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However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"oa_version":"Published Version","acknowledgement":"We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. We thank Paul Henderson for advice on deep-learning training and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag ligand. "},{"department":[{"_id":"TiVo"}],"title":"douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation","article_processing_charge":"No","author":[{"full_name":"Feitosa Tomé, Douglas","last_name":"Feitosa Tomé","first_name":"Douglas","id":"0eed2d40-3d48-11ec-8d38-f789cc2e40b2"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-29T09:22:01Z","citation":{"chicago":"Feitosa Tomé, Douglas. “Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.10251087.","ista":"Feitosa Tomé D. 2023. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation, Zenodo, 10.5281/ZENODO.10251087.","mla":"Feitosa Tomé, Douglas. Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation. 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Dynamic and selective engrams emerge with memory consolidation. 2023.","lang":"eng"}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"GLACIER METEOROLOGICAL DATA SWISS ALPS -2022\r\n"}],"month":"08","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.8277285","open_access":"1"}],"oa":1,"publisher":"Zenodo","day":"23","year":"2023","date_created":"2024-01-31T12:08:26Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14885"}]},"date_published":"2023-08-23T00:00:00Z","doi":"10.5281/ZENODO.8277285","_id":"14919","status":"public","type":"research_data_reference","ddc":["550"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-06T08:44:01Z","citation":{"chicago":"Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan Miles, and Francesca Pellicciotti. “Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8277285.","ista":"Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. 2023. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer, Zenodo, 10.5281/ZENODO.8277285.","mla":"Shaw, Thomas, et al. Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer. Zenodo, 2023, doi:10.5281/ZENODO.8277285.","ama":"Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. 2023. doi:10.5281/ZENODO.8277285","apa":"Shaw, T., Buri, P., McCarthy, M., Miles, E., & Pellicciotti, F. (2023). Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. Zenodo. https://doi.org/10.5281/ZENODO.8277285","ieee":"T. Shaw, P. Buri, M. McCarthy, E. Miles, and F. Pellicciotti, “Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer.” Zenodo, 2023.","short":"T. Shaw, P. Buri, M. McCarthy, E. Miles, F. Pellicciotti, (2023)."},"department":[{"_id":"FrPe"}],"title":"Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer","article_processing_charge":"No","author":[{"id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas","last_name":"Shaw","full_name":"Shaw, Thomas","orcid":"0000-0001-7640-6152"},{"last_name":"Buri","full_name":"Buri, Pascal","id":"317987aa-9421-11ee-ac5a-b941b041abba","first_name":"Pascal"},{"first_name":"Michael","full_name":"McCarthy, Michael","last_name":"McCarthy"},{"first_name":"Evan","full_name":"Miles, Evan","last_name":"Miles"},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture."}],"month":"03","oa":1,"publisher":"Institute of Science and Technology Austria","day":"23","file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","checksum":"fd9a28620a81a82991fb70f4fd6591d9","file_id":"12743","file_size":87018103,"date_updated":"2023-03-24T09:34:20Z","creator":"lbecker","file_name":"Research_Data.zip","date_created":"2023-03-23T10:03:16Z"},{"file_id":"12755","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","content_type":"text/plain","access_level":"open_access","relation":"main_file","date_created":"2023-03-24T07:13:55Z","file_name":"README.txt","date_updated":"2023-03-24T09:42:03Z","file_size":747,"creator":"dernst"}],"year":"2023","has_accepted_license":"1","date_created":"2023-02-03T08:08:02Z","contributor":[{"last_name":"Berbon","contributor_type":"researcher","first_name":"Mélanie"},{"contributor_type":"researcher","first_name":"Alicia","last_name":"Vallet"},{"first_name":"Axelle","contributor_type":"researcher","last_name":"Grelard"},{"first_name":"Estelle","contributor_type":"researcher","last_name":"Morvan"},{"first_name":"Benjamin","contributor_type":"researcher","last_name":"Bardiaux"},{"contributor_type":"researcher","first_name":"Roman","last_name":"Lichtenecker"},{"last_name":"Ernst","contributor_type":"researcher","first_name":"Matthias"},{"last_name":"Loquet","contributor_type":"researcher","first_name":"Antoine"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","contributor_type":"contact_person","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"orcid":"0000-0002-6401-5151","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","contributor_type":"researcher"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12675"}]},"date_published":"2023-03-23T00:00:00Z","doi":"10.15479/AT:ISTA:12497","_id":"12497","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data","ddc":["572"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:14:06Z","citation":{"chicago":"Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12497.","ista":"Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12497.","mla":"Becker, Lea Marie, and Paul Schanda. Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12497.","ama":"Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:10.15479/AT:ISTA:12497","apa":"Becker, L. M., & Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12497","short":"L.M. Becker, P. Schanda, (2023).","ieee":"L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023."},"file_date_updated":"2023-03-24T09:42:03Z","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","article_processing_charge":"No","author":[{"id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","last_name":"Becker"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}]},{"day":"04","has_accepted_license":"1","year":"2023","date_published":"2023-08-04T00:00:00Z","doi":"10.15479/AT:ISTA:13126","date_created":"2023-06-07T07:15:12Z","acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13126.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13126","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","short":"J.G. 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During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. "}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). 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Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13116.","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13116.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:10.15479/AT:ISTA:13116","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023).","mla":"Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116."},"date_updated":"2024-02-21T12:19:09Z","ddc":["539"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"}],"status":"public","_id":"13116"},{"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","file_date_updated":"2023-11-30T14:16:59Z","department":[{"_id":"BeVi"}],"article_processing_charge":"No","author":[{"id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","first_name":"Clementine","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","last_name":"Lasne"},{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"}],"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:18:35Z","citation":{"ieee":"C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023.","short":"C. Lasne, M.N. Elkrewi, (2023).","ama":"Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:10.15479/AT:ISTA:14614","apa":"Lasne, C., & Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14614","mla":"Lasne, Clementine, and Marwan N. Elkrewi. The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14614.","ista":"Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14614.","chicago":"Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14614."},"keyword":["Panorpa","scorpionfly","genome","transcriptome"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","_id":"14614","contributor":[{"contributor_type":"researcher","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi"}],"date_created":"2023-11-27T16:39:19Z","doi":"10.15479/AT:ISTA:14614","date_published":"2023-12-01T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"14613","status":"public"}]},"file":[{"checksum":"cd0f13322b5156819ecaebd2bc8e7d12","file_id":"14625","success":1,"content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2023-11-28T13:15:26Z","file_name":"panorpaX.zip","date_updated":"2023-11-28T13:15:26Z","file_size":404968272,"creator":"clasne"},{"creator":"clasne","date_updated":"2023-11-30T14:16:59Z","file_size":2625,"date_created":"2023-11-30T14:16:59Z","file_name":"panorpa_readme.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"9ff600416577687a737cb3c96dfcb26c","file_id":"14634","success":1}],"day":"01","year":"2023","has_accepted_license":"1","month":"12","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}]},{"abstract":[{"text":"This data repository underpins the paper, published in PNAS (doi pending) and bioarxiv (doi: https://doi.org/10.1101/2023.07.05.547777).","lang":"eng"}],"oa_version":"Published Version","publisher":"Figshare","oa":1,"main_file_link":[{"open_access":"1","url":"https://figshare.com/s/85798bba4ebc68d822ed"}],"month":"12","has_accepted_license":"1","year":"2023","day":"13","date_published":"2023-12-13T00:00:00Z","related_material":{"record":[{"id":"15001","status":"public","relation":"used_in_publication"}]},"date_created":"2024-02-26T08:37:57Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"15027","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","citation":{"chicago":"Curk, Samo. “Aggregation_data.” Figshare, 2023.","ista":"Curk S. 2023. aggregation_data, Figshare.","mla":"Curk, Samo. Aggregation_data. Figshare, 2023.","apa":"Curk, S. (2023). aggregation_data. Figshare.","ama":"Curk S. aggregation_data. 2023.","short":"S. Curk, (2023).","ieee":"S. Curk, “aggregation_data.” Figshare, 2023."},"date_updated":"2024-02-26T08:45:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"author":[{"last_name":"Curk","orcid":"0000-0001-6160-9766","full_name":"Curk, Samo","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","first_name":"Samo"}],"article_processing_charge":"No","department":[{"_id":"AnSa"}],"title":"aggregation_data"},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14654"}]},"date_published":"2023-06-23T00:00:00Z","doi":"10.5281/ZENODO.7757041","date_created":"2024-02-14T14:37:57Z","ec_funded":1,"day":"23","has_accepted_license":"1","year":"2023","month":"06","publisher":"Zenodo","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7757041"}],"oa_version":"Published Version","abstract":[{"text":"This repository contains the data, scripts, WRF codes and files required to reproduce the results of the manuscript \"Assessing Memory in Convection Schemes Using Idealized Tests\" submitted to the Journal of Advances in Modeling Earth Systems (JAMES).","lang":"eng"}],"department":[{"_id":"CaMu"}],"title":"Data-assessing memory in convection schemes using idealized tests","author":[{"orcid":"0000-0001-9281-3479","full_name":"Hwong, Yi-Ling","last_name":"Hwong","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22"},{"first_name":"Maxime","full_name":"Colin, Maxime","last_name":"Colin"},{"first_name":"Philipp","id":"02eace56-97fc-11ee-b81a-f0939ca85a77","last_name":"Aglas","full_name":"Aglas, Philipp"},{"last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J"},{"full_name":"Sherwood, Steven C.","last_name":"Sherwood","first_name":"Steven C."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["550"],"date_updated":"2024-02-27T07:26:31Z","citation":{"mla":"Hwong, Yi-Ling, et al. Data-Assessing Memory in Convection Schemes Using Idealized Tests. Zenodo, 2023, doi:10.5281/ZENODO.7757041.","short":"Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, (2023).","ieee":"Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. C. Sherwood, “Data-assessing memory in convection schemes using idealized tests.” Zenodo, 2023.","apa":"Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., & Sherwood, S. C. (2023). Data-assessing memory in convection schemes using idealized tests. Zenodo. https://doi.org/10.5281/ZENODO.7757041","ama":"Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. Data-assessing memory in convection schemes using idealized tests. 2023. doi:10.5281/ZENODO.7757041","chicago":"Hwong, Yi-Ling, Maxime Colin, Philipp Aglas, Caroline J Muller, and Steven C. Sherwood. “Data-Assessing Memory in Convection Schemes Using Idealized Tests.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7757041.","ista":"Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. 2023. Data-assessing memory in convection schemes using idealized tests, Zenodo, 10.5281/ZENODO.7757041."},"project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14991"},{"has_accepted_license":"1","year":"2023","day":"18","related_material":{"record":[{"relation":"used_in_publication","id":"13139","status":"public"}]},"date_published":"2023-01-18T00:00:00Z","doi":"10.5281/ZENODO.7548214","date_created":"2024-02-14T14:27:06Z","abstract":[{"lang":"eng","text":"The software artefact to evaluate the approximation of stationary distributions implementation."}],"oa_version":"Published Version","publisher":"Zenodo","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7548214","open_access":"1"}],"oa":1,"month":"01","date_updated":"2024-02-27T07:19:32Z","citation":{"chicago":"Meggendorfer, Tobias. “Artefact for: Correct Approximation of Stationary Distributions.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7548214.","ista":"Meggendorfer T. 2023. Artefact for: Correct Approximation of Stationary Distributions, Zenodo, 10.5281/ZENODO.7548214.","mla":"Meggendorfer, Tobias. Artefact for: Correct Approximation of Stationary Distributions. Zenodo, 2023, doi:10.5281/ZENODO.7548214.","ama":"Meggendorfer T. Artefact for: Correct Approximation of Stationary Distributions. 2023. doi:10.5281/ZENODO.7548214","apa":"Meggendorfer, T. (2023). Artefact for: Correct Approximation of Stationary Distributions. Zenodo. https://doi.org/10.5281/ZENODO.7548214","short":"T. Meggendorfer, (2023).","ieee":"T. Meggendorfer, “Artefact for: Correct Approximation of Stationary Distributions.” Zenodo, 2023."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias"}],"article_processing_charge":"No","title":"Artefact for: Correct Approximation of Stationary Distributions","department":[{"_id":"KrCh"}],"_id":"14990","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"_id":"14995","status":"public","type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2024-02-27T07:46:52Z","citation":{"ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. 2023. doi:10.5281/ZENODO.7877757","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. Zenodo. https://doi.org/10.5281/ZENODO.7877757","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM.” Zenodo, 2023.","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, (2023).","mla":"Koval, Nikita, et al. Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM. Zenodo, 2023, doi:10.5281/ZENODO.7877757.","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM, Zenodo, 10.5281/ZENODO.7877757.","chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7877757."},"department":[{"_id":"DaAl"}],"title":"Lincheck: A practical framework for testing concurrent data structures on JVM","article_processing_charge":"No","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval","full_name":"Koval, Nikita"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander"},{"full_name":"Sokolova, Maria","last_name":"Sokolova","first_name":"Maria"},{"first_name":"Dmitry","last_name":"Tsitelov","full_name":"Tsitelov, Dmitry"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"oa_version":"Published Version","abstract":[{"text":"Lincheck is a new practical and user-friendly framework for testing concurrent data structures on the Java Virtual Machine (JVM). It provides a simple and declarative way to write concurrent tests. Instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. \r\nThe artifact presents a collection of Lincheck tests that discover new bugs in popular libraries and implementations from the concurrency literature -- they are listed in Table 1, Section 3. To evaluate the performance of Lincheck analysis, the collection of tests also includes those which check correct data structures and, thus, always succeed. Similarly to Table 2, Section 3, the experiments demonstrate the reasonable time to perform a test. Finally, Lincheck provides user-friendly output with an easy-to-follow trace to reproduce a detected error, significantly simplifying further investigation.","lang":"eng"}],"month":"04","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7877757"}],"publisher":"Zenodo","day":"28","year":"2023","date_created":"2024-02-14T15:14:13Z","date_published":"2023-04-28T00:00:00Z","doi":"10.5281/ZENODO.7877757","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14260"}]}},{"type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14994","author":[{"first_name":"Rupak","full_name":"Majumdar, Rupak","last_name":"Majumdar"},{"first_name":"Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","last_name":"Mallik"},{"last_name":"Rychlicki","full_name":"Rychlicki, Mateusz","first_name":"Mateusz"},{"full_name":"Schmuck, Anne-Kathrin","last_name":"Schmuck","first_name":"Anne-Kathrin"},{"last_name":"Soudjani","full_name":"Soudjani, Sadegh","first_name":"Sadegh"}],"article_processing_charge":"No","title":"A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties","department":[{"_id":"ToHe"}],"citation":{"mla":"Majumdar, Rupak, et al. A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties. Zenodo, 2023, doi:10.5281/ZENODO.7877790.","ieee":"R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, and S. Soudjani, “A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties.” Zenodo, 2023.","short":"R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, S. Soudjani, (2023).","apa":"Majumdar, R., Mallik, K., Rychlicki, M., Schmuck, A.-K., & Soudjani, S. (2023). A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. Zenodo. https://doi.org/10.5281/ZENODO.7877790","ama":"Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. 2023. doi:10.5281/ZENODO.7877790","chicago":"Majumdar, Rupak, Kaushik Mallik, Mateusz Rychlicki, Anne-Kathrin Schmuck, and Sadegh Soudjani. “A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7877790.","ista":"Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. 2023. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties, Zenodo, 10.5281/ZENODO.7877790."},"date_updated":"2024-02-27T07:39:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"publisher":"Zenodo","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7877790","open_access":"1"}],"oa":1,"month":"04","abstract":[{"text":"This resource contains the artifacts for reproducing the experimental results presented in the paper titled \"A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties\" that has been submitted in CAV 2023.","lang":"eng"}],"oa_version":"Published Version","date_published":"2023-04-28T00:00:00Z","doi":"10.5281/ZENODO.7877790","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14758"}]},"date_created":"2024-02-14T15:13:00Z","has_accepted_license":"1","year":"2023","day":"28"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2024-02-28T12:33:09Z","citation":{"apa":"Chalupa, M., & Henzinger, T. A. (2023). Monitoring hyperproperties with prefix transducers. Zenodo. https://doi.org/10.5281/ZENODO.8191723","ama":"Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers. 2023. doi:10.5281/ZENODO.8191723","short":"M. Chalupa, T.A. Henzinger, (2023).","ieee":"M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers.” Zenodo, 2023.","mla":"Chalupa, Marek, and Thomas A. Henzinger. Monitoring Hyperproperties with Prefix Transducers. Zenodo, 2023, doi:10.5281/ZENODO.8191723.","ista":"Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers, Zenodo, 10.5281/ZENODO.8191723.","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8191723."},"title":"Monitoring hyperproperties with prefix transducers","department":[{"_id":"ToHe"}],"article_processing_charge":"No","author":[{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"_id":"15035","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","day":"28","year":"2023","has_accepted_license":"1","ec_funded":1,"date_created":"2024-02-28T07:34:34Z","date_published":"2023-07-28T00:00:00Z","doi":"10.5281/ZENODO.8191723","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14076"}]},"oa_version":"Published Version","abstract":[{"text":"This artifact aims to reproduce experiments from the paper Monitoring Hyperproperties With Prefix Transducers accepted at RV'23, and give further pointers to implementation of prefix transducers.\r\nIt has two parts: a pre-compiled docker image and sources that one can use to compile (locally or in docker) the software and run the experiments.","lang":"eng"}],"month":"07","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8191722","open_access":"1"}],"publisher":"Zenodo"},{"citation":{"ama":"Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995","apa":"Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995","ieee":"S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.","short":"S. Stankowski, (2023).","mla":"Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.","ista":"Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.","chicago":"Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995."},"date_updated":"2024-03-05T09:35:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"article_processing_charge":"No","author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","department":[{"_id":"NiBa"}],"_id":"14812","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","year":"2023","has_accepted_license":"1","day":"05","date_created":"2024-01-16T10:23:01Z","contributor":[{"last_name":"Zagrodzka","first_name":"Zusanna"},{"first_name":"Martin","last_name":"Garlovsky"},{"orcid":"0000-0002-4530-8469","last_name":"Pal","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","orcid":"0000-0002-1145-9226"},{"last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando"},{"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"},{"first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Butlin","first_name":"Roger"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14796"}]},"doi":"10.5281/ZENODO.8318995","date_published":"2023-09-05T00:00:00Z","abstract":[{"lang":"eng","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"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8318995","open_access":"1"}],"oa":1,"publisher":"Zenodo","month":"09"},{"file":[{"file_size":542873672,"date_updated":"2023-11-17T14:30:44Z","creator":"shigemot","file_name":"Raw data for Koppensteiner et al.zip","title":"Outdated Version","date_created":"2023-06-29T13:11:22Z","description":"After review an updated version of the data is provided","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"closed","file_id":"13174","checksum":"ed59170869ba621f89f7c1894092192f"},{"file_name":"11-17-23 Updated Koppensteiner et al. raw data.xlsx","date_created":"2023-11-17T14:13:02Z","creator":"patrickd","file_size":915079,"date_updated":"2023-11-17T14:13:02Z","success":1,"file_id":"14550","checksum":"c07860eb82b4d367245f1b589fe5c250","relation":"main_file","access_level":"open_access","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"},{"file_size":544868924,"date_updated":"2024-02-06T07:21:43Z","creator":"dernst","file_name":"EM_Images.zip","date_created":"2024-02-06T07:21:43Z","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","success":1,"file_id":"14942","checksum":"abf84b1699edac4349dc3a92d466fb7b"}],"day":"29","has_accepted_license":"1","year":"2023","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15084"}]},"date_published":"2023-07-29T00:00:00Z","doi":"10.15479/AT:ISTA:13173","date_created":"2023-06-29T13:16:42Z","oa_version":"Published Version","abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles at the presynaptic active zone (AZ). Strikingly, tonic and phasic release exhibit distinct coupling distances and are selectively affected by deletion of synaptoporin (SPO) and Ca2+-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. Double pre-embedding immunolabeling confirmed the co-localization of CAPS2 and SPO inside the same terminal. The cytosolic protein CAPS2 showed a synaptic vesicle (SV)-associated distribution similar to the vesicular transmembrane protein SPO. A newly developed “Flash and Freeze-fracture” method revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to a persistent RRP increase. Thus, we discovered structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"month":"07","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["571"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Shigemoto, Ryuichi. Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13173.","ieee":"R. Shigemoto, “Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals.” Institute of Science and Technology Austria, 2023.","short":"R. Shigemoto, (2023).","apa":"Shigemoto, R. (2023). Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13173","ama":"Shigemoto R. Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals. 2023. doi:10.15479/AT:ISTA:13173","chicago":"Shigemoto, Ryuichi. “Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13173.","ista":"Shigemoto R. 2023. Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13173."},"date_updated":"2024-03-12T13:44:18Z","title":"Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals","department":[{"_id":"RySh"}],"file_date_updated":"2024-02-06T07:21:43Z","author":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"article_processing_charge":"No","_id":"13173","status":"public","keyword":["medial habenula","GABAB receptor","vesicle release","Flash and Freeze","Flash and Freeze-fracture"],"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"}},{"abstract":[{"lang":"eng","text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes."}],"oa_version":"Published Version","acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25338/B81931"}],"oa":1,"month":"01","year":"2022","day":"06","related_material":{"record":[{"status":"public","id":"10604","relation":"used_in_publication"}]},"date_published":"2022-01-06T00:00:00Z","doi":"10.25338/B81931","date_created":"2022-07-29T06:45:41Z","_id":"11686","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","keyword":["Biological sciences"],"date_updated":"2023-08-02T13:50:08Z","citation":{"mla":"Turelli, Michael, and Nicholas H. Barton. Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control. Dryad, 2022, doi:10.25338/B81931.","short":"M. Turelli, N.H. Barton, (2022).","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","apa":"Turelli, M., & Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. https://doi.org/10.25338/B81931","ama":"Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:10.25338/B81931","chicago":"Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. https://doi.org/10.25338/B81931.","ista":"Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control, Dryad, 10.25338/B81931."},"ddc":["570"],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Turelli","full_name":"Turelli, Michael","first_name":"Michael"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control"},{"_id":"10833","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","ddc":["540"],"citation":{"ista":"Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device, Zenodo, 10.5281/ZENODO.5500360.","chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.5500360.","ieee":"R. Hasler et al., “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device.” Zenodo, 2022.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, (2022).","apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. Zenodo. https://doi.org/10.5281/ZENODO.5500360","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. 2022. doi:10.5281/ZENODO.5500360","mla":"Hasler, Roger, et al. Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device. Zenodo, 2022, doi:10.5281/ZENODO.5500360."},"date_updated":"2023-08-02T14:46:16Z","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","department":[{"_id":"MaIb"}],"article_processing_charge":"No","author":[{"last_name":"Hasler","full_name":"Hasler, Roger","first_name":"Roger"},{"full_name":"Reiner-Rozman, Ciril","last_name":"Reiner-Rozman","first_name":"Ciril"},{"first_name":"Stefan","full_name":"Fossati, Stefan","last_name":"Fossati"},{"last_name":"Aspermair","full_name":"Aspermair, Patrik","first_name":"Patrik"},{"full_name":"Dostalek, Jakub","last_name":"Dostalek","first_name":"Jakub"},{"last_name":"Lee","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez"},{"full_name":"Bintinger, Johannes","last_name":"Bintinger","first_name":"Johannes"},{"full_name":"Knoll, Wolfgang","last_name":"Knoll","first_name":"Wolfgang"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Detailed information about the data set see \"dataset description.txt\" file."}],"month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5500360"}],"oa":1,"publisher":"Zenodo","day":"08","year":"2022","date_created":"2022-03-07T08:19:11Z","doi":"10.5281/ZENODO.5500360","related_material":{"record":[{"id":"10829","status":"public","relation":"used_in_publication"}]},"date_published":"2022-02-08T00:00:00Z"},{"doi":"10.5281/ZENODO.5733408","date_published":"2022-01-03T00:00:00Z","related_material":{"record":[{"id":"11180","status":"public","relation":"used_in_publication"}],"link":[{"url":"https://github.com/npostnikova/mq-based-schedulers/tree/v1.1","relation":"software"}]},"date_created":"2023-05-23T17:05:40Z","year":"2022","day":"03","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5813846","open_access":"1"}],"month":"01","abstract":[{"text":"The source code for replicating experiments presented in the paper.\r\n\r\nThe implementation of the designed priority schedulers can be found in Galois-2.2.1/include/Galois/WorkList/:\r\nStealingMultiQueue.h is the StealingMultiQueue.\r\nMQOptimized/ contains MQ Optimized variants.\r\n\r\nWe provide images that contain all the dependencies and datasets. Images can be pulled from npostnikova/mq-based-schedulers repository, or downloaded from Zenodo. See readme for more detail.","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Anastasiia","full_name":"Postnikova, Anastasiia","last_name":"Postnikova"},{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","full_name":"Koval, Nikita","last_name":"Koval"},{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"article_processing_charge":"No","department":[{"_id":"DaAl"}],"title":"Multi-queues can be state-of-the-art priority schedulers","citation":{"ama":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. Multi-queues can be state-of-the-art priority schedulers. 2022. doi:10.5281/ZENODO.5733408","apa":"Postnikova, A., Koval, N., Nadiradze, G., & Alistarh, D.-A. (2022). Multi-queues can be state-of-the-art priority schedulers. Zenodo. https://doi.org/10.5281/ZENODO.5733408","ieee":"A. Postnikova, N. Koval, G. Nadiradze, and D.-A. Alistarh, “Multi-queues can be state-of-the-art priority schedulers.” Zenodo, 2022.","short":"A. Postnikova, N. Koval, G. Nadiradze, D.-A. Alistarh, (2022).","mla":"Postnikova, Anastasiia, et al. Multi-Queues Can Be State-of-the-Art Priority Schedulers. Zenodo, 2022, doi:10.5281/ZENODO.5733408.","ista":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. 2022. Multi-queues can be state-of-the-art priority schedulers, Zenodo, 10.5281/ZENODO.5733408.","chicago":"Postnikova, Anastasiia, Nikita Koval, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.5733408."},"date_updated":"2023-08-03T06:48:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"type":"research_data_reference","status":"public","_id":"13076"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Data underlying the figures in the publication \"The chemistry of Cu3N and Cu3PdN nanocrystals\" "}],"month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6542908"}],"publisher":"Zenodo","day":"12","year":"2022","date_created":"2022-07-29T09:31:13Z","date_published":"2022-05-12T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"11451","status":"public"}]},"doi":"10.5281/ZENODO.6542908","_id":"11695","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","ddc":["540"],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-03T07:19:12Z","citation":{"chicago":"Parvizian, Mahsa, Alejandra Duran Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “Data for ‘The Chemistry of Cu3N and Cu3PdN Nanocrystals.’” Zenodo, 2022. https://doi.org/10.5281/ZENODO.6542908.","ista":"Parvizian M, Duran Balsa A, Pokratath R, Kalha C, Lee S, Van den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals’, Zenodo, 10.5281/ZENODO.6542908.","mla":"Parvizian, Mahsa, et al. Data for “The Chemistry of Cu3N and Cu3PdN Nanocrystals.” Zenodo, 2022, doi:10.5281/ZENODO.6542908.","ama":"Parvizian M, Duran Balsa A, Pokratath R, et al. Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” 2022. doi:10.5281/ZENODO.6542908","apa":"Parvizian, M., Duran Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van den Eynden, D., … De Roo, J. (2022). Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” Zenodo. https://doi.org/10.5281/ZENODO.6542908","short":"M. Parvizian, A. Duran Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, (2022).","ieee":"M. Parvizian et al., “Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals.’” Zenodo, 2022."},"title":"Data for \"The chemistry of Cu3N and Cu3PdN nanocrystals\"","department":[{"_id":"MaIb"}],"article_processing_charge":"No","author":[{"first_name":"Mahsa","full_name":"Parvizian, Mahsa","last_name":"Parvizian"},{"last_name":"Duran Balsa","full_name":"Duran Balsa, Alejandra","first_name":"Alejandra"},{"first_name":"Rohan","last_name":"Pokratath","full_name":"Pokratath, Rohan"},{"full_name":"Kalha, Curran","last_name":"Kalha","first_name":"Curran"},{"full_name":"Lee, Seungho","last_name":"Lee","first_name":"Seungho"},{"first_name":"Dietger","last_name":"Van den Eynden","full_name":"Van den Eynden, Dietger"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"first_name":"Anna","full_name":"Regoutz, Anna","last_name":"Regoutz"},{"last_name":"De Roo","full_name":"De Roo, Jonathan","first_name":"Jonathan"}]},{"day":"06","year":"2022","has_accepted_license":"1","date_created":"2022-08-01T08:06:33Z","date_published":"2022-07-06T00:00:00Z","doi":"10.5281/ZENODO.6802720","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11704"}]},"oa_version":"Published Version","abstract":[{"text":"Codes and data for reproducing the results of N. B. Budanur and B. Hof \"An autonomous compartmental model for accelerating epidemics\"","lang":"eng"}],"month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6802720"}],"oa":1,"publisher":"Zenodo","ddc":["000"],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-03T12:24:21Z","citation":{"ista":"Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, 10.5281/ZENODO.6802720.","chicago":"Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.6802720.","short":"N.B. Budanur, (2022).","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","apa":"Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. https://doi.org/10.5281/ZENODO.6802720","ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:10.5281/ZENODO.6802720","mla":"Budanur, Nazmi B. Burakbudanur/Autoacc-Public. Zenodo, 2022, doi:10.5281/ZENODO.6802720."},"department":[{"_id":"BjHo"}],"title":"burakbudanur/autoacc-public","article_processing_charge":"No","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur"}],"_id":"11711","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference"},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.gtht76hmz","open_access":"1"}],"publisher":"Dryad","month":"09","abstract":[{"lang":"eng","text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R 2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h SNP 2 . We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies."}],"oa_version":"Published Version","date_created":"2023-05-23T16:28:13Z","date_published":"2022-09-02T00:00:00Z","doi":"10.5061/DRYAD.GTHT76HMZ","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11733"}]},"year":"2022","day":"02","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","_id":"13064","article_processing_charge":"No","author":[{"first_name":"Etienne","last_name":"Orliac","full_name":"Orliac, Etienne"},{"first_name":"Daniel","last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel"},{"full_name":"Ojavee, Sven","last_name":"Ojavee","first_name":"Sven"},{"full_name":"Läll, Kristi","last_name":"Läll","first_name":"Kristi"},{"first_name":"Reedik","full_name":"Mägi, Reedik","last_name":"Mägi"},{"last_name":"Visscher","full_name":"Visscher, Peter","first_name":"Peter"},{"last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"department":[{"_id":"MaRo"}],"title":"Improving genome-wide association discovery and genomic prediction accuracy in biobank data","citation":{"mla":"Orliac, Etienne, et al. Improving Genome-Wide Association Discovery and Genomic Prediction Accuracy in Biobank Data. Dryad, 2022, doi:10.5061/DRYAD.GTHT76HMZ.","ama":"Orliac E, Trejo Banos D, Ojavee S, et al. Improving genome-wide association discovery and genomic prediction accuracy in biobank data. 2022. doi:10.5061/DRYAD.GTHT76HMZ","apa":"Orliac, E., Trejo Banos, D., Ojavee, S., Läll, K., Mägi, R., Visscher, P., & Robinson, M. R. (2022). Improving genome-wide association discovery and genomic prediction accuracy in biobank data. Dryad. https://doi.org/10.5061/DRYAD.GTHT76HMZ","ieee":"E. Orliac et al., “Improving genome-wide association discovery and genomic prediction accuracy in biobank data.” Dryad, 2022.","short":"E. Orliac, D. Trejo Banos, S. Ojavee, K. Läll, R. Mägi, P. Visscher, M.R. Robinson, (2022).","chicago":"Orliac, Etienne, Daniel Trejo Banos, Sven Ojavee, Kristi Läll, Reedik Mägi, Peter Visscher, and Matthew Richard Robinson. “Improving Genome-Wide Association Discovery and Genomic Prediction Accuracy in Biobank Data.” Dryad, 2022. https://doi.org/10.5061/DRYAD.GTHT76HMZ.","ista":"Orliac E, Trejo Banos D, Ojavee S, Läll K, Mägi R, Visscher P, Robinson MR. 2022. Improving genome-wide association discovery and genomic prediction accuracy in biobank data, Dryad, 10.5061/DRYAD.GTHT76HMZ."},"date_updated":"2023-08-03T12:40:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"]},{"article_processing_charge":"No","author":[{"id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella","last_name":"Tomanek","orcid":"0000-0001-6197-363X","full_name":"Tomanek, Isabella"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"department":[{"_id":"CaGu"}],"title":"Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose","date_updated":"2023-08-03T14:23:06Z","citation":{"apa":"Tomanek, I., & Guet, C. C. (2022). Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. Dryad. https://doi.org/10.5061/dryad.rfj6q57ds","ama":"Tomanek I, Guet CC. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. 2022. doi:10.5061/dryad.rfj6q57ds","short":"I. Tomanek, C.C. Guet, (2022).","ieee":"I. Tomanek and C. C. Guet, “Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose.” Dryad, 2022.","mla":"Tomanek, Isabella, and Calin C. Guet. Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose. Dryad, 2022, doi:10.5061/dryad.rfj6q57ds.","ista":"Tomanek I, Guet CC. 2022. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose, Dryad, 10.5061/dryad.rfj6q57ds.","chicago":"Tomanek, Isabella, and Calin C Guet. “Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose.” Dryad, 2022. https://doi.org/10.5061/dryad.rfj6q57ds."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","status":"public","_id":"12339","date_created":"2023-01-23T09:00:37Z","doi":"10.5061/dryad.rfj6q57ds","date_published":"2022-12-23T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12333"}]},"year":"2022","day":"23","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.rfj6q57ds","open_access":"1"}],"publisher":"Dryad","month":"12","abstract":[{"lang":"eng","text":"Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also constrain sequence divergence over evolutionary time scales."}],"oa_version":"Published Version"},{"title":"Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution","department":[{"_id":"NiBa"}],"author":[{"first_name":"Eva","full_name":"Koch, Eva","last_name":"Koch"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Kerstin","last_name":"Jonannesson","full_name":"Jonannesson, Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"article_processing_charge":"No","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-04T09:42:10Z","citation":{"ista":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. 2022. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution, Dryad, 10.5061/DRYAD.M905QFV4B.","chicago":"Koch, Eva, Mark Ravinet, Anja M Westram, Kerstin Jonannesson, and Roger Butlin. “Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution.” Dryad, 2022. https://doi.org/10.5061/DRYAD.M905QFV4B.","apa":"Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., & Butlin, R. (2022). Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Dryad. https://doi.org/10.5061/DRYAD.M905QFV4B","ama":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. 2022. doi:10.5061/DRYAD.M905QFV4B","short":"E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022).","ieee":"E. Koch, M. Ravinet, A. M. Westram, K. Jonannesson, and R. Butlin, “Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution.” Dryad, 2022.","mla":"Koch, Eva, et al. Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution. Dryad, 2022, doi:10.5061/DRYAD.M905QFV4B."},"status":"public","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"13066","date_published":"2022-07-28T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12247"}]},"doi":"10.5061/DRYAD.M905QFV4B","date_created":"2023-05-23T16:33:12Z","day":"28","year":"2022","month":"07","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.m905qfv4b"}],"oa":1,"oa_version":"Published Version","abstract":[{"text":"Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.","lang":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"date_updated":"2023-11-13T09:22:48Z","citation":{"short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, (2022).","ieee":"M. Zemlicka et al., “Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses.” Zenodo, 2022.","ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. 2022. doi:10.5281/ZENODO.8408897","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., & Fink, J. M. (2022). Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Zenodo. https://doi.org/10.5281/ZENODO.8408897","mla":"Zemlicka, Martin, et al. Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses. Zenodo, 2022, doi:10.5281/ZENODO.8408897.","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2022. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses, Zenodo, 10.5281/ZENODO.8408897.","chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.8408897."},"department":[{"_id":"JoFi"}],"title":"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses","author":[{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","full_name":"Redchenko, Elena","last_name":"Redchenko"},{"last_name":"Peruzzo","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Trioni","full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea"},{"last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","_id":"14520","status":"public","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"day":"28","has_accepted_license":"1","year":"2022","date_published":"2022-06-28T00:00:00Z","doi":"10.5281/ZENODO.8408897","related_material":{"record":[{"relation":"used_in_publication","id":"14517","status":"public"}]},"date_created":"2023-11-13T08:09:10Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses\" at arxiv.org/abs/2206.14104. Additional raw data are available from the corresponding author on reasonable request."}],"month":"06","publisher":"Zenodo","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8408897"}]},{"author":[{"orcid":" 0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"In vitro reconstitution of Escherichia coli divisome activation","citation":{"ieee":"P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022.","short":"P. Radler, (2022).","apa":"Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10934","ama":"Radler P. In vitro reconstitution of Escherichia coli divisome activation. 2022. doi:10.15479/AT:ISTA:10934","mla":"Radler, Philipp. In Vitro Reconstitution of Escherichia Coli Divisome Activation. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10934.","ista":"Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:10934.","chicago":"Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10934."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"date_published":"2022-04-05T00:00:00Z","doi":"10.15479/AT:ISTA:10934","date_created":"2022-03-31T11:32:32Z","has_accepted_license":"1","year":"2022","day":"05","publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","file_date_updated":"2022-04-22T10:15:19Z","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"date_updated":"2024-02-21T12:35:18Z","ddc":["572"],"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Bacterial cell division","in vitro reconstitution","FtsZ","FtsN","FtsA"],"_id":"10934","related_material":{"record":[{"id":"11373","status":"public","relation":"used_in_publication"},{"relation":"used_in_publication","status":"public","id":"14280"}],"link":[{"description":"A custom written code (FRAPdiff) to quantify the Off binding rate and Diffusion coefficient of membrane bound proteins. 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FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments. Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. 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Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses). 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Valentini, et. al. The transport data are saved with hdf5 file format. 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Data for ‘Majorana-like Coulomb spectroscopy in the absence of zero bias peaks’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12102.","chicago":"Valentini, Marco, Pablo San-Jose, Jordi Arbiol, Sara Marti-Sanchez, and Marc Botifoll. “Data for ‘Majorana-like Coulomb Spectroscopy in the Absence of Zero Bias Peaks.’” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:12102.","ieee":"M. Valentini, P. San-Jose, J. Arbiol, S. Marti-Sanchez, and M. Botifoll, “Data for ‘Majorana-like Coulomb spectroscopy in the absence of zero bias peaks.’” Institute of Science and Technology Austria, 2022.","short":"M. Valentini, P. San-Jose, J. Arbiol, S. Marti-Sanchez, M. Botifoll, (2022).","ama":"Valentini M, San-Jose P, Arbiol J, Marti-Sanchez S, Botifoll M. Data for “Majorana-like Coulomb spectroscopy in the absence of zero bias peaks.” 2022. doi:10.15479/AT:ISTA:12102","apa":"Valentini, M., San-Jose, P., Arbiol, J., Marti-Sanchez, S., & Botifoll, M. (2022). Data for “Majorana-like Coulomb spectroscopy in the absence of zero bias peaks.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12102","mla":"Valentini, Marco, et al. Data for “Majorana-like Coulomb Spectroscopy in the Absence of Zero Bias Peaks.” Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:12102."},"title":"Data for \"Majorana-like Coulomb spectroscopy in the absence of zero bias peaks\"","department":[{"_id":"GeKa"}],"file_date_updated":"2023-02-07T08:18:24Z","article_processing_charge":"No","author":[{"last_name":"Valentini","full_name":"Valentini, Marco","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"},{"last_name":"San-Jose","full_name":"San-Jose, Pablo","first_name":"Pablo"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"last_name":"Marti-Sanchez","full_name":"Marti-Sanchez, Sara","first_name":"Sara"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"}]},{"_id":"11321","status":"public","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2024-02-21T12:41:09Z","citation":{"ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11321","mla":"Surendranadh, Parvathy, et al. 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Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/at:ista:11321.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321."},"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","file_date_updated":"2022-04-22T09:39:03Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"author":[{"last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy"},{"last_name":"Arathoon","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. "}],"month":"04","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"checksum":"96c1b86cdf25481f2a52972fcc45ca7f","file_id":"11326","creator":"larathoo","file_size":13260571,"date_updated":"2022-04-22T09:39:03Z","file_name":"Data_Code.zip","date_created":"2022-04-22T09:39:03Z"}],"day":"28","has_accepted_license":"1","year":"2022","date_published":"2022-04-28T00:00:00Z","doi":"10.15479/at:ista:11321","related_material":{"record":[{"relation":"used_in_publication","id":"11411","status":"public"},{"relation":"earlier_version","status":"public","id":"9192"},{"status":"public","id":"8254","relation":"earlier_version"}]},"contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","contributor_type":"project_member","last_name":"Arathoon"},{"orcid":"0000-0002-7354-8574","last_name":"Baskett","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","contributor_type":"project_member","last_name":"Field","orcid":"0000-0002-4014-8478"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"first_name":"Nicholas H","contributor_type":"project_member","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"date_created":"2022-04-22T09:42:24Z"},{"abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"08","year":"2022","has_accepted_license":"1","day":"05","file":[{"creator":"melkrewi","file_size":2209382998,"date_updated":"2022-08-08T22:30:04Z","file_name":"Data.zip","date_created":"2022-07-26T12:37:52Z","title":"Supplementary Datasets","relation":"main_file","access_level":"open_access","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","content_type":"application/x-zip-compressed","embargo":"2022-08-07","file_id":"11655","checksum":"5f1d7c6d7ab5375ed2564521432bed0c"}],"contributor":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups"},{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"},{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sax","first_name":"Luca"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"last_name":"Hontoria ","first_name":"Francisco"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"date_created":"2022-07-26T11:01:47Z","doi":"10.15479/AT:ISTA:11653","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12248"}]},"date_published":"2022-08-05T00:00:00Z","_id":"11653","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","status":"public","citation":{"chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653.","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653.","mla":"Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653","short":"M.N. Elkrewi, (2022).","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022."},"date_updated":"2024-02-21T12:35:53Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file_date_updated":"2022-08-08T22:30:04Z","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\""},{"date_created":"2023-05-23T16:46:20Z","related_material":{"record":[{"status":"public","id":"10702","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.5794028","date_published":"2021-12-20T00:00:00Z","year":"2021","day":"20","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5794029"}],"oa":1,"publisher":"Zenodo","month":"12","abstract":[{"text":"CpGs and corresponding mean weights for DNAm-based prediction of cognitive abilities (6 traits)","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Daniel L","last_name":"McCartney","full_name":"McCartney, Daniel L"},{"first_name":"Robert F","full_name":"Hillary, Robert F","last_name":"Hillary"},{"last_name":"Conole","full_name":"Conole, Eleanor LS","first_name":"Eleanor LS"},{"last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel","first_name":"Daniel"},{"full_name":"Gadd, Danni A","last_name":"Gadd","first_name":"Danni A"},{"first_name":"Rosie M","last_name":"Walker","full_name":"Walker, Rosie M"},{"full_name":"Nangle, Cliff","last_name":"Nangle","first_name":"Cliff"},{"first_name":"Robin","last_name":"Flaig","full_name":"Flaig, Robin"},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"last_name":"Murray","full_name":"Murray, Alison D","first_name":"Alison D"},{"last_name":"Munoz Maniega","full_name":"Munoz Maniega, Susana","first_name":"Susana"},{"first_name":"Maria","last_name":"del C Valdes-Hernandez","full_name":"del C Valdes-Hernandez, Maria"},{"first_name":"Mathew A","full_name":"Harris, Mathew A","last_name":"Harris"},{"full_name":"Bastin, Mark E","last_name":"Bastin","first_name":"Mark E"},{"last_name":"Wardlaw","full_name":"Wardlaw, Joanna M","first_name":"Joanna M"},{"last_name":"Harris","full_name":"Harris, Sarah E","first_name":"Sarah E"},{"first_name":"David J","full_name":"Porteous, David J","last_name":"Porteous"},{"last_name":"Tucker-Drob","full_name":"Tucker-Drob, Elliot M","first_name":"Elliot M"},{"first_name":"Andrew M","full_name":"McIntosh, Andrew M","last_name":"McIntosh"},{"first_name":"Kathryn L","full_name":"Evans, Kathryn L","last_name":"Evans"},{"first_name":"Ian J","full_name":"Deary, Ian J","last_name":"Deary"},{"full_name":"Cox, Simon R","last_name":"Cox","first_name":"Simon R"},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Riccardo E","full_name":"Marioni, Riccardo E","last_name":"Marioni"}],"title":"Blood-based epigenome-wide analyses of cognitive abilities","department":[{"_id":"MaRo"}],"date_updated":"2023-08-02T14:05:12Z","citation":{"apa":"McCartney, D. L., Hillary, R. F., Conole, E. L., Trejo Banos, D., Gadd, D. A., Walker, R. M., … Marioni, R. E. (2021). Blood-based epigenome-wide analyses of cognitive abilities. Zenodo. https://doi.org/10.5281/ZENODO.5794028","ama":"McCartney DL, Hillary RF, Conole EL, et al. Blood-based epigenome-wide analyses of cognitive abilities. 2021. doi:10.5281/ZENODO.5794028","ieee":"D. L. McCartney et al., “Blood-based epigenome-wide analyses of cognitive abilities.” Zenodo, 2021.","short":"D.L. McCartney, R.F. Hillary, E.L. Conole, D. Trejo Banos, D.A. Gadd, R.M. Walker, C. Nangle, R. Flaig, A. Campbell, A.D. Murray, S. Munoz Maniega, M. del C Valdes-Hernandez, M.A. Harris, M.E. Bastin, J.M. Wardlaw, S.E. Harris, D.J. Porteous, E.M. Tucker-Drob, A.M. McIntosh, K.L. Evans, I.J. Deary, S.R. Cox, M.R. Robinson, R.E. Marioni, (2021).","mla":"McCartney, Daniel L., et al. Blood-Based Epigenome-Wide Analyses of Cognitive Abilities. Zenodo, 2021, doi:10.5281/ZENODO.5794028.","ista":"McCartney DL, Hillary RF, Conole EL, Trejo Banos D, Gadd DA, Walker RM, Nangle C, Flaig R, Campbell A, Murray AD, Munoz Maniega S, del C Valdes-Hernandez M, Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. 2021. Blood-based epigenome-wide analyses of cognitive abilities, Zenodo, 10.5281/ZENODO.5794028.","chicago":"McCartney, Daniel L, Robert F Hillary, Eleanor LS Conole, Daniel Trejo Banos, Danni A Gadd, Rosie M Walker, Cliff Nangle, et al. “Blood-Based Epigenome-Wide Analyses of Cognitive Abilities.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5794028."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"13072"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","_id":"13068","title":"Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids","department":[{"_id":"EdHa"}],"article_processing_charge":"No","author":[{"last_name":"Randriamanantsoa","full_name":"Randriamanantsoa, Samuel","first_name":"Samuel"},{"first_name":"Aristeidis","last_name":"Papargyriou","full_name":"Papargyriou, Aristeidis"},{"first_name":"Carlo","full_name":"Maurer, Carlo","last_name":"Maurer"},{"first_name":"Katja","full_name":"Peschke, Katja","last_name":"Peschke"},{"first_name":"Maximilian","last_name":"Schuster","full_name":"Schuster, Maximilian"},{"first_name":"Giulia","last_name":"Zecchin","full_name":"Zecchin, Giulia"},{"full_name":"Steiger, Katja","last_name":"Steiger","first_name":"Katja"},{"first_name":"Rupert","full_name":"Öllinger, Rupert","last_name":"Öllinger"},{"first_name":"Dieter","last_name":"Saur","full_name":"Saur, Dieter"},{"last_name":"Scheel","full_name":"Scheel, Christina","first_name":"Christina"},{"first_name":"Roland","last_name":"Rad","full_name":"Rad, Roland"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"first_name":"Maximilian","full_name":"Reichert, Maximilian","last_name":"Reichert"},{"first_name":"Andreas R.","full_name":"Bausch, Andreas R.","last_name":"Bausch"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-04T09:25:23Z","citation":{"ama":"Randriamanantsoa S, Papargyriou A, Maurer C, et al. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. 2021. doi:10.5281/ZENODO.5148117","apa":"Randriamanantsoa, S., Papargyriou, A., Maurer, C., Peschke, K., Schuster, M., Zecchin, G., … Bausch, A. R. (2021). Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Zenodo. https://doi.org/10.5281/ZENODO.5148117","ieee":"S. Randriamanantsoa et al., “Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids.” Zenodo, 2021.","short":"S. Randriamanantsoa, A. Papargyriou, C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo, M. Reichert, A.R. Bausch, (2021).","mla":"Randriamanantsoa, Samuel, et al. Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids. Zenodo, 2021, doi:10.5281/ZENODO.5148117.","ista":"Randriamanantsoa S, Papargyriou A, Maurer C, Peschke K, Schuster M, Zecchin G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch AR. 2021. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids, Zenodo, 10.5281/ZENODO.5148117.","chicago":"Randriamanantsoa, Samuel, Aristeidis Papargyriou, Carlo Maurer, Katja Peschke, Maximilian Schuster, Giulia Zecchin, Katja Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5148117."},"month":"07","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.6577226","open_access":"1"}],"oa":1,"publisher":"Zenodo","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Source data and source code for the graphs in \"Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids\"."}],"date_created":"2023-05-23T16:39:24Z","date_published":"2021-07-30T00:00:00Z","doi":"10.5281/ZENODO.5148117","related_material":{"record":[{"status":"public","id":"12217","relation":"used_in_publication"}]},"day":"30","year":"2021"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome."}],"month":"04","main_file_link":[{"url":"https://doi.org/10.5061/dryad.zgmsbccb4","open_access":"1"}],"oa":1,"publisher":"Dryad","day":"10","year":"2021","has_accepted_license":"1","date_created":"2023-05-16T12:34:09Z","related_material":{"record":[{"relation":"used_in_publication","id":"9394","status":"public"}]},"date_published":"2021-04-10T00:00:00Z","doi":"10.5061/DRYAD.ZGMSBCCB4","_id":"12987","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.","ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4","apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4","short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021).","ieee":"E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","mla":"Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4."},"date_updated":"2023-08-08T13:34:07Z","department":[{"_id":"NiBa"}],"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","article_processing_charge":"No","author":[{"first_name":"Eva","last_name":"Koch","full_name":"Koch, Eva"},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"first_name":"E. Moriarty","last_name":"Lemmon","full_name":"Lemmon, E. Moriarty"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}]},{"year":"2021","day":"09","date_created":"2023-05-23T17:11:28Z","related_material":{"link":[{"relation":"software","url":"https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3"}],"record":[{"relation":"used_in_publication","id":"9570","status":"public"}]},"doi":"10.5281/ZENODO.4592435","date_published":"2021-03-09T00:00:00Z","abstract":[{"lang":"eng","text":"Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the raw data for these extended datasets as well."}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4592460","open_access":"1"}],"publisher":"Zenodo","month":"03","citation":{"chicago":"Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435.","ista":"Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R, Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435.","mla":"Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435.","ieee":"D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021.","short":"D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher, M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021).","apa":"Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G., … Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435","ama":"Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435"},"date_updated":"2023-08-08T14:08:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"article_processing_charge":"No","author":[{"first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","last_name":"Puglia"},{"full_name":"Martinez, Esteban","last_name":"Martinez","first_name":"Esteban"},{"first_name":"Gerbold","full_name":"Menard, Gerbold","last_name":"Menard"},{"first_name":"Andreas","full_name":"Pöschl, Andreas","last_name":"Pöschl"},{"first_name":"Sergei","full_name":"Gronin, Sergei","last_name":"Gronin"},{"last_name":"Gardner","full_name":"Gardner, Geoffrey","first_name":"Geoffrey"},{"full_name":"Kallaher, Ray","last_name":"Kallaher","first_name":"Ray"},{"full_name":"Manfra, Michael","last_name":"Manfra","first_name":"Michael"},{"first_name":"Charles","full_name":"Marcus, Charles","last_name":"Marcus"},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"},{"first_name":"Lucas","full_name":"Casparis, Lucas","last_name":"Casparis"}],"title":"Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire","department":[{"_id":"AnHi"}],"_id":"13080","type":"research_data_reference","status":"public"},{"title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","department":[{"_id":"JoFi"}],"article_processing_charge":"No","author":[{"first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani"},{"first_name":"Grisha","last_name":"Szep","full_name":"Szep, Grisha"},{"first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea","last_name":"Trioni"},{"full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","last_name":"Zemlicka"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.","ista":"Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction, Zenodo, 10.5281/ZENODO.5592103.","mla":"Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.","apa":"Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., & Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. Zenodo. https://doi.org/10.5281/ZENODO.5592103","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, (2021).","ieee":"M. Peruzzo et al., “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction.” Zenodo, 2021."},"date_updated":"2023-08-11T10:44:21Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","_id":"13057","date_created":"2023-05-23T13:42:27Z","date_published":"2021-10-22T00:00:00Z","doi":"10.5281/ZENODO.5592103","related_material":{"record":[{"relation":"used_in_publication","id":"9928","status":"public"}]},"day":"22","year":"2021","month":"10","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5592104"}],"publisher":"Zenodo","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction\". Additional raw data are available from the corresponding author on reasonable request."}]},{"type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"_id":"13061","author":[{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","last_name":"Pull"},{"first_name":"Filip","full_name":"Naiser, Filip","last_name":"Naiser"},{"first_name":"Elisabeth","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth"},{"full_name":"Matas, Jiri","last_name":"Matas","first_name":"Jiri"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"article_processing_charge":"No","title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","department":[{"_id":"SyCr"}],"date_updated":"2023-08-14T11:45:28Z","citation":{"chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021. https://doi.org/10.5061/DRYAD.7PVMCVDTJ.","ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies, Dryad, 10.5061/DRYAD.7PVMCVDTJ.","mla":"Casillas Perez, Barbara E., et al. Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies. Dryad, 2021, doi:10.5061/DRYAD.7PVMCVDTJ.","ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies.” Dryad, 2021.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021).","apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., & Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Dryad. https://doi.org/10.5061/DRYAD.7PVMCVDTJ","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. 2021. doi:10.5061/DRYAD.7PVMCVDTJ"},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7pvmcvdtj"}],"month":"10","abstract":[{"text":"Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10284"}]},"date_published":"2021-10-29T00:00:00Z","doi":"10.5061/DRYAD.7PVMCVDTJ","date_created":"2023-05-23T16:14:35Z","ec_funded":1,"year":"2021","day":"29"},{"_id":"13069","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans. Zenodo, 2021, doi:10.5281/ZENODO.5519410.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans.” Zenodo, 2021.","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. 2021. doi:10.5281/ZENODO.5519410","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. Zenodo. https://doi.org/10.5281/ZENODO.5519410","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410.","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans, Zenodo, 10.5281/ZENODO.5519410."},"date_updated":"2023-08-14T11:53:26Z","title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","department":[{"_id":"MaDe"}],"article_processing_charge":"No","author":[{"last_name":"Chauve","full_name":"Chauve, Laetitia","first_name":"Laetitia"},{"last_name":"Hodge","full_name":"Hodge, Francesca","first_name":"Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"last_name":"Masoudzadeh","full_name":"Masoudzadeh, Fatemah","first_name":"Fatemah"},{"first_name":"Harry-Jack","full_name":"Mann, Harry-Jack","last_name":"Mann"},{"first_name":"Andrea","full_name":"Lopez-Clavijo, Andrea","last_name":"Lopez-Clavijo"},{"full_name":"Okkenhaug, Hanneke","last_name":"Okkenhaug","first_name":"Hanneke"},{"first_name":"Greg","last_name":"West","full_name":"West, Greg"},{"first_name":"Bebiana C.","full_name":"Sousa, Bebiana C.","last_name":"Sousa"},{"first_name":"Anne","full_name":"Segonds-Pichon, Anne","last_name":"Segonds-Pichon"},{"full_name":"Li, Cheryl","last_name":"Li","first_name":"Cheryl"},{"full_name":"Wingett, Steven","last_name":"Wingett","first_name":"Steven"},{"full_name":"Kienberger, Hermine","last_name":"Kienberger","first_name":"Hermine"},{"full_name":"Kleigrewe, Karin","last_name":"Kleigrewe","first_name":"Karin"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"},{"first_name":"Michael","full_name":"Wakelam, Michael","last_name":"Wakelam"},{"first_name":"Olivia","last_name":"Casanueva","full_name":"Casanueva, Olivia"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal."}],"month":"12","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5547464"}],"publisher":"Zenodo","day":"25","year":"2021","date_created":"2023-05-23T16:40:56Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10322"}]},"doi":"10.5281/ZENODO.5519410","date_published":"2021-12-25T00:00:00Z"},{"date_created":"2023-05-23T13:46:34Z","date_published":"2021-08-25T00:00:00Z","doi":"10.5281/ZENODO.5257160","related_material":{"record":[{"id":"10402","status":"public","relation":"used_in_publication"}]},"year":"2021","day":"25","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5257161"}],"publisher":"Zenodo","month":"08","abstract":[{"lang":"eng","text":"The zip file includes source data used in the main text of the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar"}],"title":"Source data for the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\"","department":[{"_id":"EdHa"}],"date_updated":"2023-08-14T13:18:46Z","citation":{"chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160.","ista":"Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160.","mla":"Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160.","ieee":"M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021.","short":"M.C. Ucar, (2021).","apa":"Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160","ama":"Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160"},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"13058"},{"department":[{"_id":"NiBa"}],"title":"Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model","author":[{"last_name":"Szep","full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"ista":"Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1.","chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.","short":"E. Szep, H. Sachdeva, N.H. Barton, (2021).","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1","ama":"Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1","mla":"Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1."},"date_updated":"2023-09-05T15:44:05Z","status":"public","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"13062","date_published":"2021-03-02T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9252"}]},"doi":"10.5061/DRYAD.8GTHT76P1","date_created":"2023-05-23T16:17:02Z","day":"02","year":"2021","month":"03","publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.8gtht76p1","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments."}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\\leq$ 10\\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. 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The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. 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Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192"},"date_updated":"2024-02-21T12:41:09Z","month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document.","lang":"eng"}],"date_published":"2021-02-26T00:00:00Z","doi":"10.15479/AT:ISTA:9192","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11411"},{"relation":"later_version","status":"public","id":"11321"},{"relation":"earlier_version","status":"public","id":"8254"}]},"date_created":"2021-02-24T17:49:21Z","contributor":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","contributor_type":"project_member","last_name":"Surendranadh"},{"contributor_type":"project_member","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","last_name":"Arathoon"},{"first_name":"Carina","contributor_type":"project_member","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett"},{"last_name":"Field","orcid":"0000-0002-4014-8478","first_name":"David","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","contributor_type":"project_member","last_name":"Pickup","orcid":"0000-0001-6118-0541"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","contributor_type":"project_leader","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"day":"26","file":[{"file_name":"Data_Code.zip","date_created":"2021-02-24T17:45:13Z","creator":"larathoo","file_size":5934452,"date_updated":"2021-02-24T17:45:13Z","success":1,"file_id":"9193","checksum":"f85537815809a8a4b7da9d01163f88c0","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed"}],"has_accepted_license":"1","year":"2021"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:40:30Z","citation":{"chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9949.","ista":"Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9949.","mla":"Vicoso, Beatriz. Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9949.","short":"B. Vicoso, (2021).","ieee":"B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021.","apa":"Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9949","ama":"Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:10.15479/AT:ISTA:9949"},"file_date_updated":"2021-08-21T13:43:59Z","title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","department":[{"_id":"BeVi"}],"article_processing_charge":"No","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"_id":"9949","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","file":[{"file_size":139188306,"date_updated":"2021-08-21T13:43:59Z","creator":"bvicoso","file_name":"Data.zip","date_created":"2021-08-21T13:43:59Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"file_id":"9950","checksum":"90461837eed66beac6fa302993cf0ca9"}],"day":"24","year":"2021","has_accepted_license":"1","date_created":"2021-08-21T13:44:22Z","date_published":"2021-08-24T00:00:00Z","doi":"10.15479/AT:ISTA:9949","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10166"}]},"oa_version":"None","month":"08","oa":1,"publisher":"Institute of Science and Technology Austria"},{"date_created":"2023-05-23T16:48:27Z","date_published":"2020-09-22T00:00:00Z","related_material":{"record":[{"status":"public","id":"8708","relation":"used_in_publication"}]},"doi":"10.5061/DRYAD.R4XGXD29N","year":"2020","day":"22","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"oa":1,"publisher":"Dryad","month":"09","abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Alexis","last_name":"Simon","full_name":"Simon, Alexis"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"El Ayari, Tahani","last_name":"El Ayari","first_name":"Tahani"},{"last_name":"Liautard-Haag","full_name":"Liautard-Haag, Cathy","first_name":"Cathy"},{"full_name":"Strelkov, Petr","last_name":"Strelkov","first_name":"Petr"},{"last_name":"Welch","full_name":"Welch, John","first_name":"John"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","department":[{"_id":"NiBa"}],"citation":{"short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N","mla":"Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N.","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N."},"date_updated":"2023-08-04T11:04:11Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","_id":"13073"},{"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"first_name":"Stephanie","last_name":"Arnoux","full_name":"Arnoux, Stephanie"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"last_name":"Sauvage","full_name":"Sauvage, Christopher","first_name":"Christopher"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-04T11:19:26Z","citation":{"chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD.","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD.","mla":"Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD"},"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","_id":"13065","date_created":"2023-05-23T16:30:20Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8928"}],"link":[{"url":"https://github.com/starnoux/arnoux_et_al_2019","relation":"software"}]},"doi":"10.5061/DRYAD.Q2BVQ83HD","date_published":"2020-10-19T00:00:00Z","day":"19","year":"2020","month":"10","main_file_link":[{"url":"https://doi.org/10.5061/dryad.q2bvq83hd","open_access":"1"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.","lang":"eng"}]},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)"}],"month":"01","publisher":"American Chemical Society ","day":"08","year":"2020","doi":"10.1021/acs.nanolett.9b04445.s002","date_published":"2020-01-08T00:00:00Z","related_material":{"record":[{"status":"public","id":"7166","relation":"used_in_publication"}]},"date_created":"2021-08-11T13:16:03Z","_id":"9885","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-17T14:07:52Z","citation":{"mla":"Ucar, Mehmet C., and Reinhard Lipowsky. MURL_Dataz. American Chemical Society , 2020, doi:10.1021/acs.nanolett.9b04445.s002.","ieee":"M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society , 2020.","short":"M.C. Ucar, R. Lipowsky, (2020).","apa":"Ucar, M. C., & Lipowsky, R. (2020). MURL_Dataz. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s002","ama":"Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:10.1021/acs.nanolett.9b04445.s002","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical Society , 2020. https://doi.org/10.1021/acs.nanolett.9b04445.s002.","ista":"Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society , 10.1021/acs.nanolett.9b04445.s002."},"department":[{"_id":"EdHa"}],"title":"MURL_Dataz","author":[{"last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"full_name":"Lipowsky, Reinhard","last_name":"Lipowsky","first_name":"Reinhard"}],"article_processing_charge":"No"},{"oa_version":"Published Version","publisher":"Public Library of Science","month":"02","year":"2020","day":"25","related_material":{"record":[{"status":"public","id":"7569","relation":"research_data"}]},"date_published":"2020-02-25T00:00:00Z","doi":"10.1371/journal.pcbi.1007642.s003","date_created":"2021-08-06T07:24:37Z","_id":"9779","type":"research_data_reference","status":"public","citation":{"mla":"Grah, Rok, and Tamar Friedlander. Distribution of Crosstalk Values. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s003.","ama":"Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003","apa":"Grah, R., & Friedlander, T. (2020). Distribution of crosstalk values. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s003","short":"R. Grah, T. Friedlander, (2020).","ieee":"R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020.","chicago":"Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s003.","ista":"Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library of Science, 10.1371/journal.pcbi.1007642.s003."},"date_updated":"2023-08-18T06:47:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok"},{"first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"title":"Distribution of crosstalk values"},{"publisher":"Public Library of Science","month":"02","oa_version":"Published Version","doi":"10.1371/journal.pcbi.1007642.s001","date_published":"2020-02-25T00:00:00Z","related_material":{"record":[{"status":"public","id":"7569","relation":"used_in_publication"}]},"date_created":"2021-08-06T07:15:04Z","year":"2020","day":"25","type":"research_data_reference","status":"public","_id":"9776","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"},{"first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"title":"Supporting information","date_updated":"2023-08-18T06:47:47Z","citation":{"ista":"Grah R, Friedlander T. 2020. Supporting information, Public Library of Science, 10.1371/journal.pcbi.1007642.s001.","chicago":"Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s001.","ama":"Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001","apa":"Grah, R., & Friedlander, T. (2020). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s001","short":"R. Grah, T. Friedlander, (2020).","ieee":"R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020.","mla":"Grah, Rok, and Tamar Friedlander. Supporting Information. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"day":"29","year":"2020","has_accepted_license":"1","date_created":"2021-07-23T10:00:35Z","doi":"10.17863/cam.50169","date_published":"2020-05-29T00:00:00Z","related_material":{"record":[{"status":"public","id":"7942","relation":"used_in_publication"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided."}],"month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.17863/CAM.50169"}],"oa":1,"publisher":"Apollo - University of Cambridge","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-21T07:06:48Z","citation":{"chicago":"Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169.","ista":"Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, 10.17863/cam.50169.","mla":"Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169.","ama":"Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:10.17863/cam.50169","apa":"Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169","ieee":"M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020.","short":"M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020)."},"title":"Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'","department":[{"_id":"KiMo"}],"article_processing_charge":"No","author":[{"first_name":"Mate","last_name":"Hartstein","full_name":"Hartstein, Mate"},{"last_name":"Hsu","full_name":"Hsu, Yu-Te","first_name":"Yu-Te"},{"last_name":"Modic","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A"},{"last_name":"Porras","full_name":"Porras, Juan","first_name":"Juan"},{"full_name":"Loew, Toshinao","last_name":"Loew","first_name":"Toshinao"},{"first_name":"Matthieu","full_name":"Le Tacon, Matthieu","last_name":"Le Tacon"},{"last_name":"Zuo","full_name":"Zuo, Huakun","first_name":"Huakun"},{"last_name":"Wang","full_name":"Wang, Jinhua","first_name":"Jinhua"},{"first_name":"Zengwei","last_name":"Zhu","full_name":"Zhu, Zengwei"},{"full_name":"Chan, Mun","last_name":"Chan","first_name":"Mun"},{"full_name":"McDonald, Ross","last_name":"McDonald","first_name":"Ross"},{"last_name":"Lonzarich","full_name":"Lonzarich, Gilbert","first_name":"Gilbert"},{"last_name":"Keimer","full_name":"Keimer, Bernhard","first_name":"Bernhard"},{"first_name":"Suchitra","full_name":"Sebastian, Suchitra","last_name":"Sebastian"},{"last_name":"Harrison","full_name":"Harrison, Neil","first_name":"Neil"}],"_id":"9708","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference"},{"date_published":"2020-07-01T00:00:00Z","doi":"10.5061/dryad.qrfj6q5cn","related_material":{"record":[{"id":"7995","status":"public","relation":"used_in_publication"}]},"date_created":"2020-11-25T11:07:25Z","has_accepted_license":"1","year":"2020","day":"01","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.qrfj6q5cn","open_access":"1"}],"oa":1,"month":"07","abstract":[{"text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.","lang":"eng"}],"oa_version":"Published Version","author":[{"full_name":"Perini, Samuel","last_name":"Perini","first_name":"Samuel"},{"last_name":"Rafajlovic","full_name":"Rafajlovic, Marina","first_name":"Marina"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"article_processing_charge":"No","title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","department":[{"_id":"NiBa"}],"date_updated":"2023-08-22T07:13:37Z","citation":{"mla":"Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.","ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","_id":"8809"},{"date_created":"2021-04-14T12:05:20Z","doi":"10.1021/jacs.9b13450.s002","date_published":"2020-05-20T00:00:00Z","related_material":{"record":[{"id":"8040","status":"public","relation":"used_in_publication"}]},"day":"20","year":"2020","month":"05","main_file_link":[{"open_access":"1"}],"oa":1,"publisher":"American Chemical Society","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I."}],"title":"Charge transfer and chemo-mechanical coupling in respiratory complex I","department":[{"_id":"LeSa"}],"article_processing_charge":"No","author":[{"first_name":"Chitrak","full_name":"Gupta, Chitrak","last_name":"Gupta"},{"last_name":"Khaniya","full_name":"Khaniya, Umesh","first_name":"Umesh"},{"first_name":"Chun","full_name":"Chan, Chun","last_name":"Chan"},{"first_name":"Francois","full_name":"Dehez, Francois","last_name":"Dehez"},{"first_name":"Mrinal","full_name":"Shekhar, Mrinal","last_name":"Shekhar"},{"first_name":"M. R.","full_name":"Gunner, M. R.","last_name":"Gunner"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov"},{"first_name":"Christophe","last_name":"Chipot","full_name":"Chipot, Christophe"},{"last_name":"Singharoy","full_name":"Singharoy, Abhishek","first_name":"Abhishek"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-22T07:49:37Z","citation":{"mla":"Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","ama":"Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002","apa":"Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020.","short":"C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.","ista":"Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I, American Chemical Society, 10.1021/jacs.9b13450.s002."},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data_reference","_id":"9326"},{"date_created":"2021-07-23T12:02:39Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8040"}]},"doi":"10.1021/jacs.9b13450.s001","date_published":"2020-05-20T00:00:00Z","year":"2020","day":"20","publisher":"American Chemical Society ","month":"05","abstract":[{"lang":"eng","text":"Additional analyses of the trajectories"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Chitrak","full_name":"Gupta, Chitrak","last_name":"Gupta"},{"full_name":"Khaniya, Umesh","last_name":"Khaniya","first_name":"Umesh"},{"first_name":"Chun Kit","last_name":"Chan","full_name":"Chan, Chun Kit"},{"first_name":"Francois","full_name":"Dehez, Francois","last_name":"Dehez"},{"first_name":"Mrinal","full_name":"Shekhar, Mrinal","last_name":"Shekhar"},{"last_name":"Gunner","full_name":"Gunner, M.R.","first_name":"M.R."},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"},{"first_name":"Christophe","full_name":"Chipot, Christophe","last_name":"Chipot"},{"first_name":"Abhishek","full_name":"Singharoy, Abhishek","last_name":"Singharoy"}],"title":"Supporting information","department":[{"_id":"LeSa"}],"citation":{"chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society , 2020. https://doi.org/10.1021/jacs.9b13450.s001.","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society , 10.1021/jacs.9b13450.s001.","mla":"Gupta, Chitrak, et al. Supporting Information. American Chemical Society , 2020, doi:10.1021/jacs.9b13450.s001.","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ieee":"C. Gupta et al., “Supporting information.” American Chemical Society , 2020.","ama":"Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . https://doi.org/10.1021/jacs.9b13450.s001"},"date_updated":"2023-08-22T07:49:38Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9713"},{"department":[{"_id":"LeSa"}],"title":"Movies","article_processing_charge":"No","author":[{"last_name":"Gupta","full_name":"Gupta, Chitrak","first_name":"Chitrak"},{"first_name":"Umesh","full_name":"Khaniya, Umesh","last_name":"Khaniya"},{"first_name":"Chun Kit","full_name":"Chan, Chun Kit","last_name":"Chan"},{"first_name":"Francois","full_name":"Dehez, Francois","last_name":"Dehez"},{"first_name":"Mrinal","full_name":"Shekhar, Mrinal","last_name":"Shekhar"},{"first_name":"M.R.","full_name":"Gunner, M.R.","last_name":"Gunner"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chipot","full_name":"Chipot, Christophe","first_name":"Christophe"},{"last_name":"Singharoy","full_name":"Singharoy, Abhishek","first_name":"Abhishek"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Gupta, Chitrak, et al. Movies. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Movies. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","ama":"Gupta C, Khaniya U, Chan CK, et al. Movies. 2020. doi:10.1021/jacs.9b13450.s002","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ieee":"C. Gupta et al., “Movies.” American Chemical Society, 2020.","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Movies.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Movies, American Chemical Society, 10.1021/jacs.9b13450.s002."},"date_updated":"2023-08-22T07:49:38Z","status":"public","type":"research_data_reference","_id":"9878","date_created":"2021-08-11T09:18:54Z","date_published":"2020-05-20T00:00:00Z","related_material":{"record":[{"status":"public","id":"8040","relation":"used_in_publication"}]},"doi":"10.1021/jacs.9b13450.s002","day":"20","year":"2020","month":"05","publisher":"American Chemical Society","oa_version":"Published Version"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"9706","article_processing_charge":"No","author":[{"full_name":"Hillary, Robert F.","last_name":"Hillary","first_name":"Robert F."},{"last_name":"Trejo-Banos","full_name":"Trejo-Banos, Daniel","first_name":"Daniel"},{"first_name":"Athanasios","last_name":"Kousathanas","full_name":"Kousathanas, Athanasios"},{"first_name":"Daniel L.","full_name":"McCartney, Daniel L.","last_name":"McCartney"},{"first_name":"Sarah E.","last_name":"Harris","full_name":"Harris, Sarah E."},{"last_name":"Stevenson","full_name":"Stevenson, Anna J.","first_name":"Anna J."},{"full_name":"Patxot, Marion","last_name":"Patxot","first_name":"Marion"},{"full_name":"Ojavee, Sven Erik","last_name":"Ojavee","first_name":"Sven Erik"},{"first_name":"Qian","full_name":"Zhang, Qian","last_name":"Zhang"},{"full_name":"Liewald, David C.","last_name":"Liewald","first_name":"David C."},{"last_name":"Ritchie","full_name":"Ritchie, Craig W.","first_name":"Craig W."},{"first_name":"Kathryn L.","full_name":"Evans, Kathryn L.","last_name":"Evans"},{"full_name":"Tucker-Drob, Elliot M.","last_name":"Tucker-Drob","first_name":"Elliot M."},{"first_name":"Naomi R.","last_name":"Wray","full_name":"Wray, Naomi R."},{"last_name":"McRae","full_name":"McRae, Allan F. ","first_name":"Allan F. "},{"last_name":"Visscher","full_name":"Visscher, Peter M.","first_name":"Peter M."},{"first_name":"Ian J.","full_name":"Deary, Ian J.","last_name":"Deary"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"},{"first_name":"Riccardo E. ","last_name":"Marioni","full_name":"Marioni, Riccardo E. "}],"department":[{"_id":"MaRo"}],"title":"Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","citation":{"ista":"Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020).","ieee":"R. F. Hillary et al., “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020.","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:10.6084/m9.figshare.12629697.v1","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1","mla":"Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults. Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1."},"date_updated":"2023-08-22T07:55:36Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.12629697.v1","open_access":"1"}],"publisher":"Springer Nature","other_data_license":"CC0 + CC BY (4.0)","month":"07","abstract":[{"text":"Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).","lang":"eng"}],"oa_version":"Published Version","date_created":"2021-07-23T08:59:15Z","date_published":"2020-07-09T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"8133","status":"public"}]},"doi":"10.6084/m9.figshare.12629697.v1","year":"2020","has_accepted_license":"1","day":"09"},{"department":[{"_id":"JoFi"}],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","article_processing_charge":"No","author":[{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","last_name":"Arnold","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M"},{"first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf"},{"orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Hease","orcid":"0000-0001-9868-2166","full_name":"Hease, William J"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"citation":{"chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561.","mla":"Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561.","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561"},"date_updated":"2023-08-22T09:27:11Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","_id":"13056","date_created":"2023-05-23T13:37:41Z","date_published":"2020-07-27T00:00:00Z","doi":"10.5281/ZENODO.3961561","related_material":{"record":[{"id":"8529","status":"public","relation":"used_in_publication"}]},"day":"27","year":"2020","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3961562"}],"oa":1,"publisher":"Zenodo","oa_version":"Published Version","abstract":[{"text":"This datasets comprises all data shown in plots of the submitted article \"Converting microwave and telecom photons with a silicon photonic nanomechanical interface\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}]},{"date_created":"2023-05-23T16:42:30Z","date_published":"2020-09-27T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8755"}]},"doi":"10.5281/ZENODO.4052882","day":"27","year":"2020","month":"09","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4052883","open_access":"1"}],"publisher":"Zenodo","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request."}],"title":"Surpassing the resistance quantum with a geometric superinductor","department":[{"_id":"JoFi"}],"article_processing_charge":"No","author":[{"last_name":"Peruzzo","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda"},{"first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","full_name":"Trioni, Andrea"},{"last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-22T13:23:57Z","citation":{"mla":"Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882.","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882."},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","_id":"13070"},{"date_created":"2023-05-23T16:44:11Z","date_published":"2020-11-10T00:00:00Z","doi":"10.5281/ZENODO.4266025","related_material":{"record":[{"status":"public","id":"9114","relation":"used_in_publication"}]},"day":"10","year":"2020","month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4266026"}],"publisher":"Zenodo","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the plots of the main part of the submitted article \"Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State\". Additional raw data are available from the corresponding author on reasonable request."}],"title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","department":[{"_id":"JoFi"}],"article_processing_charge":"No","author":[{"last_name":"Hease","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez"},{"full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","last_name":"Sahu","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"},{"id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Wulf","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378"},{"first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876","last_name":"Arnold"},{"first_name":"Harald","last_name":"Schwefel","full_name":"Schwefel, Harald"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"date_updated":"2023-08-24T11:16:35Z","citation":{"ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel H, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state, Zenodo, 10.5281/ZENODO.4266025.","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4266025.","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H. Schwefel, J.M. Fink, (2020).","ieee":"W. J. Hease et al., “Bidirectional electro-optic wavelength conversion in the quantum ground state.” Zenodo, 2020.","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. 2020. doi:10.5281/ZENODO.4266025","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H., & Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. Zenodo. https://doi.org/10.5281/ZENODO.4266025","mla":"Hease, William J., et al. Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State. Zenodo, 2020, doi:10.5281/ZENODO.4266025."},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","_id":"13071"},{"abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"oa_version":"Published Version","publisher":"Royal Society of London","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957469.v1","open_access":"1"}],"oa":1,"month":"10","year":"2020","day":"15","related_material":{"record":[{"relation":"used_in_publication","id":"6467","status":"public"}]},"doi":"10.6084/m9.figshare.7957469.v1","date_published":"2020-10-15T00:00:00Z","date_created":"2021-08-06T11:26:57Z","_id":"9799","type":"research_data_reference","status":"public","date_updated":"2023-08-25T10:34:41Z","citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957469.v1.","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957469.v1.","mla":"Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957469.v1.","apa":"Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957469.v1","ama":"Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957469.v1","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","short":"C. Fraisse, J.J. Welch, (2020)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"first_name":"John J.","full_name":"Welch, John J.","last_name":"Welch"}],"article_processing_charge":"No","title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes","department":[{"_id":"BeVi"},{"_id":"NiBa"}]},{"status":"public","type":"research_data_reference","_id":"9798","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"first_name":"John J.","full_name":"Welch, John J.","last_name":"Welch"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-25T10:34:41Z","citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957472.v1.","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957472.v1.","mla":"Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957472.v1.","apa":"Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957472.v1","ama":"Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957472.v1","short":"C. Fraisse, J.J. Welch, (2020).","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020."},"month":"10","publisher":"Royal Society of London","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7957472.v1"}],"oa_version":"Published Version","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"doi":"10.6084/m9.figshare.7957472.v1","date_published":"2020-10-15T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6467"}]},"date_created":"2021-08-06T11:18:15Z","day":"15","year":"2020"},{"day":"19","year":"2020","date_created":"2023-05-23T16:11:22Z","doi":"10.5061/DRYAD.CRJDFN318","related_material":{"record":[{"status":"public","id":"7343","relation":"used_in_publication"}]},"date_published":"2020-12-19T00:00:00Z","oa_version":"Published Version","abstract":[{"text":"Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level.","lang":"eng"}],"month":"12","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.crjdfn318"}],"publisher":"Dryad","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-05T16:04:48Z","citation":{"mla":"Milutinovic, Barbara, et al. Social Immunity Modulates Competition between Coinfecting Pathogens. Dryad, 2020, doi:10.5061/DRYAD.CRJDFN318.","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020).","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:10.5061/DRYAD.CRJDFN318","apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. https://doi.org/10.5061/DRYAD.CRJDFN318","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318.","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318."},"title":"Social immunity modulates competition between coinfecting pathogens","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"article_processing_charge":"No","author":[{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Milutinovic","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758"},{"last_name":"Stock","full_name":"Stock, Miriam","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V","last_name":"Grasse"},{"full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"_id":"13060","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference"},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8329"}]},"doi":"10.5517/ccdc.csd.cc24vsrk","date_published":"2020-03-22T00:00:00Z","date_created":"2021-08-06T07:41:07Z","day":"22","year":"2020","month":"03","publisher":"CCDC","oa":1,"main_file_link":[{"url":"https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°"}],"title":"CCDC 1991959: Experimental Crystal Structure Determination","department":[{"_id":"StFr"}],"author":[{"full_name":"Schlemmer, Werner","last_name":"Schlemmer","first_name":"Werner"},{"last_name":"Nothdurft","full_name":"Nothdurft, Philipp","first_name":"Philipp"},{"last_name":"Petzold","full_name":"Petzold, Alina","first_name":"Alina"},{"first_name":"Gisbert","full_name":"Riess, Gisbert","last_name":"Riess"},{"first_name":"Philipp","full_name":"Frühwirt, Philipp","last_name":"Frühwirt"},{"full_name":"Schmallegger, Max","last_name":"Schmallegger","first_name":"Max"},{"full_name":"Gescheidt-Demner, Georg","last_name":"Gescheidt-Demner","first_name":"Georg"},{"first_name":"Roland","last_name":"Fischer","full_name":"Fischer, Roland"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"},{"full_name":"Kern, Wolfgang","last_name":"Kern","first_name":"Wolfgang"},{"last_name":"Spirk","full_name":"Spirk, Stefan","first_name":"Stefan"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-05T16:03:47Z","citation":{"chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020. https://doi.org/10.5517/ccdc.csd.cc24vsrk.","ista":"Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. 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Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8834.","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","short":"G. Katsaros, (2020).","ama":"Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:10.15479/AT:ISTA:8834","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8834","chicago":"Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8834.","ista":"Katsaros G. 2020. Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8834."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.","short":"B. Kavcic, (2020).","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097","ama":"Kavcic B. 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Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097."},"date_updated":"2024-02-21T12:40:51Z","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:48:09Z","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","article_processing_charge":"No","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic"}],"_id":"8097","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","day":"15","file":[{"date_updated":"2020-07-14T12:48:09Z","file_size":255770756,"creator":"bkavcic","date_created":"2020-07-06T20:38:27Z","file_name":"natComm_2020_scripts.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","file_id":"8098"}],"year":"2020","has_accepted_license":"1","contributor":[{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","contributor_type":"research_group","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","contributor_type":"research_group","first_name":"Tobias"}],"date_created":"2020-07-06T20:40:19Z","date_published":"2020-07-15T00:00:00Z","doi":"10.15479/AT:ISTA:8097","oa_version":"Published Version","abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"month":"07","oa":1,"publisher":"Institute of Science and Technology Austria"},{"date_created":"2020-08-12T12:49:23Z","contributor":[{"last_name":"Arathoon","first_name":"Louise S","contributor_type":"data_collector","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Parvathy","last_name":"Surendranadh"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Melinda"},{"last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","contributor_type":"project_member"}],"date_published":"2020-08-18T00:00:00Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"11321"},{"relation":"later_version","status":"public","id":"9192"}]},"doi":"10.15479/AT:ISTA:8254","day":"18","file":[{"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","file_id":"8280","checksum":"4f1382ed4384751b6013398c11557bf6","success":1,"date_updated":"2020-08-18T08:03:23Z","file_size":5778420,"creator":"dernst","date_created":"2020-08-18T08:03:23Z","file_name":"Data_Rcode_MathematicaNB.zip"}],"year":"2020","has_accepted_license":"1","month":"08","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","department":[{"_id":"NiBa"}],"file_date_updated":"2020-08-18T08:03:23Z","article_processing_charge":"No","author":[{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"}],"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254.","short":"L.S. Arathoon, (2020).","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254."},"date_updated":"2024-02-21T12:41:09Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","_id":"8254"},{"article_processing_charge":"No","author":[{"first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor"}],"title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","department":[{"_id":"GaTk"}],"file_date_updated":"2020-12-09T15:00:19Z","date_updated":"2024-02-21T12:41:42Z","citation":{"apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","short":"B. Kavcic, (2020).","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"status":"public","_id":"8930","contributor":[{"contributor_type":"supervisor","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","last_name":"Bollenbach"}],"date_created":"2020-12-09T15:04:02Z","date_published":"2020-12-10T00:00:00Z","doi":"10.15479/AT:ISTA:8930","related_material":{"record":[{"status":"public","id":"8997","relation":"used_in_publication"}]},"year":"2020","has_accepted_license":"1","day":"10","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","file_id":"8932","success":1,"creator":"bkavcic","date_updated":"2020-12-09T15:00:19Z","file_size":315494370,"date_created":"2020-12-09T15:00:19Z","file_name":"PLoSCompBiol2020_datarep.zip"}],"oa":1,"publisher":"Institute of Science and Technology Austria","month":"12","abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"oa_version":"Published Version"},{"_id":"8951","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:41:57Z","citation":{"chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","short":"A.A. Nagy-Staron, (2020).","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020."},"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","file_date_updated":"2020-12-20T22:01:44Z","department":[{"_id":"CaGu"}],"article_processing_charge":"No","author":[{"first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A"}],"oa_version":"Published Version","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.","lang":"eng"}],"month":"12","oa":1,"publisher":"Institute of Science and Technology Austria","day":"21","file":[{"creator":"bkavcic","date_updated":"2020-12-20T09:52:52Z","file_size":523,"date_created":"2020-12-20T09:52:52Z","file_name":"readme.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","file_id":"8952","checksum":"f57862aeee1690c7effd2b1117d40ed1","success":1},{"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","file_id":"8954","checksum":"f2c6d5232ec6d551b6993991e8689e9f","success":1,"creator":"bkavcic","date_updated":"2020-12-20T22:01:44Z","file_size":379228,"date_created":"2020-12-20T22:01:44Z","file_name":"GRNs Research depository.gb"}],"year":"2020","has_accepted_license":"1","date_created":"2020-12-20T10:00:26Z","contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Anna A","last_name":"Nagy-Staron"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","contributor_type":"project_member","last_name":"Tomasek"},{"last_name":"Caruso Carter","first_name":"Caroline","contributor_type":"project_member"},{"last_name":"Sonnleitner","contributor_type":"project_member","first_name":"Elisabeth"},{"orcid":"0000-0001-6041-254X","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","contributor_type":"project_member"},{"first_name":"Tiago","contributor_type":"project_member","last_name":"Paixão"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","contributor_type":"project_manager","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"doi":"10.15479/AT:ISTA:8951","date_published":"2020-12-21T00:00:00Z","related_material":{"record":[{"status":"public","id":"9283","relation":"used_in_publication"}]}},{"has_accepted_license":"1","year":"2020","day":"28","file":[{"date_updated":"2020-07-14T12:47:57Z","file_size":73363365,"creator":"rgrah","date_created":"2020-01-28T10:39:40Z","file_name":"Scripts.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"9d292cf5207b3829225f44c044cdb3fd","file_id":"7384"},{"date_created":"2020-01-28T10:39:30Z","file_name":"READ_ME_MAIN.txt","creator":"rgrah","date_updated":"2020-07-14T12:47:57Z","file_size":962,"checksum":"4076ceab32ef588cc233802bab24c1ab","file_id":"7385","access_level":"open_access","relation":"main_file","content_type":"text/plain"}],"related_material":{"record":[{"id":"7652","status":"public","relation":"used_in_publication"}]},"date_published":"2020-01-28T00:00:00Z","doi":"10.15479/AT:ISTA:7383","contributor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","contributor_type":"project_leader","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-01-28T10:41:49Z","abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"01","citation":{"mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383.","short":"R. Grah, (2020).","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383."},"date_updated":"2024-02-21T12:42:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"7383","type":"research_data","status":"public","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"]},{"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"03","has_accepted_license":"1","year":"2020","day":"16","file":[{"date_created":"2021-03-05T17:50:45Z","file_name":"DOI_SiteControlledHWs.zip","date_updated":"2021-03-05T17:50:45Z","file_size":13317557,"creator":"gkatsaro","file_id":"9223","checksum":"41b66e195ed3dbd73077feee77b05652","content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file"},{"file_size":3515,"date_updated":"2021-03-10T07:31:50Z","creator":"dernst","file_name":"Readme.txt","date_created":"2021-03-10T07:31:50Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","success":1,"checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","file_id":"9233"}],"date_published":"2020-03-16T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"7541","status":"public"}]},"doi":"10.15479/AT:ISTA:9222","contributor":[{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","contributor_type":"research_group","first_name":"Georgios"}],"date_created":"2021-03-05T18:00:47Z","_id":"9222","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","citation":{"ista":"Katsaros G. 2020. 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Guseinov, “Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter.’” Institute of Science and Technology Austria, 2020.","short":"R. Guseinov, (2020).","ama":"Guseinov R. Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” 2020. doi:10.15479/AT:ISTA:8375","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8375","mla":"Guseinov, Ruslan. Supplementary Data for “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8375.","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8375.","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8375."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Katsaros, Georgios. Supplementary Data for “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7689.","short":"G. Katsaros, (2020).","ieee":"G. Katsaros, “Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots.’” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7689","ama":"Katsaros G. Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” 2020. doi:10.15479/AT:ISTA:7689","chicago":"Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7689.","ista":"Katsaros G. 2020. 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All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\r\n"}],"month":"05","publisher":"Institute of Science and Technology Austria","oa":1},{"author":[{"last_name":"Guseinov","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","file_date_updated":"2020-11-18T10:04:59Z","department":[{"_id":"BeBi"}],"title":"Supplementary data for \"Computational design of cold bent glass façades\"","date_updated":"2024-02-21T12:43:22Z","citation":{"chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8761.","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of cold bent glass façades’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8761.","mla":"Guseinov, Ruslan. Supplementary Data for “Computational Design of Cold Bent Glass Façades.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8761.","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020.","short":"R. Guseinov, (2020).","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of cold bent glass façades.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8761","ama":"Guseinov R. 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Optogenetic Alteration of Hippocampal Network Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563.","short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","chicago":"Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8563.","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563."},"date_updated":"2024-02-21T12:43:41Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Institute of Science and Technology Austria","month":"10","abstract":[{"lang":"eng","text":"Supplementary data provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife."}],"oa_version":"Published Version","contributor":[{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader"}],"date_created":"2020-09-23T14:39:54Z","doi":"10.15479/AT:ISTA:8563","date_published":"2020-10-19T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"8740","status":"public"}]},"year":"2020","has_accepted_license":"1","day":"19","file":[{"file_name":"upload.tgz","date_created":"2020-09-23T14:36:17Z","creator":"jozsef","file_size":145243906,"date_updated":"2020-09-23T14:36:17Z","success":1,"checksum":"a16098a6d172f9c42ab5af5f6991668c","file_id":"8564","relation":"main_file","access_level":"open_access","content_type":"application/x-compressed"},{"access_level":"open_access","relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"0bfc54b7e14c0694cd081617318ba606","file_id":"8675","success":1,"creator":"jozsef","date_updated":"2020-10-19T10:12:29Z","file_size":11648,"date_created":"2020-10-19T10:12:29Z","file_name":"redme.docx"}]},{"status":"public","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"research_data","_id":"14592","department":[{"_id":"FlSc"}],"file_date_updated":"2023-12-01T10:39:59Z","title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","article_processing_charge":"No","author":[{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","short":"F.K. Schur, (2020).","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592."},"date_updated":"2024-02-21T12:44:48Z","month":"12","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"date_created":"2023-11-22T15:00:57Z","contributor":[{"last_name":"Fäßler","orcid":"0000-0001-7149-769X","first_name":"Florian","contributor_type":"researcher","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Zens"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Hauschild"},{"orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Florian KM"}],"date_published":"2020-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14592","related_material":{"record":[{"relation":"research_data","status":"public","id":"8586"}]},"file":[{"success":1,"file_id":"14593","checksum":"0108616e2a59e51879ea51299a29b091","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_name":"3Dprint-files_download_v2.zip","date_created":"2023-11-22T14:58:44Z","file_size":49297,"date_updated":"2023-11-22T14:58:44Z","creator":"fschur"},{"access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"4c66ddedee4d01c1c4a7978208350cfc","file_id":"14637","success":1,"creator":"cchlebak","date_updated":"2023-12-01T10:39:59Z","file_size":641,"date_created":"2023-12-01T10:39:59Z","file_name":"readme.txt"}],"day":"01","year":"2020","has_accepted_license":"1"},{"_id":"9784","type":"research_data_reference","status":"public","date_updated":"2023-02-23T12:52:29Z","citation":{"ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019).","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1","mla":"Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1.","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Antoniou, Michael N.","last_name":"Antoniou","first_name":"Michael N."},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","last_name":"Nicolas","full_name":"Nicolas, Armel"},{"full_name":"Mesnage, Robin","last_name":"Mesnage","first_name":"Robin"},{"first_name":"Martina","full_name":"Biserni, Martina","last_name":"Biserni"},{"first_name":"Francesco V.","full_name":"Rao, Francesco V.","last_name":"Rao"},{"last_name":"Martin","full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez"}],"article_processing_charge":"No","title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","department":[{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures."}],"oa_version":"Published Version","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9411761.v1","open_access":"1"}],"oa":1,"month":"08","year":"2019","day":"09","date_published":"2019-08-09T00:00:00Z","doi":"10.6084/m9.figshare.9411761.v1","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6819"}]},"date_created":"2021-08-06T08:14:05Z"},{"abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.5vv37"}],"publisher":"Dryad","month":"06","year":"2019","day":"22","date_created":"2021-08-09T13:07:28Z","date_published":"2019-06-22T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"315","status":"public"}]},"doi":"10.5061/dryad.5vv37","_id":"9839","type":"research_data_reference","status":"public","citation":{"chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.","ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.","mla":"Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.","ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37","short":"J. Polechova, (2019).","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019."},"date_updated":"2023-02-23T11:14:30Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova"}],"department":[{"_id":"NiBa"}],"title":"Data from: Is the sky the limit? On the expansion threshold of a species' range"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs."}],"month":"10","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.n0r525h"}],"publisher":"Dryad","day":"28","year":"2019","date_created":"2023-05-23T17:09:30Z","related_material":{"record":[{"status":"public","id":"11060","relation":"used_in_publication"}]},"doi":"10.5061/DRYAD.N0R525H","date_published":"2019-10-28T00:00:00Z","_id":"13079","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Data from: Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” Dryad, 2019. https://doi.org/10.5061/DRYAD.N0R525H.","ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. 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Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. 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Armitage. “Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance.” Dryad, 2019. https://doi.org/10.5061/dryad.9kj41f0.","ista":"Kutzer M, Kurtz J, Armitage SAO. 2019. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance, Dryad, 10.5061/dryad.9kj41f0.","mla":"Kutzer, Megan, et al. Data from: A Multi-Faceted Approach Testing the Effects of Previous Bacterial Exposure on Resistance and Tolerance. Dryad, 2019, doi:10.5061/dryad.9kj41f0.","ama":"Kutzer M, Kurtz J, Armitage SAO. Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. 2019. doi:10.5061/dryad.9kj41f0","apa":"Kutzer, M., Kurtz, J., & Armitage, S. A. O. (2019). Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance. Dryad. https://doi.org/10.5061/dryad.9kj41f0","short":"M. Kutzer, J. Kurtz, S.A.O. Armitage, (2019).","ieee":"M. Kutzer, J. Kurtz, and S. A. O. Armitage, “Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance.” Dryad, 2019."},"date_updated":"2023-08-25T08:04:52Z","month":"02","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.9kj41f0","open_access":"1"}],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. 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Bogatyreva, et al. “Multiple Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library of Science, 10.1371/journal.pgen.1008079.s010."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9789","date_created":"2021-08-06T08:38:50Z","date_published":"2019-04-10T00:00:00Z","related_material":{"record":[{"id":"6419","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pgen.1008079.s010","year":"2019","day":"10","publisher":"Public Library of Science","month":"04","oa_version":"Published Version"},{"status":"public","type":"research_data_reference","_id":"9804","department":[{"_id":"NiBa"}],"title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","article_processing_charge":"No","author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"first_name":"Michelle N.","last_name":"Yancoskie","full_name":"Yancoskie, Michelle N."},{"first_name":"Marta","full_name":"Marchini, Marta","last_name":"Marchini"},{"last_name":"Belohlavy","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie","first_name":"Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hiramatsu, Layla","last_name":"Hiramatsu","first_name":"Layla"},{"full_name":"Kučka, Marek","last_name":"Kučka","first_name":"Marek"},{"first_name":"William H.","full_name":"Beluch, William H.","last_name":"Beluch"},{"full_name":"Naumann, Ronald","last_name":"Naumann","first_name":"Ronald"},{"full_name":"Skuplik, Isabella","last_name":"Skuplik","first_name":"Isabella"},{"first_name":"John","full_name":"Cobb, John","last_name":"Cobb"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Campbell","full_name":"Rolian, Campbell","last_name":"Rolian"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","ieee":"J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:10.5061/dryad.0q2h6tk","mla":"Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk.","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, 10.5061/dryad.0q2h6tk.","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk."},"date_updated":"2023-08-29T06:41:51Z","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0q2h6tk"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"date_created":"2021-08-06T11:52:54Z","doi":"10.5061/dryad.0q2h6tk","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6713"}]},"date_published":"2019-06-06T00:00:00Z","day":"06","year":"2019"},{"status":"public","type":"research_data_reference","_id":"9802","department":[{"_id":"NiBa"}],"title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","article_processing_charge":"No","author":[{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-29T06:43:57Z","citation":{"chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900.","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900.","mla":"Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","short":"H. Sachdeva, (2019).","ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900"},"month":"07","main_file_link":[{"url":"https://doi.org/10.5061/dryad.8tp0900","open_access":"1"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.","lang":"eng"}],"date_created":"2021-08-06T11:45:11Z","doi":"10.5061/dryad.8tp0900","related_material":{"record":[{"id":"6680","status":"public","relation":"used_in_publication"}]},"date_published":"2019-07-16T00:00:00Z","day":"16","year":"2019"},{"month":"07","publisher":"Public Library of Science","oa_version":"Published Version","date_published":"2019-07-02T00:00:00Z","related_material":{"record":[{"id":"6784","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pcbi.1007168.s001","date_created":"2021-08-06T08:23:43Z","day":"02","year":"2019","status":"public","type":"research_data_reference","_id":"9786","title":"Supporting text and results","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","last_name":"Ruess","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pleska","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"apa":"Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Supporting text and results. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168.s001","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019.","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).","mla":"Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public Library of Science, 10.1371/journal.pcbi.1007168.s001.","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.s001."},"date_updated":"2023-08-29T07:10:05Z"},{"month":"07","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.n1701c9","open_access":"1"}],"publisher":"Dryad","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle."}],"date_created":"2021-08-06T11:48:42Z","date_published":"2019-07-22T00:00:00Z","doi":"10.5061/dryad.n1701c9","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14058"},{"status":"public","id":"6831","relation":"used_in_publication"}]},"day":"22","year":"2019","status":"public","type":"research_data_reference","_id":"9803","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"title":"Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics","article_processing_charge":"No","author":[{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala"},{"last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"first_name":"David","last_name":"Field","full_name":"Field, David"},{"first_name":"Spencer C.H.","last_name":"Barrett","full_name":"Barrett, Spencer C.H."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-29T07:17:07Z","citation":{"chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. https://doi.org/10.5061/dryad.n1701c9.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, 10.5061/dryad.n1701c9.","mla":"Puixeu Sala, Gemma, et al. Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics. Dryad, 2019, doi:10.5061/dryad.n1701c9.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:10.5061/dryad.n1701c9","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. Dryad. https://doi.org/10.5061/dryad.n1701c9","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019).","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics.” Dryad, 2019."}},{"date_created":"2021-07-27T14:09:11Z","doi":"10.6084/m9.figshare.9808772.v1","date_published":"2019-09-12T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"year":"2019","day":"12","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808772.v1","open_access":"1"}],"oa":1,"publisher":"Springer Nature","month":"09","abstract":[{"text":"OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb)","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"full_name":"Sigalova, Olga","last_name":"Sigalova","first_name":"Olga"},{"first_name":"Andrei","full_name":"Chaplin, Andrei","last_name":"Chaplin"},{"first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva"},{"full_name":"Shelyakin, Pavel","last_name":"Shelyakin","first_name":"Pavel"},{"first_name":"Vsevolod","full_name":"Filaretov, Vsevolod","last_name":"Filaretov"},{"first_name":"Evgeny","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny"},{"last_name":"Burskaia","full_name":"Burskaia, Valentina","first_name":"Valentina"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"department":[{"_id":"FyKo"}],"title":"Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","citation":{"ista":"Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E, Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808772.v1.","chicago":"Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808772.v1.","ieee":"O. Sigalova et al., “Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","short":"O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ama":"Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1","apa":"Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov, E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808772.v1","mla":"Sigalova, Olga, et al. Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808772.v1."},"date_updated":"2023-08-30T06:20:21Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9731"},{"article_processing_charge":"No","author":[{"first_name":"Olga M.","last_name":"Sigalova","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov"},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"department":[{"_id":"FyKo"}],"title":"Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","date_updated":"2023-08-30T06:20:21Z","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808760.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808760.v1.","mla":"Sigalova, Olga M., et al. Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808760.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808760.v1","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808760.v1","ieee":"O. M. Sigalova et al., “Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9783","date_created":"2021-08-06T07:59:56Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"doi":"10.6084/m9.figshare.9808760.v1","date_published":"2019-09-12T00:00:00Z","year":"2019","day":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808760.v1"}],"oa":1,"publisher":"Springer Nature","month":"09","abstract":[{"lang":"eng","text":"Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb)"}],"oa_version":"Published Version"},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808850.v1","open_access":"1"}],"publisher":"Springer Nature","month":"09","abstract":[{"text":"Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes. Only 374 genes with typical length and domain composition were considered. 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