[{"oa_version":"Published Version","file":[{"file_id":"14707","relation":"main_file","date_created":"2023-12-22T13:54:21Z","date_updated":"2023-12-22T13:54:21Z","success":1,"checksum":"bdaf1392867786634ec5466d528c36ca","file_name":"readme.txt.txt","access_level":"open_access","creator":"melkrewi","content_type":"text/plain","file_size":847},{"creator":"melkrewi","file_size":343632753,"content_type":"application/x-zip-compressed","access_level":"open_access","file_name":"data_artemia_franciscana_genome.zip","success":1,"checksum":"973e1cbdab923a71709782177980829f","date_created":"2023-12-22T14:14:06Z","date_updated":"2023-12-22T14:14:06Z","file_id":"14708","relation":"main_file"}],"date_updated":"2024-02-26T09:59:29Z","date_created":"2023-12-22T13:40:48Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"15009"}]},"contributor":[{"first_name":"Vincent K","contributor_type":"researcher","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"first_name":"Ariana","contributor_type":"project_member","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","contributor_type":"supervisor","first_name":"Beatriz"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","contributor_type":"researcher","last_name":"Elkrewi"}],"author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"status":"public","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14705","year":"2024","abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"file_date_updated":"2023-12-22T14:14:06Z","type":"research_data","doi":"10.15479/AT:ISTA:14705","date_published":"2024-01-02T00:00:00Z","project":[{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14705","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14705.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705","chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705.","short":"M.N. Elkrewi, (2024).","mla":"Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705."},"oa":1,"article_processing_charge":"No","has_accepted_license":"1","day":"02","month":"01","keyword":["sex chromosome evolution","genome assembly","dosage compensation"]},{"author":[{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"contributor":[{"contributor_type":"researcher","last_name":"Troussicot","first_name":"Laura"},{"first_name":"Björn M.","contributor_type":"researcher","last_name":"Burmann"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13095"}]},"date_created":"2023-04-10T05:55:56Z","date_updated":"2023-08-01T14:48:08Z","file":[{"date_updated":"2023-04-14T09:39:33Z","date_created":"2023-04-14T09:39:33Z","success":1,"checksum":"54a619605e44c871214fb0e07b05c6bf","file_id":"12823","relation":"main_file","creator":"pschanda","file_size":54184807,"content_type":"application/zip","file_name":"data_deposition.zip","access_level":"open_access"},{"file_name":"README","access_level":"open_access","file_size":4978,"content_type":"application/octet-stream","creator":"pschanda","relation":"main_file","file_id":"12824","date_created":"2023-04-14T09:39:58Z","date_updated":"2023-04-14T09:39:58Z","checksum":"8dede9fc78399d13144eb05c62bf5750","success":1}],"oa_version":"Published Version","_id":"12820","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","ddc":["570"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"PaSc"}],"abstract":[{"lang":"eng","text":"Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript"}],"file_date_updated":"2023-04-14T09:39:58Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","type":"research_data","doi":"10.15479/AT:ISTA:12820","date_published":"2023-04-18T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"citation":{"chicago":"Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820.","mla":"Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820.","short":"P. Schanda, (2023).","ista":"Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820.","apa":"Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820","ieee":"P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023.","ama":"Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820"},"month":"04","day":"18","article_processing_charge":"No","has_accepted_license":"1"},{"abstract":[{"text":"basic data for use in code for experimental data analysis for manuscript under revision: \r\nDynamic pathogen detection and social feedback shape collective hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S","lang":"eng"}],"file_date_updated":"2023-05-12T08:04:08Z","type":"research_data","date_updated":"2023-08-07T13:09:09Z","date_created":"2023-05-11T21:35:17Z","oa_version":"None","file":[{"success":1,"checksum":"3eadf17fd59ad8c98bf10bf63061863c","date_created":"2023-05-12T08:04:04Z","date_updated":"2023-05-12T08:04:04Z","file_id":"12947","relation":"main_file","creator":"scremer","file_size":3414674,"content_type":"application/zip","access_level":"open_access","file_name":"Experimental_data.zip"},{"creator":"scremer","content_type":"application/octet-stream","file_size":2113,"access_level":"open_access","file_name":"README_Experimental_Data.md","success":1,"checksum":"1b5e8e01a0989154a76b44e6d8d68f89","date_updated":"2023-05-12T08:04:08Z","date_created":"2023-05-12T08:04:08Z","file_id":"12948","relation":"main_file"}],"author":[{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"contributor":[{"last_name":"Casillas Perez","contributor_type":"data_collector","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","contributor_type":"data_collector","last_name":"Grasse","first_name":"Anna V"},{"first_name":"Katarina","contributor_type":"researcher","last_name":"Bodova"},{"first_name":"Gašper","last_name":"Tkačik","contributor_type":"supervisor","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"related_material":{"record":[{"id":"13127","relation":"used_in_publication","status":"public"}]},"ddc":["570"],"title":"Data from: \"Dynamic pathogen detection and social feedback shape collective hygiene in ants\" ","status":"public","department":[{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","year":"2023","_id":"12945","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"12","month":"05","article_processing_charge":"No","has_accepted_license":"1","keyword":["collective behavior","host-pathogen interactions","social immunity","epidemiology","social insects","probabilistic modeling"],"acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2023-05-12T00:00:00Z","doi":"10.15479/AT:ISTA:12945","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"citation":{"chicago":"Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12945.","short":"S. Cremer, (2023).","mla":"Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12945.","ieee":"S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.","apa":"Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12945","ista":"Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12945.","ama":"Cremer S. Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945"},"oa":1},{"month":"01","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","name":"Circuits of Visual Attention","call_identifier":"H2020"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"doi":"10.15479/AT:ISTA:12370","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-01-26T10:51:34Z","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","year":"2023","date_updated":"2023-10-04T11:41:04Z","date_created":"2023-01-25T12:45:18Z","author":[{"id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","first_name":"Divyansh","last_name":"Gupta","full_name":"Gupta, Divyansh"},{"full_name":"Sumser, Anton L","first_name":"Anton L","last_name":"Sumser","id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12349"}]},"contributor":[{"first_name":"Olga","contributor_type":"researcher","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","contributor_type":"researcher","last_name":"Mlynarski"},{"last_name":"Svaton","contributor_type":"researcher","first_name":"Jan","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2"}],"day":"26","article_processing_charge":"No","has_accepted_license":"1","citation":{"mla":"Gupta, Divyansh, et al. Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12370.","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023).","chicago":"Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12370.","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:10.15479/AT:ISTA:12370","ista":"Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12370.","ieee":"D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.","apa":"Gupta, D., Sumser, A. L., & Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12370"},"date_published":"2023-01-26T00:00:00Z","type":"research_data","abstract":[{"text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. 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Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562.","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562."},"date_published":"2023-11-21T00:00:00Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","file_date_updated":"2023-11-20T11:49:58Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"FlSc"}],"year":"2023","acknowledgement":"We would like to thank K. von Peinen and B. 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We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","date_updated":"2023-11-21T08:05:34Z","date_created":"2023-11-20T09:22:33Z","contributor":[{"last_name":"Fäßler","contributor_type":"researcher","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","contributor_type":"researcher","first_name":"Manjunath"},{"orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","contributor_type":"researcher","first_name":"Julia"},{"contributor_type":"researcher","last_name":"Döring","first_name":"Hermann"},{"first_name":"Florian","last_name":"Hofer","contributor_type":"researcher","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6"},{"last_name":"Dimchev","contributor_type":"researcher","first_name":"Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau","contributor_type":"researcher"},{"first_name":"Jan","last_name":"Faix","contributor_type":"researcher"},{"last_name":"Rottner","contributor_type":"researcher","first_name":"Klemens"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Schur","first_name":"Florian KM"}],"related_material":{"record":[{"id":"12334","status":"public","relation":"used_in_publication"}]},"author":[{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"month":"11","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"doi":"10.15479/AT:ISTA:14562"},{"type":"research_data","abstract":[{"text":"Data related to the following paper:\r\n\"Stress granules plug and stabilize damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract: \r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in \"Stress granules plug and stabilize damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.","lang":"eng"}],"file_date_updated":"2023-10-31T08:57:50Z","department":[{"_id":"AnSa"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["570"],"title":"Stress granules plug and stabilize damaged endolysosomal membranes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14472","year":"2023","file":[{"file_size":62821432,"content_type":"application/zip","creator":"ipalaia","file_name":"SGporecondensation-main.zip","access_level":"open_access","date_updated":"2023-10-30T16:31:08Z","date_created":"2023-10-30T16:31:08Z","checksum":"a18706e952e8660c51ede52a167270b7","success":1,"relation":"main_file","file_id":"14473"},{"file_size":1697,"content_type":"text/plain","creator":"dernst","access_level":"open_access","file_name":"README.txt","checksum":"389eab31c6509dbc05795017fb618758","success":1,"date_updated":"2023-10-31T08:57:50Z","date_created":"2023-10-31T08:57:50Z","relation":"main_file","file_id":"14474"}],"oa_version":"Published Version","date_created":"2023-10-30T16:38:32Z","date_updated":"2023-11-27T09:05:07Z","related_material":{"record":[{"id":"14610","status":"public","relation":"used_in_publication"}]},"author":[{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"article_processing_charge":"No","has_accepted_license":"1","day":"31","month":"10","tmp":{"short":"CC0 (1.0)","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)"},"oa":1,"citation":{"short":"C.E. Vanhille-Campos, A. Šarić, (2023).","mla":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14472.","chicago":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472.","ama":"Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:10.15479/AT:ISTA:14472","apa":"Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14472","ieee":"C. E. Vanhille-Campos and A. 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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. ","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"file_date_updated":"2023-05-18T19:51:52Z","type":"research_data"},{"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"}],"file_date_updated":"2023-03-24T09:42:03Z","type":"research_data","date_created":"2023-02-03T08:08:02Z","date_updated":"2024-02-21T12:14:06Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Research_Data.zip","file_size":87018103,"content_type":"application/zip","creator":"lbecker","relation":"main_file","file_id":"12743","checksum":"fd9a28620a81a82991fb70f4fd6591d9","date_created":"2023-03-23T10:03:16Z","date_updated":"2023-03-24T09:34:20Z"},{"file_size":747,"content_type":"text/plain","creator":"dernst","file_name":"README.txt","access_level":"open_access","date_created":"2023-03-24T07:13:55Z","date_updated":"2023-03-24T09:42:03Z","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","relation":"main_file","file_id":"12755"}],"author":[{"first_name":"Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie"},{"last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"contributor":[{"contributor_type":"researcher","last_name":"Berbon","first_name":"Mélanie"},{"contributor_type":"researcher","last_name":"Vallet","first_name":"Alicia"},{"last_name":"Grelard","contributor_type":"researcher","first_name":"Axelle"},{"last_name":"Morvan","contributor_type":"researcher","first_name":"Estelle"},{"first_name":"Benjamin","contributor_type":"researcher","last_name":"Bardiaux"},{"first_name":"Roman","last_name":"Lichtenecker","contributor_type":"researcher"},{"first_name":"Matthias","last_name":"Ernst","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Loquet","first_name":"Antoine"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","contributor_type":"contact_person","first_name":"Paul"},{"first_name":"Lea Marie","last_name":"Becker","contributor_type":"researcher","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151"}],"related_material":{"record":[{"id":"12675","status":"public","relation":"used_in_publication"}]},"title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","status":"public","ddc":["572"],"department":[{"_id":"GradSch"},{"_id":"PaSc"}],"publisher":"Institute of Science and Technology Austria","_id":"12497","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","day":"23","article_processing_charge":"No","has_accepted_license":"1","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"date_published":"2023-03-23T00:00:00Z","doi":"10.15479/AT:ISTA:12497","citation":{"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","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.","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","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.","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.","short":"L.M. Becker, P. Schanda, (2023).","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."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1},{"day":"04","has_accepted_license":"1","article_processing_charge":"No","date_published":"2023-08-04T00:00:00Z","citation":{"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.","mla":"Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.","short":"J.G. Danzl, (2023).","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.","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.","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126"},"abstract":[{"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 disease.","lang":"eng"}],"type":"research_data","oa_version":"Published 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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)","year":"2023"},{"day":"26","month":"07","has_accepted_license":"1","article_processing_charge":"No","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"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.","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.","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.","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, 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"},"project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments"}],"date_published":"2023-07-26T00:00:00Z","doi":"10.15479/AT:ISTA:13116","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"type":"research_data","file_date_updated":"2023-08-08T11:17:28Z","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. "}],"ec_funded":1,"_id":"13116","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). ","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["539"],"status":"public","title":"Chiral and nematic phases of flexible active filaments","department":[{"_id":"MaLo"},{"_id":"EdHa"},{"_id":"JoDa"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Dunajova","full_name":"Dunajova, Zuzana"},{"full_name":"Prats Mateu, Batirtze","first_name":"Batirtze","last_name":"Prats Mateu","id":"299FE892-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp"},{"first_name":"Keesiang","last_name":"Lim","full_name":"Lim, Keesiang"},{"full_name":"Brandis, Dörte","last_name":"Brandis","first_name":"Dörte"},{"first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","full_name":"Velicky, 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peculiar dipteran X chromosome","file_date_updated":"2023-11-30T14:16:59Z","abstract":[{"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.","lang":"eng"}],"type":"research_data","doi":"10.15479/AT:ISTA:14614","date_published":"2023-12-01T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"C. Lasne, M.N. Elkrewi, (2023).","mla":"Lasne, Clementine, and Marwan N. Elkrewi. The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome. 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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"}],"file_date_updated":"2024-02-06T07:21:43Z","citation":{"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","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.","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.","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","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.","short":"R. Shigemoto, (2023).","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."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"doi":"10.15479/AT:ISTA:13173","date_published":"2023-07-29T00:00:00Z","keyword":["medial habenula","GABAB receptor","vesicle release","Flash and Freeze","Flash and Freeze-fracture"],"day":"29","month":"07","article_processing_charge":"No","has_accepted_license":"1"},{"date_updated":"2024-02-21T12:35:18Z","date_created":"2022-03-31T11:32:32Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11373"},{"id":"14280","relation":"used_in_publication","status":"public"}],"link":[{"description":"A custom written code (FRAPdiff) to quantify the Off binding rate and Diffusion coefficient of membrane bound proteins. 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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. 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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). Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11542.","short":"R. Schulz, (2022)."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"short":"M. Valentini, P. San-Jose, J. Arbiol, S. Marti-Sanchez, M. Botifoll, (2022).","mla":"Valentini, Marco, et al. 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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."},"doi":"10.15479/AT:ISTA:12102","date_published":"2022-09-25T00:00:00Z","month":"09","day":"25","has_accepted_license":"1","article_processing_charge":"No","status":"public","ddc":["530"],"title":"Data for \"Majorana-like Coulomb spectroscopy in the absence of zero bias peaks\"","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12522","year":"2022","date_created":"2023-02-07T08:13:39Z","date_updated":"2024-02-21T12:35:34Z","file":[{"file_id":"12523","relation":"main_file","date_updated":"2023-02-07T08:18:24Z","date_created":"2023-02-07T08:18:24Z","success":1,"checksum":"0dbd6327bf84c7e81b295c4bc9d12826","file_name":"Majorana_like.zip","access_level":"open_access","creator":"dernst","content_type":"application/x-zip-compressed","file_size":3609122411}],"oa_version":"Published Version","author":[{"last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco"},{"full_name":"San-Jose, Pablo","last_name":"San-Jose","first_name":"Pablo"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"last_name":"Marti-Sanchez","first_name":"Sara","full_name":"Marti-Sanchez, Sara"},{"first_name":"Marc","last_name":"Botifoll","full_name":"Botifoll, Marc"}],"contributor":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","contributor_type":"contact_person","last_name":"Valentini"}],"related_material":{"record":[{"id":"12118","status":"public","relation":"used_in_publication"},{"id":"13286","status":"public","relation":"used_in_publication"}]},"type":"research_data","file_date_updated":"2023-02-07T08:18:24Z","abstract":[{"lang":"eng","text":"This .zip File contains the transport data, the codes for the data analysis, the microscopy analysis and the codes for the theoretical simulations for \"Majorana-like Coulomb spectroscopy in the absence of zero bias peaks\" by M. Valentini, et. al. The transport data are saved with hdf5 file format. The files can be open with the log browser of Labber."}]},{"citation":{"ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 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, 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","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.","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","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.","mla":"Surendranadh, Parvathy, et al. 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, doi:10.15479/at:ista:11321.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022)."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/at:ista:11321","date_published":"2022-04-28T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","month":"04","day":"28","_id":"11321","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"status":"public","ddc":["570"],"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","related_material":{"record":[{"id":"11411","status":"public","relation":"used_in_publication"},{"id":"9192","relation":"earlier_version","status":"public"},{"id":"8254","status":"public","relation":"earlier_version"}]},"contributor":[{"last_name":"Arathoon","contributor_type":"project_member","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Baskett","contributor_type":"project_member","first_name":"Carina","orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","contributor_type":"project_member","last_name":"Field"},{"last_name":"Pickup","contributor_type":"project_member","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","contributor_type":"project_member"}],"author":[{"full_name":"Surendranadh, Parvathy","last_name":"Surendranadh","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","first_name":"Louise S","last_name":"Arathoon","full_name":"Arathoon, Louise S"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","first_name":"Carina","last_name":"Baskett","full_name":"Baskett, Carina"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"oa_version":"Published Version","file":[{"file_name":"Data_Code.zip","access_level":"open_access","creator":"larathoo","file_size":13260571,"content_type":"application/x-zip-compressed","file_id":"11326","relation":"main_file","date_created":"2022-04-22T09:39:03Z","date_updated":"2022-04-22T09:39:03Z","success":1,"checksum":"96c1b86cdf25481f2a52972fcc45ca7f"}],"date_created":"2022-04-22T09:42:24Z","date_updated":"2024-02-21T12:41:09Z","type":"research_data","abstract":[{"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. ","lang":"eng"}],"file_date_updated":"2022-04-22T09:39:03Z"},{"file":[{"embargo":"2022-08-07","file_id":"11655","title":"Supplementary Datasets","relation":"main_file","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","date_created":"2022-07-26T12:37:52Z","date_updated":"2022-08-08T22:30:04Z","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","file_name":"Data.zip","creator":"melkrewi","content_type":"application/x-zip-compressed","file_size":2209382998}],"oa_version":"Published Version","date_updated":"2024-02-21T12:35:53Z","date_created":"2022-07-26T11:01:47Z","contributor":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups"},{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","first_name":"Vincent K"},{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","last_name":"Mrnjavac"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse"},{"first_name":"Luca","last_name":"Sax"},{"first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hontoria ","first_name":"Francisco"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"12248","status":"public","relation":"used_in_publication"}]},"author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"status":"public","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","_id":"11653","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","file_date_updated":"2022-08-08T22:30:04Z","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"}],"type":"research_data","date_published":"2022-08-05T00:00:00Z","doi":"10.15479/AT:ISTA:11653","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"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.","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.","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","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.","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.","short":"M.N. Elkrewi, (2022)."},"has_accepted_license":"1","article_processing_charge":"No","day":"05","month":"08"},{"day":"29","month":"03","article_processing_charge":"No","has_accepted_license":"1","tmp":{"short":"CC0 (1.0)","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)"},"citation":{"chicago":"Katsaros, Georgios. “Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9291.","mla":"Katsaros, Georgios. Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9291.","short":"G. Katsaros, (2021).","ista":"Katsaros G. 2021. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9291.","apa":"Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9291","ieee":"G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium.” Institute of Science and Technology Austria, 2021.","ama":"Katsaros G. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. 2021. doi:10.15479/AT:ISTA:9291"},"oa":1,"doi":"10.15479/AT:ISTA:9291","date_published":"2021-03-29T00:00:00Z","type":"research_data","file_date_updated":"2021-04-01T07:52:56Z","abstract":[{"lang":"eng","text":"This .zip File contains the transport data for figures presented in the main text and supplementary material of \"Enhancement of Proximity Induced Superconductivity in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. 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)."}],"status":"public","title":"Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium","ddc":["530"],"department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","year":"2021","_id":"9291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:37:14Z","date_created":"2021-03-27T13:47:49Z","oa_version":"Published Version","file":[{"file_id":"9292","relation":"main_file","success":1,"checksum":"635df3c08fc13c3dac008cd421aefbe4","date_updated":"2021-03-27T13:46:17Z","date_created":"2021-03-27T13:46:17Z","access_level":"open_access","file_name":"Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip","creator":"gkatsaro","file_size":10616071,"content_type":"application/x-zip-compressed"},{"creator":"dernst","content_type":"text/plain","file_size":470,"access_level":"open_access","file_name":"README.txt","success":1,"checksum":"12b3ca69ae7509a346711baae0b02a75","date_created":"2021-04-01T07:52:56Z","date_updated":"2021-04-01T07:52:56Z","file_id":"9302","relation":"main_file"}],"author":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios"}]},{"department":[{"_id":"AnHi"}],"publisher":"Institute of Science and Technology Austria","title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","status":"public","year":"2021","_id":"9636","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"figures_data.zip","access_level":"open_access","content_type":"application/zip","file_size":3345244,"creator":"ahigginb","relation":"main_file","file_id":"9637","date_created":"2021-07-07T20:37:28Z","date_updated":"2021-07-07T20:37:28Z","checksum":"18e90687ec7bbd75f8bfea4d8293fb30","success":1}],"oa_version":"Submitted Version","date_updated":"2024-02-21T12:36:52Z","date_created":"2021-07-07T20:43:10Z","related_material":{"record":[{"id":"10029","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P"}],"type":"research_data","file_date_updated":"2021-07-07T20:37:28Z","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"citation":{"chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","short":"A.P. Higginbotham, (2021).","mla":"Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology Austria, 2021.","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021."},"date_published":"2021-01-01T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1"},{"has_accepted_license":"1","article_processing_charge":"No","day":"14","month":"04","tmp":{"short":"CC0 (1.0)","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)"},"citation":{"ista":"Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar Ge’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9323.","apa":"Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar Ge.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9323","ieee":"D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’” Institute of Science and Technology Austria, 2021.","ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:10.15479/AT:ISTA:9323","chicago":"Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit Planar Ge.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9323.","mla":"Jirovec, Daniel. Research Data for “A Singlet-Triplet Hole Spin Qubit Planar Ge.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9323.","short":"D. Jirovec, (2021)."},"oa":1,"doi":"10.15479/AT:ISTA:9323","date_published":"2021-04-14T00:00:00Z","type":"research_data","abstract":[{"lang":"eng","text":"This .zip File contains the data for figures presented in the main text and supplementary material of \"A singlet triplet hole spin qubit in planar Ge\" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. 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. The code for simulations is as well provided in Python."}],"file_date_updated":"2021-04-14T09:49:30Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\"","ddc":["530"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9323","year":"2021","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9324","checksum":"c569d2a2ce1694445cdbca19cf8ae023","success":1,"date_updated":"2021-04-14T09:48:47Z","date_created":"2021-04-14T09:48:47Z","access_level":"open_access","file_name":"DataRepositorySTqubit.zip","content_type":"application/x-zip-compressed","file_size":221832287,"creator":"djirovec"},{"date_updated":"2021-04-14T09:49:30Z","date_created":"2021-04-14T09:49:30Z","success":1,"checksum":"845bdf87430718ad6aff47eda7b5fc92","file_id":"9325","relation":"main_file","creator":"djirovec","file_size":4323,"content_type":"application/octet-stream","file_name":"ReadMe","access_level":"open_access"}],"date_updated":"2024-02-21T12:39:15Z","date_created":"2021-04-14T09:50:22Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8909"}]},"contributor":[{"contributor_type":"project_member","last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Jirovec, Daniel","last_name":"Jirovec","first_name":"Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"}]},{"file_date_updated":"2021-05-14T11:56:48Z","abstract":[{"text":"This .zip File contains the transport data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. 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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."}],"file_date_updated":"2020-08-18T08:03:23Z","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8254","year":"2020","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8280","date_updated":"2020-08-18T08:03:23Z","date_created":"2020-08-18T08:03:23Z","checksum":"4f1382ed4384751b6013398c11557bf6","success":1,"file_name":"Data_Rcode_MathematicaNB.zip","access_level":"open_access","file_size":5778420,"content_type":"application/x-zip-compressed","creator":"dernst"}],"date_created":"2020-08-12T12:49:23Z","date_updated":"2024-02-21T12:41:09Z","contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","contributor_type":"data_collector","first_name":"Louise S"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Surendranadh","first_name":"Parvathy"},{"first_name":"Nicholas H","contributor_type":"project_member","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"first_name":"David","contributor_type":"project_member","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","contributor_type":"project_member"},{"contributor_type":"project_member","last_name":"Baskett","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"11321","status":"public","relation":"later_version"},{"relation":"later_version","status":"public","id":"9192"}]},"author":[{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S","full_name":"Arathoon, Louise S"}],"has_accepted_license":"1","article_processing_charge":"No","day":"18","month":"08","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"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.","short":"L.S. Arathoon, (2020).","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.","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","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.","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.","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254"},"doi":"10.15479/AT:ISTA:8254","date_published":"2020-08-18T00:00:00Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"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.","short":"B. Kavcic, (2020).","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.","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","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.","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","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."},"date_published":"2020-12-10T00:00:00Z","doi":"10.15479/AT:ISTA:8930","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"has_accepted_license":"1","article_processing_charge":"No","day":"10","month":"12","_id":"8930","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","status":"public","ddc":["570"],"contributor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","contributor_type":"supervisor","last_name":"Tkačik"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bollenbach","contributor_type":"supervisor"}],"related_material":{"record":[{"id":"8997","relation":"used_in_publication","status":"public"}]},"author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic","full_name":"Kavcic, Bor"}],"oa_version":"Published Version","file":[{"file_name":"PLoSCompBiol2020_datarep.zip","access_level":"open_access","creator":"bkavcic","file_size":315494370,"content_type":"application/zip","file_id":"8932","relation":"main_file","date_updated":"2020-12-09T15:00:19Z","date_created":"2020-12-09T15:00:19Z","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18"}],"date_updated":"2024-02-21T12:41:42Z","date_created":"2020-12-09T15:04:02Z","type":"research_data","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-12-09T15:00:19Z"},{"related_material":{"record":[{"id":"9283","relation":"used_in_publication","status":"public"}]},"contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","contributor_type":"project_member","first_name":"Anna A"},{"first_name":"Kathrin","contributor_type":"project_member","last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","last_name":"Caruso Carter","first_name":"Caroline"},{"first_name":"Elisabeth","last_name":"Sonnleitner","contributor_type":"project_member"},{"last_name":"Kavcic","contributor_type":"project_member","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","last_name":"Paixão","first_name":"Tiago"},{"contributor_type":"project_manager","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Nagy-Staron, Anna A","orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","first_name":"Anna A"}],"file":[{"file_name":"readme.txt","access_level":"open_access","creator":"bkavcic","content_type":"text/plain","file_size":523,"file_id":"8952","relation":"main_file","date_created":"2020-12-20T09:52:52Z","date_updated":"2020-12-20T09:52:52Z","success":1,"checksum":"f57862aeee1690c7effd2b1117d40ed1"},{"access_level":"open_access","file_name":"GRNs Research depository.gb","file_size":379228,"content_type":"application/octet-stream","creator":"bkavcic","relation":"main_file","file_id":"8954","checksum":"f2c6d5232ec6d551b6993991e8689e9f","success":1,"date_updated":"2020-12-20T22:01:44Z","date_created":"2020-12-20T22:01:44Z"}],"oa_version":"Published Version","date_created":"2020-12-20T10:00:26Z","date_updated":"2024-02-21T12:41:57Z","year":"2020","_id":"8951","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"ddc":["570"],"status":"public","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","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"}],"file_date_updated":"2020-12-20T22:01:44Z","type":"research_data","date_published":"2020-12-21T00:00:00Z","doi":"10.15479/AT:ISTA:8951","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"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.","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.","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","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.","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.","short":"A.A. Nagy-Staron, (2020)."},"article_processing_charge":"No","has_accepted_license":"1","month":"12","day":"21","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"]},{"date_published":"2020-01-28T00:00:00Z","doi":"10.15479/AT:ISTA:7383","oa":1,"citation":{"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.","short":"R. Grah, (2020).","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.","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","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.","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.","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"},"day":"28","month":"01","has_accepted_license":"1","article_processing_charge":"No","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","first_name":"Rok","last_name":"Grah","full_name":"Grah, Rok"}],"contributor":[{"contributor_type":"project_leader","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"7652","status":"public","relation":"used_in_publication"}]},"date_created":"2020-01-28T10:41:49Z","date_updated":"2024-02-21T12:42:31Z","file":[{"access_level":"open_access","file_name":"Scripts.zip","creator":"rgrah","content_type":"application/zip","file_size":73363365,"file_id":"7384","relation":"main_file","checksum":"9d292cf5207b3829225f44c044cdb3fd","date_created":"2020-01-28T10:39:40Z","date_updated":"2020-07-14T12:47:57Z"},{"content_type":"text/plain","file_size":962,"creator":"rgrah","access_level":"open_access","file_name":"READ_ME_MAIN.txt","checksum":"4076ceab32ef588cc233802bab24c1ab","date_created":"2020-01-28T10:39:30Z","date_updated":"2020-07-14T12:47:57Z","relation":"main_file","file_id":"7385"}],"oa_version":"Published Version","year":"2020","_id":"7383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"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"}],"file_date_updated":"2020-07-14T12:47:57Z","type":"research_data"},{"ddc":["530"],"status":"public","title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GeKa"}],"_id":"9222","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","date_updated":"2024-02-21T12:42:13Z","date_created":"2021-03-05T18:00:47Z","oa_version":"Published Version","file":[{"content_type":"application/x-zip-compressed","file_size":13317557,"creator":"gkatsaro","file_name":"DOI_SiteControlledHWs.zip","access_level":"open_access","date_created":"2021-03-05T17:50:45Z","date_updated":"2021-03-05T17:50:45Z","checksum":"41b66e195ed3dbd73077feee77b05652","relation":"main_file","file_id":"9223"},{"date_updated":"2021-03-10T07:31:50Z","date_created":"2021-03-10T07:31:50Z","checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","success":1,"relation":"main_file","file_id":"9233","file_size":3515,"content_type":"text/plain","creator":"dernst","file_name":"Readme.txt","access_level":"open_access"}],"author":[{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7541"}]},"contributor":[{"first_name":"Georgios","last_name":"Katsaros","contributor_type":"research_group","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","file_date_updated":"2021-03-10T07:31:50Z","tmp":{"short":"CC0 (1.0)","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)"},"oa":1,"citation":{"chicago":"Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.","short":"G. Katsaros, (2020).","mla":"Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.","apa":"Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9222","ieee":"G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling.” Institute of Science and Technology Austria, 2020.","ista":"Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9222.","ama":"Katsaros G. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222"},"date_published":"2020-03-16T00:00:00Z","doi":"10.15479/AT:ISTA:9222","month":"03","day":"16","article_processing_charge":"No","has_accepted_license":"1"},{"type":"research_data","ec_funded":1,"file_date_updated":"2020-09-11T09:52:36Z","abstract":[{"lang":"eng","text":"Supplementary movies showing the following sequences for spatio-temporarily programmed shells: input geometry and actuation time landscape; comparison of morphing processes from a camera recording and a simulation; final actuated shape."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8375","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeBi"}],"status":"public","title":"Supplementary data for \"Computational design of curved thin shells: from glass façades to programmable matter\"","ddc":["000"],"contributor":[{"orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Guseinov","first_name":"Ruslan"},{"contributor_type":"researcher","last_name":"McMahan","first_name":"Connor"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","contributor_type":"researcher","last_name":"Perez Rodriguez"},{"first_name":"Chiara","contributor_type":"researcher","last_name":"Daraio"},{"contributor_type":"researcher","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8366"}]},"author":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","last_name":"Guseinov","full_name":"Guseinov, Ruslan"}],"file":[{"file_id":"8376","relation":"main_file","success":1,"checksum":"4029ffd65fb82ef2366b2fc2a4908e16","date_created":"2020-09-11T09:45:21Z","date_updated":"2020-09-11T09:45:21Z","access_level":"open_access","file_name":"supplementary_movie_1.mp4","creator":"rguseino","content_type":"video/mp4","file_size":29214988},{"file_size":28449475,"content_type":"video/mp4","creator":"rguseino","file_name":"supplementary_movie_2.mp4","access_level":"open_access","date_updated":"2020-09-11T09:45:25Z","date_created":"2020-09-11T09:45:25Z","checksum":"8ed03b04d80f1a4e622cb22e6100afd8","success":1,"relation":"main_file","file_id":"8377"},{"file_name":"supplementary_movie_3.mp4","access_level":"open_access","content_type":"video/mp4","file_size":26315853,"creator":"rguseino","relation":"main_file","file_id":"8378","date_created":"2020-09-11T09:45:28Z","date_updated":"2020-09-11T09:45:28Z","checksum":"ad6864afb5e694e5c52a88fba4e02eea","success":1},{"access_level":"open_access","file_name":"supplementary_movie_4.mp4","creator":"rguseino","file_size":25198755,"content_type":"video/mp4","file_id":"8379","relation":"main_file","success":1,"checksum":"b079cef7871fe1afb69af0e2b099f3b1","date_updated":"2020-09-11T09:45:33Z","date_created":"2020-09-11T09:45:33Z"},{"file_name":"supplementary_movie_5.mp4","access_level":"open_access","creator":"rguseino","file_size":29011354,"content_type":"video/mp4","file_id":"8380","relation":"main_file","date_updated":"2020-09-11T09:45:36Z","date_created":"2020-09-11T09:45:36Z","success":1,"checksum":"9d1d48a8ed5c109a999c51b044ee523d"},{"date_created":"2020-09-11T09:52:36Z","date_updated":"2020-09-11T09:52:36Z","checksum":"d414d0059e982d752d218756b3c3ce05","success":1,"relation":"main_file","file_id":"8381","content_type":"text/plain","file_size":586,"creator":"rguseino","file_name":"readme.txt","access_level":"open_access"}],"oa_version":"Published Version","date_updated":"2024-02-21T12:44:29Z","date_created":"2020-09-11T09:52:54Z","article_processing_charge":"No","has_accepted_license":"1","month":"09","day":"21","citation":{"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.","short":"R. Guseinov, (2020).","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.","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","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.","ieee":"R. 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Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. 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Institute of Science and Technology Austria, 2020, doi: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.","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","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","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."},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"doi":"10.15479/AT:ISTA:8563","date_published":"2020-10-19T00:00:00Z","day":"19","month":"10","has_accepted_license":"1","article_processing_charge":"No","title":"Optogenetic alteration of hippocampal network activity","ddc":["570"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"_id":"8563","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","date_updated":"2024-02-21T12:43:41Z","date_created":"2020-09-23T14:39:54Z","file":[{"access_level":"open_access","file_name":"upload.tgz","creator":"jozsef","content_type":"application/x-compressed","file_size":145243906,"file_id":"8564","relation":"main_file","success":1,"checksum":"a16098a6d172f9c42ab5af5f6991668c","date_created":"2020-09-23T14:36:17Z","date_updated":"2020-09-23T14:36:17Z"},{"date_created":"2020-10-19T10:12:29Z","date_updated":"2020-10-19T10:12:29Z","checksum":"0bfc54b7e14c0694cd081617318ba606","success":1,"relation":"main_file","file_id":"8675","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":11648,"creator":"jozsef","file_name":"redme.docx","access_level":"open_access"}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"},{"orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn","first_name":"Igor","full_name":"Gridchyn, Igor"},{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","last_name":"Schönenberger","first_name":"Philipp","full_name":"Schönenberger, Philipp"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8740"}]},"contributor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","contributor_type":"project_leader","last_name":"Csicsvari"}],"type":"research_data","file_date_updated":"2020-10-19T10:12:29Z","abstract":[{"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.","lang":"eng"}]},{"type":"research_data","file_date_updated":"2023-12-01T10:39:59Z","abstract":[{"lang":"eng","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."}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"FlSc"}],"ddc":["570"],"status":"public","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","_id":"14592","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"3Dprint-files_download_v2.zip","access_level":"open_access","creator":"fschur","content_type":"application/zip","file_size":49297,"file_id":"14593","relation":"main_file","date_created":"2023-11-22T14:58:44Z","date_updated":"2023-11-22T14:58:44Z","success":1,"checksum":"0108616e2a59e51879ea51299a29b091"},{"creator":"cchlebak","content_type":"text/plain","file_size":641,"access_level":"open_access","file_name":"readme.txt","success":1,"checksum":"4c66ddedee4d01c1c4a7978208350cfc","date_updated":"2023-12-01T10:39:59Z","date_created":"2023-12-01T10:39:59Z","file_id":"14637","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2024-02-21T12:44:48Z","date_created":"2023-11-22T15:00:57Z","contributor":[{"first_name":"Florian","contributor_type":"researcher","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X"},{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","contributor_type":"researcher","last_name":"Zens"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Hauschild","first_name":"Robert"},{"last_name":"Schur","contributor_type":"researcher","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8586","status":"public","relation":"research_data"}]},"author":[{"full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","article_processing_charge":"No","day":"01","month":"12","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"citation":{"ama":"Schur FK. 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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.","short":"F.K. Schur, (2020).","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. 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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. 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Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","ama":"Dotter C, Novarino G. 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Novarino, (2019)."},"abstract":[{"text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:18Z","type":"research_data","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"date_updated":"2024-02-21T13:41:01Z","date_created":"2019-03-07T13:32:35Z","oa_version":"Published Version","file":[{"relation":"supplementary_material","file_id":"6084","checksum":"bc1b285edca9e98a2c63d153c79bb75b","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-07T13:37:19Z","access_level":"open_access","file_name":"Setd5_paper.zip","file_size":33202743,"content_type":"application/zip","creator":"dernst"}],"year":"2019","_id":"6074","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","department":[{"_id":"GaNo"}],"publisher":"Institute of Science and Technology Austria"},{"article_processing_charge":"No","has_accepted_license":"1","day":"29","month":"03","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"citation":{"ista":"Nardin M. 2019. 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