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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. ","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"abstract":[{"lang":"eng","text":"3D-reconstruction of living brain tissue down to individual synapse level would create opportunities for decoding the dynamics and structure-function relationships of the brain’s complex and dense information processing network. 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. 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Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12817."},"status":"public","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"type":"research_data","_id":"12817"},{"citation":{"ista":"Feitosa Tomé D. 2023. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation, Zenodo, 10.5281/ZENODO.10251087.","chicago":"Feitosa Tomé, Douglas. “Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.10251087.","ama":"Feitosa Tomé D. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. 2023. doi:10.5281/ZENODO.10251087","apa":"Feitosa Tomé, D. 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Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer, Zenodo, 10.5281/ZENODO.8277285.","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.","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).","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."},"ddc":["550"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"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","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"status":"public","_id":"12497","article_processing_charge":"No","author":[{"last_name":"Becker","full_name":"Becker, Lea Marie","orcid":"0000-0002-6401-5151","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"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","date_updated":"2024-02-21T12:14:06Z","citation":{"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","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","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.","short":"L.M. Becker, P. Schanda, (2023).","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.","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.","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."},"ddc":["572"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Institute of Science and Technology Austria","month":"03","abstract":[{"text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture.","lang":"eng"}],"oa_version":"Published Version","date_created":"2023-02-03T08:08:02Z","contributor":[{"contributor_type":"researcher","first_name":"Mélanie","last_name":"Berbon"},{"contributor_type":"researcher","first_name":"Alicia","last_name":"Vallet"},{"first_name":"Axelle","contributor_type":"researcher","last_name":"Grelard"},{"contributor_type":"researcher","first_name":"Estelle","last_name":"Morvan"},{"last_name":"Bardiaux","contributor_type":"researcher","first_name":"Benjamin"},{"first_name":"Roman","contributor_type":"researcher","last_name":"Lichtenecker"},{"contributor_type":"researcher","first_name":"Matthias","last_name":"Ernst"},{"last_name":"Loquet","contributor_type":"researcher","first_name":"Antoine"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","contributor_type":"contact_person","first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"last_name":"Becker","orcid":"0000-0002-6401-5151","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","contributor_type":"researcher"}],"doi":"10.15479/AT:ISTA:12497","related_material":{"record":[{"status":"public","id":"12675","relation":"used_in_publication"}]},"date_published":"2023-03-23T00:00:00Z","year":"2023","has_accepted_license":"1","day":"23","file":[{"creator":"lbecker","date_updated":"2023-03-24T09:34:20Z","file_size":87018103,"date_created":"2023-03-23T10:03:16Z","file_name":"Research_Data.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"fd9a28620a81a82991fb70f4fd6591d9","file_id":"12743"},{"creator":"dernst","file_size":747,"date_updated":"2023-03-24T09:42:03Z","file_name":"README.txt","date_created":"2023-03-24T07:13:55Z","relation":"main_file","access_level":"open_access","content_type":"text/plain","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","file_id":"12755"}]},{"_id":"13126","status":"public","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","ddc":["610"],"date_updated":"2024-02-21T12:18:19Z","file_date_updated":"2023-08-04T13:19:47Z","department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and 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of Science and Technology Austria","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). ","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. 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"}]},{"department":[{"_id":"BeVi"}],"file_date_updated":"2023-11-30T14:16:59Z","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","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"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"citation":{"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.","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","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","short":"C. Lasne, M.N. Elkrewi, (2023).","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.","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."},"date_updated":"2024-02-21T12:18:35Z","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","date_created":"2023-11-27T16:39:19Z","contributor":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","contributor_type":"researcher","first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi"}],"date_published":"2023-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14614","related_material":{"record":[{"id":"14613","status":"public","relation":"used_in_publication"}]},"day":"01","file":[{"date_created":"2023-11-28T13:15:26Z","file_name":"panorpaX.zip","creator":"clasne","date_updated":"2023-11-28T13:15:26Z","file_size":404968272,"checksum":"cd0f13322b5156819ecaebd2bc8e7d12","file_id":"14625","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip"},{"access_level":"open_access","relation":"main_file","content_type":"text/plain","file_id":"14634","checksum":"9ff600416577687a737cb3c96dfcb26c","success":1,"creator":"clasne","date_updated":"2023-11-30T14:16:59Z","file_size":2625,"date_created":"2023-11-30T14:16:59Z","file_name":"panorpa_readme.txt"}],"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."}]},{"related_material":{"record":[{"relation":"used_in_publication","id":"15001","status":"public"}]},"date_published":"2023-12-13T00:00:00Z","date_created":"2024-02-26T08:37:57Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","has_accepted_license":"1","year":"2023","day":"13","publisher":"Figshare","main_file_link":[{"url":"https://figshare.com/s/85798bba4ebc68d822ed","open_access":"1"}],"oa":1,"month":"12","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","author":[{"id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","first_name":"Samo","orcid":"0000-0001-6160-9766","full_name":"Curk, Samo","last_name":"Curk"}],"article_processing_charge":"No","department":[{"_id":"AnSa"}],"title":"aggregation_data","date_updated":"2024-02-26T08:45:55Z","citation":{"short":"S. Curk, (2023).","ieee":"S. Curk, “aggregation_data.” Figshare, 2023.","ama":"Curk S. aggregation_data. 2023.","apa":"Curk, S. (2023). aggregation_data. Figshare.","mla":"Curk, Samo. Aggregation_data. Figshare, 2023.","ista":"Curk S. 2023. aggregation_data, Figshare.","chicago":"Curk, Samo. “Aggregation_data.” Figshare, 2023."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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":"15027"},{"author":[{"last_name":"Hwong","full_name":"Hwong, Yi-Ling","orcid":"0000-0001-9281-3479","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","first_name":"Yi-Ling"},{"full_name":"Colin, Maxime","last_name":"Colin","first_name":"Maxime"},{"last_name":"Aglas","full_name":"Aglas, Philipp","id":"02eace56-97fc-11ee-b81a-f0939ca85a77","first_name":"Philipp"},{"last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"},{"first_name":"Steven C.","last_name":"Sherwood","full_name":"Sherwood, Steven C."}],"article_processing_charge":"No","title":"Data-assessing memory in convection schemes using idealized tests","department":[{"_id":"CaMu"}],"citation":{"mla":"Hwong, Yi-Ling, et al. Data-Assessing Memory in Convection Schemes Using Idealized Tests. Zenodo, 2023, doi: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","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","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.","short":"Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, (2023).","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."},"date_updated":"2024-02-27T07:26:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["550"],"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","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"_id":"14991","date_published":"2023-06-23T00:00:00Z","doi":"10.5281/ZENODO.7757041","related_material":{"record":[{"relation":"used_in_publication","id":"14654","status":"public"}]},"date_created":"2024-02-14T14:37:57Z","ec_funded":1,"has_accepted_license":"1","year":"2023","day":"23","publisher":"Zenodo","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7757041"}],"month":"06","abstract":[{"lang":"eng","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)."}],"oa_version":"Published Version"},{"_id":"14990","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)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"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.","apa":"Meggendorfer, T. (2023). Artefact for: Correct Approximation of Stationary Distributions. Zenodo. https://doi.org/10.5281/ZENODO.7548214","ama":"Meggendorfer T. Artefact for: Correct Approximation of Stationary Distributions. 2023. doi:10.5281/ZENODO.7548214","short":"T. Meggendorfer, (2023).","ieee":"T. Meggendorfer, “Artefact for: Correct Approximation of Stationary Distributions.” Zenodo, 2023."},"date_updated":"2024-02-27T07:19:32Z","title":"Artefact for: Correct Approximation of Stationary Distributions","department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The software artefact to evaluate the approximation of stationary distributions implementation."}],"month":"01","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7548214"}],"oa":1,"day":"18","has_accepted_license":"1","year":"2023","date_published":"2023-01-18T00:00:00Z","related_material":{"record":[{"id":"13139","status":"public","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.7548214","date_created":"2024-02-14T14:27:06Z"},{"date_updated":"2024-02-27T07:46:52Z","citation":{"mla":"Koval, Nikita, et al. Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM. Zenodo, 2023, doi:10.5281/ZENODO.7877757.","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, (2023).","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.","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","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","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.","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."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","last_name":"Koval"},{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","full_name":"Fedorov, Alexander","last_name":"Fedorov"},{"first_name":"Maria","last_name":"Sokolova","full_name":"Sokolova, Maria"},{"full_name":"Tsitelov, Dmitry","last_name":"Tsitelov","first_name":"Dmitry"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","department":[{"_id":"DaAl"}],"_id":"14995","type":"research_data_reference","status":"public","year":"2023","day":"28","date_published":"2023-04-28T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14260"}]},"doi":"10.5281/ZENODO.7877757","date_created":"2024-02-14T15:14:13Z","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"}],"oa_version":"Published Version","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7877757","open_access":"1"}],"month":"04"},{"has_accepted_license":"1","year":"2023","day":"28","doi":"10.5281/ZENODO.7877790","related_material":{"record":[{"status":"public","id":"14758","relation":"used_in_publication"}]},"date_published":"2023-04-28T00:00:00Z","date_created":"2024-02-14T15:13:00Z","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7877790","open_access":"1"}],"month":"04","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.","short":"R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, S. Soudjani, (2023).","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.","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","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","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"],"author":[{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"},{"orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","last_name":"Mallik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik"},{"first_name":"Mateusz","last_name":"Rychlicki","full_name":"Rychlicki, Mateusz"},{"full_name":"Schmuck, Anne-Kathrin","last_name":"Schmuck","first_name":"Anne-Kathrin"},{"first_name":"Sadegh","full_name":"Soudjani, Sadegh","last_name":"Soudjani"}],"article_processing_charge":"No","department":[{"_id":"ToHe"}],"title":"A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties","_id":"14994","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"},{"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","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"_id":"15035","author":[{"last_name":"Chalupa","full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"article_processing_charge":"No","department":[{"_id":"ToHe"}],"title":"Monitoring hyperproperties with prefix transducers","date_updated":"2024-02-28T12:33:09Z","citation":{"mla":"Chalupa, Marek, and Thomas A. Henzinger. Monitoring Hyperproperties with Prefix Transducers. Zenodo, 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.","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","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8191723.","ista":"Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers, Zenodo, 10.5281/ZENODO.8191723."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8191722","open_access":"1"}],"oa":1,"month":"07","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"}],"oa_version":"Published Version","date_published":"2023-07-28T00:00:00Z","related_material":{"record":[{"id":"14076","status":"public","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.8191723","date_created":"2024-02-28T07:34:34Z","ec_funded":1,"has_accepted_license":"1","year":"2023","day":"28"},{"article_processing_charge":"No","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"}],"title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","department":[{"_id":"NiBa"}],"citation":{"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.","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."},"date_updated":"2024-03-05T09:35:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"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":"14812","contributor":[{"first_name":"Zusanna","last_name":"Zagrodzka"},{"first_name":"Martin","last_name":"Garlovsky"},{"last_name":"Pal","orcid":"0000-0002-4530-8469","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","orcid":"0000-0002-1145-9226","last_name":"Shipilina"},{"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"},{"last_name":"Leder","first_name":"Erica"},{"last_name":"Reeve","first_name":"James"},{"last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Roger","last_name":"Butlin"}],"date_created":"2024-01-16T10:23:01Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14796"}]},"date_published":"2023-09-05T00:00:00Z","doi":"10.5281/ZENODO.8318995","year":"2023","has_accepted_license":"1","day":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8318995"}],"oa":1,"publisher":"Zenodo","month":"09","abstract":[{"text":"This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode","lang":"eng"}],"oa_version":"Published Version"},{"ddc":["571"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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).","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.","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.","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."},"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","article_processing_charge":"No","author":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"}],"_id":"13173","keyword":["medial habenula","GABAB receptor","vesicle release","Flash and Freeze","Flash and Freeze-fracture"],"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","file":[{"file_id":"13174","checksum":"ed59170869ba621f89f7c1894092192f","description":"After review an updated version of the data is provided","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"closed","file_name":"Raw data for Koppensteiner et al.zip","title":"Outdated Version","date_created":"2023-06-29T13:11:22Z","file_size":542873672,"date_updated":"2023-11-17T14:30:44Z","creator":"shigemot"},{"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","relation":"main_file","access_level":"open_access","success":1,"file_id":"14550","checksum":"c07860eb82b4d367245f1b589fe5c250","file_size":915079,"date_updated":"2023-11-17T14:13:02Z","creator":"patrickd","file_name":"11-17-23 Updated Koppensteiner et al. raw data.xlsx","date_created":"2023-11-17T14:13:02Z"},{"checksum":"abf84b1699edac4349dc3a92d466fb7b","file_id":"14942","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","date_created":"2024-02-06T07:21:43Z","file_name":"EM_Images.zip","creator":"dernst","date_updated":"2024-02-06T07:21:43Z","file_size":544868924}],"day":"29","year":"2023","has_accepted_license":"1","date_created":"2023-06-29T13:16:42Z","related_material":{"record":[{"relation":"used_in_publication","id":"15084","status":"public"}]},"doi":"10.15479/AT:ISTA:13173","date_published":"2023-07-29T00:00:00Z","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","oa":1,"publisher":"Institute of Science and Technology Austria"},{"article_processing_charge":"No","author":[{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"NiBa"}],"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","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.","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","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","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.","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","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","keyword":["Biological sciences"],"status":"public","_id":"11686","date_created":"2022-07-29T06:45:41Z","related_material":{"record":[{"relation":"used_in_publication","id":"10604","status":"public"}]},"date_published":"2022-01-06T00:00:00Z","doi":"10.25338/B81931","year":"2022","day":"06","main_file_link":[{"url":"https://doi.org/10.25338/B81931","open_access":"1"}],"oa":1,"publisher":"Dryad","month":"01","abstract":[{"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.","lang":"eng"}],"acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","oa_version":"Published Version"},{"related_material":{"record":[{"relation":"used_in_publication","id":"10829","status":"public"}]},"doi":"10.5281/ZENODO.5500360","date_published":"2022-02-08T00:00:00Z","date_created":"2022-03-07T08:19:11Z","year":"2022","day":"08","publisher":"Zenodo","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5500360"}],"month":"02","abstract":[{"lang":"eng","text":"Detailed information about the data set see \"dataset description.txt\" file."}],"oa_version":"Published Version","author":[{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"last_name":"Reiner-Rozman","full_name":"Reiner-Rozman, Ciril","first_name":"Ciril"},{"full_name":"Fossati, Stefan","last_name":"Fossati","first_name":"Stefan"},{"first_name":"Patrik","full_name":"Aspermair, Patrik","last_name":"Aspermair"},{"last_name":"Dostalek","full_name":"Dostalek, Jakub","first_name":"Jakub"},{"orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez"},{"last_name":"Bintinger","full_name":"Bintinger, Johannes","first_name":"Johannes"},{"first_name":"Wolfgang","full_name":"Knoll, Wolfgang","last_name":"Knoll"}],"article_processing_charge":"No","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","department":[{"_id":"MaIb"}],"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.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, (2022).","ieee":"R. Hasler et al., “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device.” Zenodo, 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","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","ddc":["540"],"type":"research_data_reference","status":"public","_id":"10833"}]