardo-Dodd","first_name":"Carlos J."},{"first_name":"Christian","last_name":"Oertlin","full_name":"Oertlin, Christian"},{"full_name":"Record, Julien","first_name":"Julien","last_name":"Record"},{"last_name":"Galvani","first_name":"Rômulo G.","full_name":"Galvani, Rômulo G."},{"full_name":"Sommerauer, Christian","first_name":"Christian","last_name":"Sommerauer"},{"last_name":"Kuznetsov","first_name":"Nikolai V.","full_name":"Kuznetsov, Nikolai V."},{"last_name":"Doukoumopoulos","first_name":"Evangelos","full_name":"Doukoumopoulos, Evangelos"},{"first_name":"Liaqat","last_name":"Ali","full_name":"Ali, Liaqat"},{"full_name":"Oliveira, Mariana M. S.","last_name":"Oliveira","first_name":"Mariana M. S."},{"first_name":"Christina","last_name":"Seitz","full_name":"Seitz, Christina"},{"first_name":"Mathias","id":"45adb726-eb97-11eb-a6c2-c7c3d3caabe9","last_name":"Percipalle","full_name":"Percipalle, Mathias"},{"full_name":"Nikić, Tijana","first_name":"Tijana","last_name":"Nikić"},{"last_name":"Sadova","first_name":"Anastasia A.","full_name":"Sadova, Anastasia A."},{"last_name":"Shulgina","first_name":"Sofia M.","full_name":"Shulgina, Sofia M."},{"last_name":"Shmarov","first_name":"Vjacheslav A.","full_name":"Shmarov, Vjacheslav A."},{"full_name":"Kutko, Olga V.","first_name":"Olga V.","last_name":"Kutko"},{"first_name":"Daria D.","last_name":"Vlasova","full_name":"Vlasova, Daria D."},{"first_name":"Kseniya D.","last_name":"Orlova","full_name":"Orlova, Kseniya D."},{"full_name":"Rykova, Marina P.","first_name":"Marina P.","last_name":"Rykova"},{"full_name":"Andersson, John","first_name":"John","last_name":"Andersson"},{"full_name":"Percipalle, Piergiorgio","first_name":"Piergiorgio","last_name":"Percipalle"},{"full_name":"Kutter, Claudia","last_name":"Kutter","first_name":"Claudia"},{"first_name":"Sergey A.","last_name":"Ponomarev","full_name":"Ponomarev, Sergey A."},{"full_name":"Westerberg, Lisa S.","first_name":"Lisa S.","last_name":"Westerberg"}],"file":[{"checksum":"b9072e20e2d5d9d34d2c53319bafee41","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":1596639,"file_id":"14809","content_type":"application/pdf","date_updated":"2024-01-16T09:35:28Z","date_created":"2024-01-16T09:35:28Z","file_name":"2023_ScienceAdvances_GallardoDodd.pdf","success":1}],"has_accepted_license":"1","publisher":"American Association for the Advancement of Science","publication_status":"published","_id":"14784","quality_controlled":"1","publication_identifier":{"issn":["2375-2548"]},"citation":{"chicago":"Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.adg1610\">https://doi.org/10.1126/sciadv.adg1610</a>.","ama":"Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. <i>Science Advances</i>. 2023;9(34). doi:<a href=\"https://doi.org/10.1126/sciadv.adg1610\">10.1126/sciadv.adg1610</a>","short":"C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V. Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova, K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev, L.S. Westerberg, Science Advances 9 (2023).","ieee":"C. J. Gallardo-Dodd <i>et al.</i>, “Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells,” <i>Science Advances</i>, vol. 9, no. 34. American Association for the Advancement of Science, 2023.","ista":"Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 9(34), adg1610.","mla":"Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” <i>Science Advances</i>, vol. 9, no. 34, adg1610, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.adg1610\">10.1126/sciadv.adg1610</a>.","apa":"Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer, C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adg1610\">https://doi.org/10.1126/sciadv.adg1610</a>"},"abstract":[{"lang":"eng","text":"The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity."}],"type":"journal_article","file_date_updated":"2024-01-16T09:35:28Z"},{"title":"Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803","author":[{"first_name":"Fabian","last_name":"Nies","full_name":"Nies, Fabian"},{"full_name":"Wein, Tanita","first_name":"Tanita","last_name":"Wein"},{"first_name":"Dustin M.","last_name":"Hanke","full_name":"Hanke, Dustin M."},{"last_name":"Springstein","orcid":"0000-0002-3461-5391","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","first_name":"Benjamin L","full_name":"Springstein, Benjamin L"},{"last_name":"Alcorta","first_name":"Jaime","full_name":"Alcorta, Jaime"},{"first_name":"Claudia","last_name":"Taubenheim","full_name":"Taubenheim, Claudia"},{"full_name":"Dagan, Tal","first_name":"Tal","last_name":"Dagan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2024-01-16T09:42:10Z","date_updated":"2024-01-16T09:42:10Z","file_name":"2023_EnvirMicroBiolReports_Nies.pdf","success":1,"checksum":"d09ebb68fee61f4e2e09ec286c9cf1d3","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":1518350,"file_id":"14810","content_type":"application/pdf"}],"has_accepted_license":"1","publisher":"Wiley","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"MaLo"}],"_id":"14785","quality_controlled":"1","publication_identifier":{"eissn":["1758-2229"]},"citation":{"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>","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.","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.","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>","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>."},"abstract":[{"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.","lang":"eng"}],"type":"journal_article","file_date_updated":"2024-01-16T09:42:10Z","publication_status":"published","keyword":["Agricultural and Biological Sciences (miscellaneous)","Ecology","Evolution","Behavior and Systematics"],"date_updated":"2024-01-16T09:46:12Z","oa":1,"issue":"6","date_published":"2023-12-01T00:00:00Z","month":"12","intvolume":"        15","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","year":"2023","external_id":{"isi":["001080203100001"],"pmid":["37794696"]},"page":"656-668","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2024-01-10T10:41:07Z","ddc":["570"],"status":"public","day":"01","volume":15,"pmid":1,"oa_version":"Published Version","isi":1,"publication":"Environmental Microbiology Reports","doi":"10.1111/1758-2229.13203"},{"article_number":"164010","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","intvolume":"       887","month":"08","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"date_updated":"2024-01-16T10:04:57Z","external_id":{"isi":["001002645100001"],"pmid":["37169189"]},"year":"2023","volume":887,"pmid":1,"day":"20","status":"public","date_created":"2024-01-10T10:43:08Z","publication":"Science of The Total Environment","doi":"10.1016/j.scitotenv.2023.164010","oa_version":"None","isi":1,"publisher":"Elsevier","title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","author":[{"first_name":"Vlatka","last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka"},{"last_name":"Subirana","first_name":"Maria Angels","full_name":"Subirana, Maria Angels"},{"first_name":"Dirk","last_name":"Schaumlöffel","full_name":"Schaumlöffel, Dirk"},{"first_name":"Josip","last_name":"Barišić","full_name":"Barišić, Josip"},{"last_name":"Gontier","first_name":"Etienne","full_name":"Gontier, Etienne"},{"last_name":"Krasnici","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","first_name":"Nesrete","full_name":"Krasnici, Nesrete"},{"full_name":"Mijošek, Tatjana","last_name":"Mijošek","first_name":"Tatjana"},{"full_name":"Hernández-Orts, Jesús S.","last_name":"Hernández-Orts","first_name":"Jesús S."},{"full_name":"Scholz, Tomáš","first_name":"Tomáš","last_name":"Scholz"},{"last_name":"Erk","first_name":"Marijana","full_name":"Erk, Marijana"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LifeSc"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"type":"journal_article","publication_identifier":{"issn":["0048-9697"]},"citation":{"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).","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.","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.","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>","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>."},"quality_controlled":"1","_id":"14786","publication_status":"published"},{"isi":1,"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.01.28.478139"}],"doi":"10.1111/mec.16849","publication":"Molecular Ecology","date_created":"2024-01-10T10:44:45Z","day":"01","status":"public","pmid":1,"volume":32,"year":"2023","external_id":{"isi":["000919244600001"],"pmid":["36651268"]},"page":"2041-2054","date_updated":"2024-01-16T10:10:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"issue":"8","oa":1,"intvolume":"        32","month":"04","date_published":"2023-04-01T00:00:00Z","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.","publication_status":"published","_id":"14787","quality_controlled":"1","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>","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>","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.","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.","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>."},"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"type":"journal_article","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","author":[{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"last_name":"Chase","first_name":"Madeline A.","full_name":"Chase, Madeline A."},{"first_name":"Hanna","last_name":"McIntosh","full_name":"McIntosh, Hanna"},{"first_name":"Matthew A.","last_name":"Streisfeld","full_name":"Streisfeld, Matthew A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley"},{"year":"2023","external_id":{"pmid":["36734980"],"isi":["000978065000001"]},"date_updated":"2024-01-16T10:17:05Z","keyword":["Cell Biology"],"issue":"3","oa":1,"intvolume":"       222","month":"02","date_published":"2023-02-03T00:00:00Z","article_number":"e202206038","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.","isi":1,"oa_version":"Published Version","doi":"10.1083/jcb.202206038","publication":"Journal of Cell Biology","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2024-01-10T10:45:55Z","status":"public","day":"03","pmid":1,"volume":222,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"AnSa"}],"file":[{"success":1,"file_name":"2023_JCB_Mund.pdf","date_updated":"2024-01-16T10:15:09Z","date_created":"2024-01-16T10:15:09Z","content_type":"application/pdf","file_id":"14811","file_size":5678069,"creator":"dernst","access_level":"open_access","checksum":"505d5cac36c14b073b68c7fed1a92bd3","relation":"main_file"}],"author":[{"first_name":"Markus","last_name":"Mund","full_name":"Mund, Markus"},{"full_name":"Tschanz, Aline","last_name":"Tschanz","first_name":"Aline"},{"first_name":"Yu-Le","last_name":"Wu","full_name":"Wu, Yu-Le"},{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F","last_name":"Frey","orcid":"0000-0001-8501-6017","full_name":"Frey, Felix F"},{"last_name":"Mehl","first_name":"Johanna L.","full_name":"Mehl, Johanna L."},{"full_name":"Kaksonen, Marko","first_name":"Marko","last_name":"Kaksonen"},{"full_name":"Avinoam, Ori","first_name":"Ori","last_name":"Avinoam"},{"full_name":"Schwarz, Ulrich S.","last_name":"Schwarz","first_name":"Ulrich S."},{"first_name":"Jonas","last_name":"Ries","full_name":"Ries, Jonas"}],"title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publisher":"Rockefeller University Press","publication_status":"published","_id":"14788","quality_controlled":"1","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"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).","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>.","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>."},"file_date_updated":"2024-01-16T10:15:09Z","type":"journal_article","abstract":[{"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.","lang":"eng"}]},{"citation":{"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>.","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>","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>.","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>","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.","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.","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."},"publication_identifier":{"isbn":["9798400703157"]},"scopus_import":"1","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"}],"type":"conference","file_date_updated":"2024-01-17T08:33:06Z","_id":"14798","quality_controlled":"1","project":[{"grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication"}],"publication_status":"published","has_accepted_license":"1","publisher":"Association for Computing Machinery","author":[{"full_name":"Chen, Bin","first_name":"Bin","last_name":"Chen"},{"first_name":"Akshay","last_name":"Jindal","full_name":"Jindal, Akshay"},{"first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","orcid":"0000-0002-5062-4474","last_name":"Piovarci","full_name":"Piovarci, Michael"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"full_name":"Seidel, Hans Peter","first_name":"Hans Peter","last_name":"Seidel"},{"last_name":"Didyk","first_name":"Piotr","full_name":"Didyk, Piotr"},{"first_name":"Karol","last_name":"Myszkowski","full_name":"Myszkowski, Karol"},{"full_name":"Serrano, Ana","first_name":"Ana","last_name":"Serrano"},{"first_name":"Rafał K.","last_name":"Mantiuk","full_name":"Mantiuk, Rafał K."}],"title":"The effect of display capabilities on the gloss consistency between real and virtual objects","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2024-01-17T08:33:06Z","date_created":"2024-01-17T08:33:06Z","success":1,"file_name":"2023_SA_Chen.pdf","access_level":"open_access","checksum":"8abe27432ed222b50d1af9b3388db1b0","relation":"main_file","file_id":"14823","content_type":"application/pdf","file_size":95967451,"creator":"dernst"}],"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"date_created":"2024-01-14T23:00:57Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"day":"10","status":"public","publication":"Proceedings of the SIGGRAPH Asia 2023 Conference","doi":"10.1145/3610548.3618226","oa_version":"Published Version","date_published":"2023-12-10T00:00:00Z","month":"12","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.","article_number":"90","date_updated":"2024-01-17T08:38:35Z","oa":1,"conference":{"location":"Sydney, Australia","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","end_date":"2023-12-15","start_date":"2023-12-12"},"year":"2023"},{"has_accepted_license":"1","file":[{"success":1,"file_name":"2023_JourApplCrystallography_Pauw.pdf","date_created":"2024-01-17T07:47:35Z","date_updated":"2024-01-17T07:47:35Z","file_id":"14822","content_type":"application/pdf","creator":"dernst","file_size":2165864,"checksum":"dab30d4556360f2cecf99f4b7efb0ee9","access_level":"open_access","relation":"main_file"}],"author":[{"first_name":"Brian R.","last_name":"Pauw","full_name":"Pauw, Brian R."},{"full_name":"Smales, Glen J.","last_name":"Smales","first_name":"Glen J."},{"full_name":"Anker, Andy S.","last_name":"Anker","first_name":"Andy S."},{"full_name":"Annadurai, Venkatasamy","first_name":"Venkatasamy","last_name":"Annadurai"},{"full_name":"Balazs, Daniel","last_name":"Balazs","orcid":"0000-0001-7597-043X","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"full_name":"Bienert, Ralf","first_name":"Ralf","last_name":"Bienert"},{"full_name":"Bouwman, Wim G.","last_name":"Bouwman","first_name":"Wim G."},{"first_name":"Ingo","last_name":"Breßler","full_name":"Breßler, Ingo"},{"last_name":"Breternitz","first_name":"Joachim","full_name":"Breternitz, Joachim"},{"full_name":"Brok, Erik S.","last_name":"Brok","first_name":"Erik S."},{"first_name":"Gary","last_name":"Bryant","full_name":"Bryant, Gary"},{"full_name":"Clulow, Andrew J.","first_name":"Andrew J.","last_name":"Clulow"},{"last_name":"Crater","first_name":"Erin R.","full_name":"Crater, Erin R."},{"last_name":"De Geuser","first_name":"Frédéric","full_name":"De Geuser, Frédéric"},{"full_name":"Giudice, Alessandra Del","last_name":"Giudice","first_name":"Alessandra Del"},{"last_name":"Deumer","first_name":"Jérôme","full_name":"Deumer, Jérôme"},{"full_name":"Disch, Sabrina","first_name":"Sabrina","last_name":"Disch"},{"last_name":"Dutt","first_name":"Shankar","full_name":"Dutt, Shankar"},{"first_name":"Kilian","last_name":"Frank","full_name":"Frank, Kilian"},{"full_name":"Fratini, Emiliano","first_name":"Emiliano","last_name":"Fratini"},{"first_name":"Paulo R.A.F.","last_name":"Garcia","full_name":"Garcia, Paulo R.A.F."},{"full_name":"Gilbert, Elliot P.","last_name":"Gilbert","first_name":"Elliot P."},{"last_name":"Hahn","first_name":"Marc B.","full_name":"Hahn, Marc B."},{"last_name":"Hallett","first_name":"James","full_name":"Hallett, James"},{"last_name":"Hohenschutz","first_name":"Max","full_name":"Hohenschutz, Max"},{"full_name":"Hollamby, Martin","first_name":"Martin","last_name":"Hollamby"},{"last_name":"Huband","first_name":"Steven","full_name":"Huband, Steven"},{"full_name":"Ilavsky, Jan","last_name":"Ilavsky","first_name":"Jan"},{"first_name":"Johanna K.","last_name":"Jochum","full_name":"Jochum, Johanna K."},{"full_name":"Juelsholt, Mikkel","first_name":"Mikkel","last_name":"Juelsholt"},{"full_name":"Mansel, Bradley W.","first_name":"Bradley W.","last_name":"Mansel"},{"full_name":"Penttilä, Paavo","first_name":"Paavo","last_name":"Penttilä"},{"full_name":"Pittkowski, Rebecca K.","last_name":"Pittkowski","first_name":"Rebecca K."},{"full_name":"Portale, Giuseppe","first_name":"Giuseppe","last_name":"Portale"},{"full_name":"Pozzo, Lilo D.","first_name":"Lilo D.","last_name":"Pozzo"},{"last_name":"Rochels","first_name":"Leonhard","full_name":"Rochels, Leonhard"},{"last_name":"Rosalie","first_name":"Julian M.","full_name":"Rosalie, Julian M."},{"full_name":"Saloga, Patrick E.J.","last_name":"Saloga","first_name":"Patrick E.J."},{"full_name":"Seibt, Susanne","last_name":"Seibt","first_name":"Susanne"},{"full_name":"Smith, Andrew J.","last_name":"Smith","first_name":"Andrew J."},{"full_name":"Smith, Gregory N.","first_name":"Gregory N.","last_name":"Smith"},{"first_name":"Glenn A.","last_name":"Spiering","full_name":"Spiering, Glenn A."},{"full_name":"Stawski, Tomasz M.","last_name":"Stawski","first_name":"Tomasz M."},{"full_name":"Taché, Olivier","last_name":"Taché","first_name":"Olivier"},{"last_name":"Thünemann","first_name":"Andreas F.","full_name":"Thünemann, Andreas F."},{"full_name":"Toth, Kristof","last_name":"Toth","first_name":"Kristof"},{"full_name":"Whitten, Andrew E.","last_name":"Whitten","first_name":"Andrew E."},{"last_name":"Wuttke","first_name":"Joachim","full_name":"Wuttke, Joachim"}],"title":"The human factor: Results of a small-angle scattering data analysis round robin","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"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>","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.","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.","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.","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>.","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>"},"publication_identifier":{"issn":["0021-8898"],"eissn":["1600-5767"]},"type":"journal_article","file_date_updated":"2024-01-17T07:47:35Z","scopus_import":"1","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."}],"arxiv":1,"_id":"14799","quality_controlled":"1","publication_status":"published","month":"12","intvolume":"        56","date_published":"2023-12-01T00:00:00Z","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_updated":"2024-01-17T07:49:52Z","issue":"6","oa":1,"external_id":{"arxiv":["2303.03772"]},"page":"1618-1629","year":"2023","volume":56,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["540"],"date_created":"2024-01-14T23:00:57Z","day":"01","status":"public","doi":"10.1107/S1600576723008324","publication":"Journal of Applied Crystallography","oa_version":"Published Version"},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","author":[{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"}],"date_updated":"2025-08-12T09:04:30Z","publisher":"Zenodo","month":"09","has_accepted_license":"1","date_published":"2023-09-05T00:00:00Z","year":"2023","department":[{"_id":"NiBa"}],"article_processing_charge":"No","status":"public","day":"05","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2024-01-16T10:23:01Z","_id":"14812","ddc":["570"],"type":"research_data_reference","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"}],"citation":{"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>.","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>","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>.","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.","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>.","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>"},"oa_version":"Published Version","related_material":{"record":[{"id":"14796","relation":"used_in_publication","status":"for_moderation"}]},"contributor":[{"last_name":"Zagrodzka","first_name":"Zusanna"},{"first_name":"Martin","last_name":"Garlovsky"},{"last_name":"Pal","orcid":"0000-0002-4530-8469","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","last_name":"Shipilina","orcid":"0000-0002-1145-9226"},{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","last_name":"Garcia Castillo"},{"id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","first_name":"Hila","last_name":"Lifchitz"},{"last_name":"Le Moan","first_name":"Alan"},{"first_name":"Erica","last_name":"Leder"},{"first_name":"James","last_name":"Reeve"},{"last_name":"Johannesson","first_name":"Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969"},{"last_name":"Butlin","first_name":"Roger"}],"doi":"10.5281/ZENODO.8318995","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8318995"}]},{"department":[{"_id":"DaAl"}],"article_processing_charge":"Yes (in subscription journal)","article_type":"original","language":[{"iso":"eng"}],"publisher":"Journal of Machine Learning Research","has_accepted_license":"1","file":[{"relation":"main_file","checksum":"c50f2b9db53938b755e30a085f464059","access_level":"open_access","file_id":"14816","content_type":"application/pdf","file_size":1510993,"creator":"dernst","date_created":"2024-01-16T12:13:27Z","date_updated":"2024-01-16T12:13:27Z","success":1,"file_name":"2023_JMLR_Beznosikov.pdf"}],"title":"On biased compression for distributed learning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Aleksandr","last_name":"Beznosikov","full_name":"Beznosikov, Aleksandr"},{"full_name":"Horvath, Samuel","first_name":"Samuel","last_name":"Horvath"},{"full_name":"Richtarik, Peter","first_name":"Peter","last_name":"Richtarik"},{"full_name":"Safaryan, Mher","last_name":"Safaryan","first_name":"Mher","id":"dd546b39-0804-11ed-9c55-ef075c39778d"}],"publication_status":"published","type":"journal_article","file_date_updated":"2024-01-16T12:13:27Z","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"}],"arxiv":1,"publication_identifier":{"eissn":["1533-7928"]},"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.","short":"A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine Learning Research 24 (2023) 1–50.","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.","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.","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.","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."},"quality_controlled":"1","_id":"14815","external_id":{"isi":["001111578500001"],"arxiv":["2002.12410"]},"page":"1-50","year":"2023","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. ","intvolume":"        24","month":"10","date_published":"2023-10-01T00:00:00Z","oa":1,"date_updated":"2024-01-17T09:14:13Z","publication":"Journal of Machine Learning Research","isi":1,"oa_version":"Published Version","volume":24,"day":"01","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2024-01-16T12:13:36Z","ddc":["000"]},{"publisher":"The Company of Biologists","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Connecting theory and experiment in cell and tissue mechanics","author":[{"orcid":"0000-0001-5130-2226","last_name":"Schwayer","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia"},{"first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975","full_name":"Brückner, David"}],"department":[{"_id":"EdHa"},{"_id":"CaHe"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","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."}],"type":"journal_article","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"citation":{"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>","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>.","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>","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.","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).","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>."},"quality_controlled":"1","_id":"14827","publication_status":"published","project":[{"grant_number":"343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"article_number":"jcs.261515","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).","date_published":"2023-12-27T00:00:00Z","month":"12","intvolume":"       136","issue":"24","keyword":["Cell Biology"],"date_updated":"2024-01-22T13:35:48Z","external_id":{"pmid":["38149871"]},"year":"2023","volume":136,"pmid":1,"status":"public","day":"27","date_created":"2024-01-17T12:46:55Z","publication":"Journal of Cell Science","doi":"10.1242/jcs.261515","oa_version":"None"},{"author":[{"full_name":"Cohen, Shir","last_name":"Cohen","first_name":"Shir"},{"first_name":"Guy","last_name":"Goren","full_name":"Goren, Guy"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"last_name":"Sonnino","first_name":"Alberto","full_name":"Sonnino, Alberto"},{"full_name":"Spiegelman, Alexander","first_name":"Alexander","last_name":"Spiegelman"}],"title":"Proof of availability and retrieval in a modular blockchain architecture","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"ElKo"}],"_id":"14829","quality_controlled":"1","citation":{"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>.","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>","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>","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.","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.","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."},"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031477508"],"eisbn":["9783031477515"],"eissn":["1611-3349"]},"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."}],"scopus_import":"1","type":"conference","project":[{"grant_number":"F8512","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","name":"Secure Network and Hardware for Efficient Blockchains"}],"publication_status":"published","date_updated":"2024-01-22T13:58:07Z","oa":1,"date_published":"2023-12-01T00:00:00Z","alternative_title":["LNCS"],"intvolume":"     13951","month":"12","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.","year":"2023","page":"36-53","conference":{"location":"Bol, Brac, Croatia","end_date":"2023-05-05","start_date":"2023-05-01","name":"FC: Financial Cryptography and Data Security"},"date_created":"2024-01-18T07:41:12Z","status":"public","day":"01","volume":13951,"oa_version":"Submitted Version","publication":"27th International Conference on Financial Cryptography and Data Security","main_file_link":[{"open_access":"1","url":"https://fc23.ifca.ai/preproceedings/150.pdf"}],"doi":"10.1007/978-3-031-47751-5_3"},{"title":"Learning control policies for stochastic systems with reach-avoid guarantees","author":[{"orcid":"0000-0002-4681-1699","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","full_name":"Zikelic, Dorde"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for the Advancement of Artificial Intelligence","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"_id":"14830","quality_controlled":"1","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"]},"citation":{"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>.","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.","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.","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.","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>","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>.","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>"},"type":"conference","arxiv":1,"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"}],"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","date_updated":"2025-07-14T09:10:02Z","keyword":["General Medicine"],"issue":"10","month":"06","intvolume":"        37","date_published":"2023-06-26T00:00:00Z","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.","year":"2023","page":"11926-11935","external_id":{"arxiv":["2210.05308"]},"conference":{"location":"Washington, DC, United States","name":"AAAI: Conference on Artificial Intelligence","end_date":"2023-02-14","start_date":"2023-02-07"},"date_created":"2024-01-18T07:44:31Z","day":"26","status":"public","volume":37,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"14600"}]},"oa_version":"Preprint","ec_funded":1,"doi":"10.1609/aaai.v37i10.26407","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence"},{"year":"2023","external_id":{"isi":["001134068000001"],"arxiv":["2312.15940"]},"page":"10950-10959","issue":"51","oa":1,"date_updated":"2024-01-23T07:58:27Z","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"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.","intvolume":"       127","month":"12","date_published":"2023-12-13T00:00:00Z","isi":1,"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.15940","open_access":"1"}],"doi":"10.1021/acs.jpcb.3c04627","publication":"The Journal of Physical Chemistry B","status":"public","day":"13","date_created":"2024-01-18T07:47:11Z","volume":127,"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"article_processing_charge":"No","title":"On kinetic constraints that catalysis imposes on elementary processes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Yann","last_name":"Sakref","full_name":"Sakref, Yann"},{"full_name":"Muñoz Basagoiti, Maitane","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","first_name":"Maitane","orcid":"0000-0003-1483-1457","last_name":"Muñoz Basagoiti"},{"full_name":"Zeravcic, Zorana","first_name":"Zorana","last_name":"Zeravcic"},{"first_name":"Olivier","last_name":"Rivoire","full_name":"Rivoire, Olivier"}],"publisher":"American Chemical Society","publication_status":"published","quality_controlled":"1","_id":"14831","type":"journal_article","abstract":[{"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.","lang":"eng"}],"arxiv":1,"citation":{"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>.","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>","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.","short":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical Chemistry B 127 (2023) 10950–10959.","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.","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>.","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>"},"publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]}},{"publication_identifier":{"eissn":["2752-938X"]},"citation":{"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>.","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.","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).","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>","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>.","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>"},"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"}],"type":"journal_article","file_date_updated":"2024-01-23T08:10:00Z","_id":"14833","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"Oxford University Press","author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"first_name":"Zuzanna B","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B"},{"full_name":"Galindo, Juan","first_name":"Juan","last_name":"Galindo"},{"last_name":"Montaño-Rendón","first_name":"Mauricio","full_name":"Montaño-Rendón, Mauricio"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Mikhailova, Natalia","last_name":"Mikhailova","first_name":"Natalia"},{"last_name":"Blakeslee","first_name":"April M H","full_name":"Blakeslee, April M H"},{"first_name":"Einar","last_name":"Arnason","full_name":"Arnason, Einar"},{"last_name":"Broquet","first_name":"Thomas","full_name":"Broquet, Thomas"},{"full_name":"Morales, Hernán E","first_name":"Hernán E","last_name":"Morales"},{"first_name":"John W","last_name":"Grahame","full_name":"Grahame, John W"},{"orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K","last_name":"Butlin","first_name":"Roger K"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","file":[{"date_updated":"2024-01-23T08:10:00Z","date_created":"2024-01-23T08:10:00Z","file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf","success":1,"relation":"main_file","checksum":"ba6f9102d3a9fe6631c4fa398c5e4313","access_level":"open_access","creator":"dernst","file_size":3408944,"file_id":"14875","content_type":"application/pdf"}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"article_type":"original","volume":2,"date_created":"2024-01-18T07:54:10Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["570"],"status":"public","day":"17","publication":"Evolutionary Journal of the Linnean Society","doi":"10.1093/evolinnean/kzad002","oa_version":"Published Version","date_published":"2023-08-17T00:00:00Z","intvolume":"         2","month":"08","article_number":"kzad002","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).","date_updated":"2024-01-23T08:13:43Z","oa":1,"issue":"1","year":"2023"},{"quality_controlled":"1","_id":"14835","file_date_updated":"2024-01-23T08:57:01Z","type":"journal_article","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":{"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>","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>.","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>","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.","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).","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.","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>."},"publication_identifier":{"issn":["0044-8249"],"eissn":["1521-3757"]},"publication_status":"published","file":[{"date_created":"2024-01-23T08:57:01Z","date_updated":"2024-01-23T08:57:01Z","file_name":"2023_AngewChem_Becker.pdf","success":1,"access_level":"open_access","relation":"main_file","checksum":"98e68d370159f7be52a3d7c8a8ee1198","creator":"dernst","file_size":1004676,"content_type":"application/pdf","file_id":"14876"}],"title":"Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten","author":[{"last_name":"Becker","orcid":"0000-0002-6401-5151","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie"},{"full_name":"Berbon, Mélanie","last_name":"Berbon","first_name":"Mélanie"},{"full_name":"Vallet, Alicia","last_name":"Vallet","first_name":"Alicia"},{"full_name":"Grelard, Axelle","last_name":"Grelard","first_name":"Axelle"},{"first_name":"Estelle","last_name":"Morvan","full_name":"Morvan, Estelle"},{"first_name":"Benjamin","last_name":"Bardiaux","full_name":"Bardiaux, Benjamin"},{"full_name":"Lichtenecker, Roman","first_name":"Roman","last_name":"Lichtenecker"},{"last_name":"Ernst","first_name":"Matthias","full_name":"Ernst, Matthias"},{"full_name":"Loquet, Antoine","first_name":"Antoine","last_name":"Loquet"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","has_accepted_license":"1","article_type":"original","language":[{"iso":"ger"}],"department":[{"_id":"PaSc"}],"article_processing_charge":"Yes (in subscription journal)","day":"02","status":"public","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"date_created":"2024-01-18T10:01:01Z","ddc":["540"],"volume":135,"oa_version":"Published Version","doi":"10.1002/ange.202219314","publication":"Angewandte Chemie","issue":"19","oa":1,"date_updated":"2024-01-23T12:23:35Z","keyword":["General Medicine"],"article_number":"e202219314","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.","month":"05","intvolume":"       135","date_published":"2023-05-02T00:00:00Z","year":"2023"}]