[{"article_processing_charge":"No","author":[{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file_date_updated":"2023-12-22T14:14:06Z","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","date_updated":"2024-02-26T09:59:29Z","citation":{"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.","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.","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.","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.","short":"M.N. Elkrewi, (2024).","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"status":"public","project":[{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"_id":"14705","contributor":[{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","contributor_type":"researcher","first_name":"Vincent K","last_name":"Bett"},{"contributor_type":"project_member","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"},{"last_name":"Elkrewi","orcid":"0000-0002-5328-7231","contributor_type":"researcher","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"}],"date_created":"2023-12-22T13:40:48Z","related_material":{"record":[{"relation":"used_in_publication","id":"15009","status":"public"}]},"date_published":"2024-01-02T00:00:00Z","doi":"10.15479/AT:ISTA:14705","year":"2024","has_accepted_license":"1","file":[{"file_size":847,"date_updated":"2023-12-22T13:54:21Z","creator":"melkrewi","file_name":"readme.txt.txt","date_created":"2023-12-22T13:54:21Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","success":1,"file_id":"14707","checksum":"bdaf1392867786634ec5466d528c36ca"},{"creator":"melkrewi","file_size":343632753,"date_updated":"2023-12-22T14:14:06Z","file_name":"data_artemia_franciscana_genome.zip","date_created":"2023-12-22T14:14:06Z","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"checksum":"973e1cbdab923a71709782177980829f","file_id":"14708"}],"day":"02","oa":1,"publisher":"Institute of Science and Technology Austria","month":"01","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"}],"oa_version":"Published Version"},{"date_created":"2023-04-10T05:55:56Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","contributor":[{"last_name":"Troussicot","first_name":"Laura","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Björn M.","last_name":"Burmann"}],"doi":"10.15479/AT:ISTA:12820","date_published":"2023-04-18T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"13095","status":"public"}]},"year":"2023","has_accepted_license":"1","file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"file_id":"12823","checksum":"54a619605e44c871214fb0e07b05c6bf","file_size":54184807,"date_updated":"2023-04-14T09:39:33Z","creator":"pschanda","file_name":"data_deposition.zip","date_created":"2023-04-14T09:39:33Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","checksum":"8dede9fc78399d13144eb05c62bf5750","file_id":"12824","success":1,"creator":"pschanda","date_updated":"2023-04-14T09:39:58Z","file_size":4978,"date_created":"2023-04-14T09:39:58Z","file_name":"README"}],"day":"18","oa":1,"publisher":"Institute of Science and Technology Austria","month":"04","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"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"file_date_updated":"2023-04-14T09:39:58Z","department":[{"_id":"PaSc"}],"title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","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.","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.","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).","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","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"},"date_updated":"2023-08-01T14:48:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data","status":"public","_id":"12820"},{"file":[{"checksum":"3eadf17fd59ad8c98bf10bf63061863c","file_id":"12947","success":1,"content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2023-05-12T08:04:04Z","file_name":"Experimental_data.zip","date_updated":"2023-05-12T08:04:04Z","file_size":3414674,"creator":"scremer"},{"creator":"scremer","file_size":2113,"date_updated":"2023-05-12T08:04:08Z","file_name":"README_Experimental_Data.md","date_created":"2023-05-12T08:04:08Z","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","success":1,"checksum":"1b5e8e01a0989154a76b44e6d8d68f89","file_id":"12948"}],"day":"12","year":"2023","has_accepted_license":"1","contributor":[{"last_name":"Casillas Perez","contributor_type":"data_collector","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E"},{"last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","contributor_type":"data_collector","first_name":"Anna V"},{"last_name":"Bodova","contributor_type":"researcher","first_name":"Katarina"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","contributor_type":"supervisor","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-05-11T21:35:17Z","date_published":"2023-05-12T00:00:00Z","doi":"10.15479/AT:ISTA:12945","related_material":{"record":[{"relation":"used_in_publication","id":"13127","status":"public"}]},"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.","oa_version":"None","abstract":[{"lang":"eng","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"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"month":"05","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2023-08-07T13:09:09Z","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.","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.","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.","short":"S. Cremer, (2023).","ama":"Cremer S. Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945","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"},"file_date_updated":"2023-05-12T08:04:08Z","department":[{"_id":"SyCr"}],"title":"Data from: \"Dynamic pathogen detection and social feedback shape collective hygiene in ants\" ","article_processing_charge":"No","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"_id":"12945","keyword":["collective behavior","host-pathogen interactions","social immunity","epidemiology","social insects","probabilistic modeling"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data"},{"_id":"12370","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"research_data","status":"public","date_updated":"2023-10-04T11:41:04Z","ddc":["571"],"file_date_updated":"2023-01-26T10:51:34Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"abstract":[{"lang":"eng","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. "}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"oa_version":"Published 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F"},{"last_name":"Svaton","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","contributor_type":"researcher","first_name":"Jan"}],"ec_funded":1,"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12349"}]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"name":"Circuits of Visual Attention","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256"},{"name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Gupta, Divyansh, et al. 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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.","ista":"Gupta D, Sumser AL, Jösch MA. 2023. 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The infinitesimal model with dominance, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12949.","chicago":"Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949."},"month":"05","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed."}],"contributor":[{"first_name":"Amandine","contributor_type":"researcher","last_name":"Veber"},{"contributor_type":"researcher","first_name":"Alison","last_name":"Etheridge"}],"date_created":"2023-05-13T09:49:09Z","date_published":"2023-05-13T00:00:00Z","doi":"10.15479/AT:ISTA:12949","related_material":{"record":[{"relation":"used_in_publication","id":"14452","status":"public"}]},"day":"13","file":[{"date_created":"2023-05-13T09:36:33Z","file_name":"Neutral identities 16th 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of Science and Technology Austria","oa":1,"month":"04","abstract":[{"text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. ","lang":"eng"}],"oa_version":"Published Version","acknowledgement":"FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ","author":[{"last_name":"Klausen","full_name":"Klausen, Frederik Ravn","first_name":"Frederik Ravn"},{"orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"article_processing_charge":"No","file_date_updated":"2023-04-26T12:30:06Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"title":"Research data for: A stochastic cellular automaton model of culture formation","citation":{"chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.","ista":"Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12869.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for: A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:10.15479/AT:ISTA:12869","apa":"Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12869","ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.","short":"F.R. Klausen, A.B. 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of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","citation":{"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.","ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562.","mla":"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, doi:10.15479/AT:ISTA:14562.","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:10.15479/AT:ISTA:14562","ieee":"F. K. Schur, “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.","short":"F.K. Schur, (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"}],"date_created":"2023-11-20T09:22:33Z","doi":"10.15479/AT:ISTA:14562","date_published":"2023-11-21T00:00:00Z","year":"2023","has_accepted_license":"1","day":"21","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). 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_created":"2023-10-30T16:38:32Z","related_material":{"record":[{"id":"14610","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:14472","date_published":"2023-10-31T00:00:00Z","year":"2023","has_accepted_license":"1","file":[{"creator":"ipalaia","file_size":62821432,"date_updated":"2023-10-30T16:31:08Z","file_name":"SGporecondensation-main.zip","date_created":"2023-10-30T16:31:08Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","success":1,"file_id":"14473","checksum":"a18706e952e8660c51ede52a167270b7"},{"access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"389eab31c6509dbc05795017fb618758","file_id":"14474","success":1,"creator":"dernst","date_updated":"2023-10-31T08:57:50Z","file_size":1697,"date_created":"2023-10-31T08:57:50Z","file_name":"README.txt"}],"day":"31","oa":1,"publisher":"Institute of Science and Technology Austria","month":"10","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"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"}],"department":[{"_id":"AnSa"}],"title":"Stress granules plug and stabilize damaged endolysosomal membranes","file_date_updated":"2023-10-31T08:57:50Z","citation":{"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.","ista":"Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.","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.","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. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023.","short":"C.E. Vanhille-Campos, A. Šarić, (2023)."},"date_updated":"2023-11-27T09:05:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","status":"public","_id":"14472"},{"article_processing_charge":"No","author":[{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"title":"Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ","department":[{"_id":"SyCr"}],"file_date_updated":"2023-02-28T06:34:12Z","date_updated":"2023-12-13T11:13:13Z","citation":{"mla":"Cremer, Sylvia. Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12693.","ieee":"S. Cremer, “Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males .” Institute of Science and Technology Austria, 2023.","short":"S. Cremer, (2023).","ama":"Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . 2023. doi:10.15479/AT:ISTA:12693","apa":"Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12693","chicago":"Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12693.","ista":"Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12693."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data","status":"public","_id":"12693","contributor":[{"contributor_type":"data_collector","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler"},{"contributor_type":"data_collector","id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3","first_name":"Jessica","last_name":"Kirchner"},{"last_name":"Grasse","contributor_type":"data_collector","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"}],"date_created":"2023-02-28T06:38:37Z","doi":"10.15479/AT:ISTA:12693","date_published":"2023-02-28T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"12696","status":"public"}]},"year":"2023","has_accepted_license":"1","file":[{"date_created":"2023-02-28T06:34:08Z","file_name":"Metzler_ReadMe.pdf","date_updated":"2023-02-28T06:34:08Z","file_size":77070,"creator":"scremer","file_id":"12694","checksum":"c1565d655ca05601acfd84e0d12b8563","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"success":1,"file_id":"12695","checksum":"75c4c4948563d6261cb7548f80d909f1","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","relation":"main_file","access_level":"open_access","file_name":"Metzler_RepositoryData.xlsx","date_created":"2023-02-28T06:34:12Z","file_size":88001,"date_updated":"2023-02-28T06:34:12Z","creator":"scremer"}],"day":"28","oa":1,"publisher":"Institute of Science and Technology Austria","month":"02","abstract":[{"text":"See Readme File for further information.","lang":"eng"}],"oa_version":"Published Version"},{"date_updated":"2023-12-13T12:15:36Z","citation":{"mla":"Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933.","ieee":"G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.","short":"G. Puixeu Sala, (2023).","apa":"Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933","ama":"Puixeu Sala G. 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Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"article_processing_charge":"No","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala"}],"title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","file_date_updated":"2023-05-11T12:50:18Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"_id":"12933","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","status":"public","year":"2023","has_accepted_license":"1","file":[{"date_created":"2023-05-10T09:41:43Z","file_name":"Dataset_S1.csv","creator":"gpuixeus","date_updated":"2023-05-10T09:41:43Z","file_size":8029982,"file_id":"12934","checksum":"0ba0bcd0bb8b18d84792136a4370df90","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/csv"},{"file_name":"Dataset_S2.csv","date_created":"2023-05-10T09:41:43Z","creator":"gpuixeus","file_size":13667640,"date_updated":"2023-05-10T09:41:43Z","success":1,"file_id":"12935","checksum":"a62aa9a6d4904e0fdb699cf752640863","relation":"main_file","access_level":"open_access","content_type":"text/csv"},{"file_size":8369141,"date_updated":"2023-05-10T09:41:48Z","creator":"gpuixeus","file_name":"Dataset_S3.csv","date_created":"2023-05-10T09:41:48Z","content_type":"text/csv","relation":"main_file","access_level":"open_access","success":1,"file_id":"12936","checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b"},{"date_updated":"2023-05-10T09:41:50Z","file_size":19543247,"creator":"gpuixeus","date_created":"2023-05-10T09:41:50Z","file_name":"Dataset_S4.csv","content_type":"text/csv","access_level":"open_access","relation":"main_file","checksum":"f6156e5fc44446c907ddd0d7289d4cf8","file_id":"12937","success":1},{"date_updated":"2023-05-11T12:50:18Z","file_size":4566,"creator":"gpuixeus","date_created":"2023-05-11T12:50:18Z","file_name":"readme.txt","content_type":"text/plain","access_level":"open_access","relation":"main_file","checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","file_id":"12944","success":1}],"day":"15","date_created":"2023-05-10T10:00:49Z","contributor":[{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14058"},{"status":"public","id":"14077","relation":"used_in_publication"}]},"date_published":"2023-05-15T00:00:00Z","doi":"10.15479/AT:ISTA:12933","abstract":[{"text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\".","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"05"},{"_id":"12817","status":"public","type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2024-01-10T08:37:48Z","citation":{"short":"J.G. Danzl, (2023).","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","ama":"Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:10.15479/AT:ISTA:12817","apa":"Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12817","mla":"Danzl, Johann G. Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12817.","ista":"Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12817.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12817."},"title":"Research data for the publication \"Dense 4D nanoscale reconstruction of living brain tissue\"","file_date_updated":"2023-05-18T19:51:52Z","department":[{"_id":"JoDa"}],"author":[{"last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"}],"article_processing_charge":"No","oa_version":"Published Version","acknowledgement":"We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. We thank Paul Henderson for advice on deep-learning training and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag ligand. ","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"abstract":[{"lang":"eng","text":"3D-reconstruction of living brain tissue down to individual synapse level would create opportunities for decoding the dynamics and structure-function relationships of the brain’s complex and dense information processing network. However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"month":"05","publisher":"Institute of Science and Technology 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Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12497.","chicago":"Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12497.","ieee":"L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023.","short":"L.M. Becker, P. Schanda, (2023).","ama":"Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:10.15479/AT:ISTA:12497","apa":"Becker, L. M., & Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12497","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. 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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"}]},{"project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020"}],"citation":{"ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13126.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.","short":"J.G. Danzl, (2023).","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.","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","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi: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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"}],"title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2023","has_accepted_license":"1","day":"04","date_created":"2023-06-07T07:15:12Z","doi":"10.15479/AT:ISTA:13126","date_published":"2023-08-04T00:00:00Z","_id":"13126","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"research_data","status":"public","date_updated":"2024-02-21T12:18:19Z","ddc":["610"],"department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"file_date_updated":"2023-08-04T13:19:47Z","abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"oa_version":"Published 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Chiral and nematic phases of flexible active filaments. 2023. doi:10.15479/AT:ISTA:13116","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023).","mla":"Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116.","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.","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."},"date_updated":"2024-02-21T12:19:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["539"],"author":[{"id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Dunajova","full_name":"Dunajova, Zuzana"},{"full_name":"Prats Mateu, Batirtze","last_name":"Prats Mateu","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze"},{"orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"first_name":"Keesiang","last_name":"Lim","full_name":"Lim, Keesiang"},{"last_name":"Brandis","full_name":"Brandis, Dörte","first_name":"Dörte"},{"first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"last_name":"Wong","full_name":"Wong, Richard W.","first_name":"Richard W."},{"last_name":"Elgeti","full_name":"Elgeti, Jens","first_name":"Jens"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"article_processing_charge":"No","department":[{"_id":"MaLo"},{"_id":"EdHa"},{"_id":"JoDa"}],"file_date_updated":"2023-08-08T11:17:28Z","title":"Chiral and nematic phases of flexible active filaments","abstract":[{"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. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). 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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."}],"oa_version":"Published Version","author":[{"last_name":"Lasne","orcid":"0000-0002-1197-8616","full_name":"Lasne, Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","first_name":"Clementine"},{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"}],"article_processing_charge":"No","file_date_updated":"2023-11-30T14:16:59Z","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","department":[{"_id":"BeVi"}],"date_updated":"2024-02-21T12:18:35Z","citation":{"chicago":"Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14614.","ista":"Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14614.","mla":"Lasne, Clementine, and Marwan N. Elkrewi. The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14614.","apa":"Lasne, C., & Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14614","ama":"Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:10.15479/AT:ISTA:14614","short":"C. Lasne, M.N. Elkrewi, (2023).","ieee":"C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023."},"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Panorpa","scorpionfly","genome","transcriptome"],"_id":"14614"},{"abstract":[{"lang":"eng","text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles at the presynaptic active zone (AZ). Strikingly, tonic and phasic release exhibit distinct coupling distances and are selectively affected by deletion of synaptoporin (SPO) and Ca2+-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. Double pre-embedding immunolabeling confirmed the co-localization of CAPS2 and SPO inside the same terminal. The cytosolic protein CAPS2 showed a synaptic vesicle (SV)-associated distribution similar to the vesicular transmembrane protein SPO. A newly developed “Flash and Freeze-fracture” method revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to a persistent RRP increase. Thus, we discovered structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals."}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"07","year":"2023","has_accepted_license":"1","day":"29","file":[{"title":"Outdated Version","date_created":"2023-06-29T13:11:22Z","file_name":"Raw data for Koppensteiner et al.zip","creator":"shigemot","date_updated":"2023-11-17T14:30:44Z","file_size":542873672,"checksum":"ed59170869ba621f89f7c1894092192f","file_id":"13174","access_level":"closed","relation":"main_file","description":"After review an updated version of the data is provided","content_type":"application/x-zip-compressed"},{"date_updated":"2023-11-17T14:13:02Z","file_size":915079,"creator":"patrickd","date_created":"2023-11-17T14:13:02Z","file_name":"11-17-23 Updated Koppensteiner et al. raw data.xlsx","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","access_level":"open_access","relation":"main_file","file_id":"14550","checksum":"c07860eb82b4d367245f1b589fe5c250","success":1},{"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","checksum":"abf84b1699edac4349dc3a92d466fb7b","file_id":"14942","success":1,"date_updated":"2024-02-06T07:21:43Z","file_size":544868924,"creator":"dernst","date_created":"2024-02-06T07:21:43Z","file_name":"EM_Images.zip"}],"date_created":"2023-06-29T13:16:42Z","date_published":"2023-07-29T00:00:00Z","related_material":{"record":[{"id":"15084","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:13173","_id":"13173","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data","keyword":["medial habenula","GABAB receptor","vesicle release","Flash and Freeze","Flash and Freeze-fracture"],"status":"public","citation":{"mla":"Shigemoto, Ryuichi. Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13173.","short":"R. Shigemoto, (2023).","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.","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","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","chicago":"Shigemoto, Ryuichi. “Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13173.","ista":"Shigemoto R. 2023. Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13173."},"date_updated":"2024-03-12T13:44:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["571"],"article_processing_charge":"No","author":[{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"}],"title":"Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals","department":[{"_id":"RySh"}],"file_date_updated":"2024-02-06T07:21:43Z"},{"_id":"10934","keyword":["Bacterial cell division","in vitro reconstitution","FtsZ","FtsN","FtsA"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","ddc":["572"],"date_updated":"2024-02-21T12:35:18Z","file_date_updated":"2022-04-22T10:15:19Z","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"oa_version":"Submitted Version","abstract":[{"text":"FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. 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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"}],"oa_version":"Published Version","related_material":{"record":[{"id":"11411","status":"public","relation":"used_in_publication"},{"relation":"earlier_version","status":"public","id":"9192"},{"relation":"earlier_version","id":"8254","status":"public"}]},"doi":"10.15479/at:ista:11321","date_published":"2022-04-28T00:00:00Z","contributor":[{"contributor_type":"project_member","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","last_name":"Arathoon"},{"last_name":"Baskett","orcid":"0000-0002-7354-8574","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"David"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"contributor_type":"project_member","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"date_created":"2022-04-22T09:42:24Z","has_accepted_license":"1","year":"2022","day":"28","file":[{"checksum":"96c1b86cdf25481f2a52972fcc45ca7f","file_id":"11326","success":1,"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","date_created":"2022-04-22T09:39:03Z","file_name":"Data_Code.zip","date_updated":"2022-04-22T09:39:03Z","file_size":13260571,"creator":"larathoo"}]},{"publisher":"Institute of Science and Technology Austria","oa":1,"month":"08","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","date_published":"2022-08-05T00:00:00Z","related_material":{"record":[{"id":"12248","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:11653","date_created":"2022-07-26T11:01:47Z","contributor":[{"orcid":"0000-0002-5328-7231","last_name":"Elkrewi","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luca","last_name":"Sax"},{"last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hontoria ","first_name":"Francisco"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"has_accepted_license":"1","year":"2022","day":"05","file":[{"content_type":"application/x-zip-compressed","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","relation":"main_file","access_level":"open_access","embargo":"2022-08-07","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","file_id":"11655","file_size":2209382998,"date_updated":"2022-08-08T22:30:04Z","creator":"melkrewi","file_name":"Data.zip","title":"Supplementary Datasets","date_created":"2022-07-26T12:37:52Z"}],"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"11653","author":[{"last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"}],"article_processing_charge":"No","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","file_date_updated":"2022-08-08T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"citation":{"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.","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.","short":"M.N. Elkrewi, (2022).","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","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","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653.","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653."},"date_updated":"2024-02-21T12:35:53Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2021-03-29T00:00:00Z","doi":"10.15479/AT:ISTA:9291","date_created":"2021-03-27T13:47:49Z","has_accepted_license":"1","year":"2021","file":[{"file_name":"Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip","date_created":"2021-03-27T13:46:17Z","file_size":10616071,"date_updated":"2021-03-27T13:46:17Z","creator":"gkatsaro","success":1,"file_id":"9292","checksum":"635df3c08fc13c3dac008cd421aefbe4","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access"},{"relation":"main_file","access_level":"open_access","content_type":"text/plain","success":1,"checksum":"12b3ca69ae7509a346711baae0b02a75","file_id":"9302","creator":"dernst","file_size":470,"date_updated":"2021-04-01T07:52:56Z","file_name":"README.txt","date_created":"2021-04-01T07:52:56Z"}],"day":"29","publisher":"Institute of Science and Technology Austria","oa":1,"month":"03","abstract":[{"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).","lang":"eng"}],"oa_version":"Published Version","author":[{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"article_processing_charge":"No","file_date_updated":"2021-04-01T07:52:56Z","title":"Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium","department":[{"_id":"GeKa"}],"date_updated":"2024-02-21T12:37:14Z","citation":{"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.","ama":"Katsaros G. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. 2021. doi: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","short":"G. Katsaros, (2021).","ieee":"G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium.” Institute of Science and Technology Austria, 2021.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","_id":"9291"},{"status":"public","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"9636","file_date_updated":"2021-07-07T20:37:28Z","department":[{"_id":"AnHi"}],"title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","author":[{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:36:52Z","citation":{"ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 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.","short":"A.P. Higginbotham, (2021).","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 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."},"publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Submitted Version","date_published":"2021-01-01T00:00:00Z","related_material":{"record":[{"id":"10029","status":"public","relation":"used_in_publication"}]},"date_created":"2021-07-07T20:43:10Z","file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"file_id":"9637","checksum":"18e90687ec7bbd75f8bfea4d8293fb30","file_size":3345244,"date_updated":"2021-07-07T20:37:28Z","creator":"ahigginb","file_name":"figures_data.zip","date_created":"2021-07-07T20:37:28Z"}],"has_accepted_license":"1","year":"2021"},{"_id":"9323","status":"public","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"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.","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.","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","ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi: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.","short":"D. Jirovec, (2021).","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."},"date_updated":"2024-02-21T12:39:15Z","title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\"","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"file_date_updated":"2021-04-14T09:49:30Z","author":[{"first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec"}],"article_processing_charge":"No","oa_version":"Published Version","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."}],"month":"04","publisher":"Institute of Science and Technology Austria","oa":1,"day":"14","file":[{"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","file_id":"9324","checksum":"c569d2a2ce1694445cdbca19cf8ae023","success":1,"date_updated":"2021-04-14T09:48:47Z","file_size":221832287,"creator":"djirovec","date_created":"2021-04-14T09:48:47Z","file_name":"DataRepositorySTqubit.zip"},{"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","file_id":"9325","checksum":"845bdf87430718ad6aff47eda7b5fc92","success":1,"date_updated":"2021-04-14T09:49:30Z","file_size":4323,"creator":"djirovec","date_created":"2021-04-14T09:49:30Z","file_name":"ReadMe"}],"has_accepted_license":"1","year":"2021","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8909"}]},"date_published":"2021-04-14T00:00:00Z","doi":"10.15479/AT:ISTA:9323","contributor":[{"last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"}],"date_created":"2021-04-14T09:50:22Z"},{"_id":"9389","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","status":"public","citation":{"chicago":"Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389.","ista":"Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9389.","mla":"Valentini, Marco. Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9389.","short":"M. Valentini, (2021).","ieee":"M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021.","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389","apa":"Valentini, M. (2021). 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Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8834.","chicago":"Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8834.","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8834","ama":"Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:10.15479/AT:ISTA:8834","short":"G. Katsaros, (2020).","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","mla":"Katsaros, Georgios. Enhancement of Proximity Induced Superconductivity in Planar Germanium. 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To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"07","has_accepted_license":"1","year":"2020","file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","file_id":"8098","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","file_size":255770756,"date_updated":"2020-07-14T12:48:09Z","creator":"bkavcic","file_name":"natComm_2020_scripts.zip","date_created":"2020-07-06T20:38:27Z"}],"day":"15","doi":"10.15479/AT:ISTA:8097","date_published":"2020-07-15T00:00:00Z","date_created":"2020-07-06T20:40:19Z","contributor":[{"first_name":"Gašper","contributor_type":"research_group","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","contributor_type":"research_group","first_name":"Tobias","last_name":"Bollenbach"}],"_id":"8097","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"date_updated":"2024-02-21T12:40:51Z","citation":{"chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097.","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.","short":"B. Kavcic, (2020).","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097","ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:48:09Z","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\""},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","status":"public","_id":"8254","article_processing_charge":"No","author":[{"first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X"}],"title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","department":[{"_id":"NiBa"}],"file_date_updated":"2020-08-18T08:03:23Z","date_updated":"2024-02-21T12:41:09Z","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.","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.","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.","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.","short":"L.S. Arathoon, (2020).","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 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"},"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Institute of Science and Technology Austria","month":"08","abstract":[{"text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192.","lang":"eng"}],"oa_version":"Published Version","date_created":"2020-08-12T12:49:23Z","contributor":[{"last_name":"Arathoon","first_name":"Louise S","contributor_type":"data_collector","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Surendranadh","contributor_type":"project_member","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy"},{"contributor_type":"project_member","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"last_name":"Baskett","first_name":"Carina","contributor_type":"project_member","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"11321"},{"relation":"later_version","status":"public","id":"9192"}]},"doi":"10.15479/AT:ISTA:8254","date_published":"2020-08-18T00:00:00Z","year":"2020","has_accepted_license":"1","file":[{"file_id":"8280","checksum":"4f1382ed4384751b6013398c11557bf6","success":1,"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","date_created":"2020-08-18T08:03:23Z","file_name":"Data_Rcode_MathematicaNB.zip","date_updated":"2020-08-18T08:03:23Z","file_size":5778420,"creator":"dernst"}],"day":"18"},{"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:41:42Z","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.","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.","short":"B. Kavcic, (2020).","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","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","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.","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."},"title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","file_date_updated":"2020-12-09T15:00:19Z","department":[{"_id":"GaTk"}],"article_processing_charge":"No","author":[{"orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"}],"_id":"8930","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","day":"10","file":[{"file_size":315494370,"date_updated":"2020-12-09T15:00:19Z","creator":"bkavcic","file_name":"PLoSCompBiol2020_datarep.zip","date_created":"2020-12-09T15:00:19Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"file_id":"8932","checksum":"60a818edeffaa7da1ebf5f8fbea9ba18"}],"year":"2020","has_accepted_license":"1","date_created":"2020-12-09T15:04:02Z","contributor":[{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","last_name":"Tkačik","orcid":"0000-0002-6699-1455"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","last_name":"Bollenbach"}],"doi":"10.15479/AT:ISTA:8930","date_published":"2020-12-10T00:00:00Z","related_material":{"record":[{"id":"8997","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"month":"12","oa":1,"publisher":"Institute of Science and Technology Austria"},{"department":[{"_id":"CaGu"}],"file_date_updated":"2020-12-20T22:01:44Z","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","author":[{"last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"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.","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.","short":"A.A. Nagy-Staron, (2020).","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","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","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","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."},"date_updated":"2024-02-21T12:41:57Z","status":"public","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8951","doi":"10.15479/AT:ISTA:8951","related_material":{"record":[{"status":"public","id":"9283","relation":"used_in_publication"}]},"date_published":"2020-12-21T00:00:00Z","date_created":"2020-12-20T10:00:26Z","contributor":[{"last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Anna A"},{"last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"first_name":"Caroline","contributor_type":"project_member","last_name":"Caruso Carter"},{"contributor_type":"project_member","first_name":"Elisabeth","last_name":"Sonnleitner"},{"last_name":"Kavcic","orcid":"0000-0001-6041-254X","contributor_type":"project_member","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"},{"contributor_type":"project_member","first_name":"Tiago","last_name":"Paixão"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","contributor_type":"project_manager","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"day":"21","file":[{"checksum":"f57862aeee1690c7effd2b1117d40ed1","file_id":"8952","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/plain","date_created":"2020-12-20T09:52:52Z","file_name":"readme.txt","creator":"bkavcic","date_updated":"2020-12-20T09:52:52Z","file_size":523},{"content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","success":1,"file_id":"8954","checksum":"f2c6d5232ec6d551b6993991e8689e9f","file_size":379228,"date_updated":"2020-12-20T22:01:44Z","creator":"bkavcic","file_name":"GRNs Research depository.gb","date_created":"2020-12-20T22:01:44Z"}],"has_accepted_license":"1","year":"2020","month":"12","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}]},{"oa_version":"Published Version","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"}],"month":"01","publisher":"Institute of Science and Technology Austria","oa":1,"day":"28","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"9d292cf5207b3829225f44c044cdb3fd","file_id":"7384","creator":"rgrah","file_size":73363365,"date_updated":"2020-07-14T12:47:57Z","file_name":"Scripts.zip","date_created":"2020-01-28T10:39:40Z"},{"file_size":962,"date_updated":"2020-07-14T12:47:57Z","creator":"rgrah","file_name":"READ_ME_MAIN.txt","date_created":"2020-01-28T10:39:30Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","checksum":"4076ceab32ef588cc233802bab24c1ab","file_id":"7385"}],"has_accepted_license":"1","year":"2020","date_published":"2020-01-28T00:00:00Z","doi":"10.15479/AT:ISTA:7383","related_material":{"record":[{"relation":"used_in_publication","id":"7652","status":"public"}]},"date_created":"2020-01-28T10:41:49Z","contributor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader","first_name":"Calin C"}],"_id":"7383","status":"public","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","short":"R. Grah, (2020).","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020."},"date_updated":"2024-02-21T12:42:31Z","file_date_updated":"2020-07-14T12:47:57Z","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"}],"article_processing_charge":"No"},{"has_accepted_license":"1","year":"2020","day":"16","file":[{"creator":"gkatsaro","file_size":13317557,"date_updated":"2021-03-05T17:50:45Z","file_name":"DOI_SiteControlledHWs.zip","date_created":"2021-03-05T17:50:45Z","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","checksum":"41b66e195ed3dbd73077feee77b05652","file_id":"9223"},{"creator":"dernst","file_size":3515,"date_updated":"2021-03-10T07:31:50Z","file_name":"Readme.txt","date_created":"2021-03-10T07:31:50Z","relation":"main_file","access_level":"open_access","content_type":"text/plain","success":1,"checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","file_id":"9233"}],"date_published":"2020-03-16T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7541"}]},"doi":"10.15479/AT:ISTA:9222","contributor":[{"first_name":"Georgios","contributor_type":"research_group","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"date_created":"2021-03-05T18:00:47Z","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"03","citation":{"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","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","short":"G. Katsaros, (2020).","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.","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.","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.","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."},"date_updated":"2024-02-21T12:42:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"author":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"article_processing_charge":"No","department":[{"_id":"GeKa"}],"file_date_updated":"2021-03-10T07:31:50Z","title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","_id":"9222","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public"},{"_id":"8375","status":"public","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2024-02-21T12:44:29Z","citation":{"apa":"Guseinov, R. (2020). Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8375","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","short":"R. Guseinov, (2020).","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter.’” Institute of Science and Technology Austria, 2020.","mla":"Guseinov, Ruslan. Supplementary Data for “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8375.","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8375.","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8375."},"department":[{"_id":"BeBi"}],"file_date_updated":"2020-09-11T09:52:36Z","title":"Supplementary data for \"Computational design of curved thin shells: from glass façades to programmable matter\"","article_processing_charge":"No","author":[{"last_name":"Guseinov","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan","first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","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."}],"month":"09","oa":1,"publisher":"Institute of Science and Technology Austria","day":"21","file":[{"file_name":"supplementary_movie_1.mp4","date_created":"2020-09-11T09:45:21Z","file_size":29214988,"date_updated":"2020-09-11T09:45:21Z","creator":"rguseino","success":1,"checksum":"4029ffd65fb82ef2366b2fc2a4908e16","file_id":"8376","content_type":"video/mp4","relation":"main_file","access_level":"open_access"},{"content_type":"video/mp4","relation":"main_file","access_level":"open_access","success":1,"file_id":"8377","checksum":"8ed03b04d80f1a4e622cb22e6100afd8","file_size":28449475,"date_updated":"2020-09-11T09:45:25Z","creator":"rguseino","file_name":"supplementary_movie_2.mp4","date_created":"2020-09-11T09:45:25Z"},{"date_created":"2020-09-11T09:45:28Z","file_name":"supplementary_movie_3.mp4","date_updated":"2020-09-11T09:45:28Z","file_size":26315853,"creator":"rguseino","checksum":"ad6864afb5e694e5c52a88fba4e02eea","file_id":"8378","success":1,"content_type":"video/mp4","access_level":"open_access","relation":"main_file"},{"creator":"rguseino","file_size":25198755,"date_updated":"2020-09-11T09:45:33Z","file_name":"supplementary_movie_4.mp4","date_created":"2020-09-11T09:45:33Z","relation":"main_file","access_level":"open_access","content_type":"video/mp4","success":1,"checksum":"b079cef7871fe1afb69af0e2b099f3b1","file_id":"8379"},{"checksum":"9d1d48a8ed5c109a999c51b044ee523d","file_id":"8380","success":1,"content_type":"video/mp4","access_level":"open_access","relation":"main_file","date_created":"2020-09-11T09:45:36Z","file_name":"supplementary_movie_5.mp4","date_updated":"2020-09-11T09:45:36Z","file_size":29011354,"creator":"rguseino"},{"file_size":586,"date_updated":"2020-09-11T09:52:36Z","creator":"rguseino","file_name":"readme.txt","date_created":"2020-09-11T09:52:36Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","success":1,"checksum":"d414d0059e982d752d218756b3c3ce05","file_id":"8381"}],"year":"2020","has_accepted_license":"1","contributor":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Ruslan","last_name":"Guseinov","orcid":"0000-0001-9819-5077"},{"last_name":"McMahan","first_name":"Connor","contributor_type":"researcher"},{"last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Jesus"},{"first_name":"Chiara","contributor_type":"researcher","last_name":"Daraio"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"}],"ec_funded":1,"date_created":"2020-09-11T09:52:54Z","doi":"10.15479/AT:ISTA:8375","related_material":{"record":[{"relation":"used_in_publication","id":"8366","status":"public"}]},"date_published":"2020-09-21T00:00:00Z"},{"has_accepted_license":"1","year":"2020","file":[{"content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","checksum":"d23c0cb9e2d19e14e2f902b88b97c05d","file_id":"7786","file_size":5514403,"date_updated":"2020-07-14T12:48:02Z","creator":"gkatsaro","file_name":"DOI_ZeroFieldSplitting.zip","date_created":"2020-05-01T15:13:28Z"}],"day":"01","doi":"10.15479/AT:ISTA:7689","related_material":{"record":[{"status":"public","id":"8203","relation":"used_in_publication"}]},"date_published":"2020-05-01T00:00:00Z","date_created":"2020-05-01T15:14:46Z","contributor":[{"contributor_type":"contact_person","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros"}],"ec_funded":1,"abstract":[{"text":"These are the supplementary research data to the publication \"Zero field splitting of heavy-hole states in quantum dots\". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\r\n","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"05","date_updated":"2024-02-21T12:44:02Z","citation":{"chicago":"Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7689.","ista":"Katsaros G. 2020. Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7689.","mla":"Katsaros, Georgios. 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Supplementary Data for “Computational Design of Cold Bent Glass Façades.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8761.","short":"R. Guseinov, (2020).","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020.","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of cold bent glass façades.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8761","ama":"Guseinov R. Supplementary data for “Computational design of cold bent glass façades.” 2020. doi:10.15479/AT:ISTA:8761","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8761.","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of cold bent glass façades’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8761."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","last_name":"Guseinov"}],"file_date_updated":"2020-11-18T10:04:59Z","department":[{"_id":"BeBi"}],"title":"Supplementary data for \"Computational design of cold bent glass façades\"","_id":"8761","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","status":"public","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}]},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","contributor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","contributor_type":"project_leader","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"}],"date_created":"2020-09-23T14:39:54Z","related_material":{"record":[{"status":"public","id":"8740","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:8563","date_published":"2020-10-19T00:00:00Z","day":"19","file":[{"success":1,"checksum":"a16098a6d172f9c42ab5af5f6991668c","file_id":"8564","relation":"main_file","access_level":"open_access","content_type":"application/x-compressed","file_name":"upload.tgz","date_created":"2020-09-23T14:36:17Z","creator":"jozsef","file_size":145243906,"date_updated":"2020-09-23T14:36:17Z"},{"success":1,"checksum":"0bfc54b7e14c0694cd081617318ba606","file_id":"8675","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"main_file","access_level":"open_access","file_name":"redme.docx","date_created":"2020-10-19T10:12:29Z","file_size":11648,"date_updated":"2020-10-19T10:12:29Z","creator":"jozsef"}],"year":"2020","has_accepted_license":"1","month":"10","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","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"}],"department":[{"_id":"JoCs"}],"title":"Optogenetic alteration of hippocampal network activity","file_date_updated":"2020-10-19T10:12:29Z","article_processing_charge":"No","author":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"},{"full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","first_name":"Igor"},{"full_name":"Schönenberger, Philipp","last_name":"Schönenberger","first_name":"Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2024-02-21T12:43:41Z","citation":{"short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","mla":"Csicsvari, Jozsef L., et al. Optogenetic Alteration of Hippocampal Network Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563.","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563.","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."},"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"research_data","_id":"8563"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"research_data","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"status":"public","_id":"14592","article_processing_charge":"No","author":[{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-12-01T10:39:59Z","department":[{"_id":"FlSc"}],"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","citation":{"mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","short":"F.K. Schur, (2020).","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592."},"date_updated":"2024-02-21T12:44:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa":1,"publisher":"Institute of Science and Technology Austria","month":"12","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."}],"oa_version":"Published Version","date_created":"2023-11-22T15:00:57Z","contributor":[{"first_name":"Florian","contributor_type":"researcher","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","orcid":"0000-0001-7149-769X"},{"last_name":"Zens","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"last_name":"Hauschild","contributor_type":"researcher","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"}],"date_published":"2020-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14592","related_material":{"record":[{"relation":"research_data","status":"public","id":"8586"}]},"year":"2020","has_accepted_license":"1","day":"01","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","success":1,"checksum":"0108616e2a59e51879ea51299a29b091","file_id":"14593","creator":"fschur","file_size":49297,"date_updated":"2023-11-22T14:58:44Z","file_name":"3Dprint-files_download_v2.zip","date_created":"2023-11-22T14:58:44Z"},{"relation":"main_file","access_level":"open_access","content_type":"text/plain","success":1,"checksum":"4c66ddedee4d01c1c4a7978208350cfc","file_id":"14637","creator":"cchlebak","file_size":641,"date_updated":"2023-12-01T10:39:59Z","file_name":"readme.txt","date_created":"2023-12-01T10:39:59Z"}]},{"author":[{"full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","last_name":"Tomanek","first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","file_date_updated":"2020-07-14T12:47:47Z","department":[{"_id":"CaGu"}],"citation":{"ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","short":"I. Tomanek, (2019).","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","apa":"Tomanek, I. (2019). Data 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:7016","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016."},"date_updated":"2024-02-21T12:45:25Z","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","status":"public","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"_id":"7016","date_published":"2019-11-13T00:00:00Z","doi":"10.15479/AT:ISTA:7016","related_material":{"record":[{"status":"public","id":"7652","relation":"used_in_publication"}]},"date_created":"2019-11-13T09:07:31Z","contributor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"has_accepted_license":"1","year":"2019","day":"13","file":[{"title":"Locus1_amplified","date_created":"2019-11-13T08:52:21Z","file_name":"D8_S35_R2_001.fastq","date_updated":"2020-07-14T12:47:47Z","file_size":2456192500,"creator":"itomanek","file_id":"7017","checksum":"72441055043eda4cbf1398a422e2c118","description":"Illumina whole genome sequence data for Locus 1 - 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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. 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."}],"oa_version":"Published Version"},{"_id":"7154","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"citation":{"chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7154.","ista":"Guseinov R. 2019. 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","article_processing_charge":"No","author":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.","apa":"Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060","ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060","short":"B. Vicoso, (2019).","ieee":"B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019.","chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060.","ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060."},"date_updated":"2024-02-21T12:45:42Z","status":"public","type":"research_data","_id":"6060"},{"status":"public","type":"research_data","_id":"6074","department":[{"_id":"GaNo"}],"title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","file_date_updated":"2020-07-14T12:47:18Z","author":[{"last_name":"Dotter","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2024-02-21T13:41:01Z","citation":{"chicago":"Dotter, Christoph, and Gaia 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. https://doi.org/10.15479/AT:ISTA:6074.","ista":"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, 10.15479/AT:ISTA:6074.","mla":"Dotter, Christoph, and Gaia 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, doi:10.15479/AT:ISTA:6074.","short":"C. Dotter, G. Novarino, (2019).","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.","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074","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"},"month":"01","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","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"}],"doi":"10.15479/AT:ISTA:6074","date_published":"2019-01-09T00:00:00Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"date_created":"2019-03-07T13:32:35Z","file":[{"date_updated":"2020-07-14T12:47:18Z","file_size":33202743,"creator":"dernst","date_created":"2019-03-07T13:37:19Z","file_name":"Setd5_paper.zip","content_type":"application/zip","access_level":"open_access","relation":"supplementary_material","file_id":"6084","checksum":"bc1b285edca9e98a2c63d153c79bb75b"}],"day":"09","has_accepted_license":"1","year":"2019"},{"publisher":"Institute of Science and Technology Austria","oa":1,"month":"03","abstract":[{"lang":"eng","text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7)."}],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:6062","related_material":{"record":[{"relation":"research_paper","id":"6194","status":"public"}]},"date_published":"2019-03-29T00:00:00Z","date_created":"2019-03-04T14:20:58Z","has_accepted_license":"1","year":"2019","file":[{"date_created":"2019-03-05T09:29:37Z","title":"Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","file_name":"Online_data.zip","creator":"mnardin","date_updated":"2020-07-14T12:47:18Z","file_size":37002186,"file_id":"6068","checksum":"48e7b9a02939b763417733239522a236","access_level":"open_access","relation":"main_file","content_type":"application/zip"}],"day":"29","type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"status":"public","_id":"6062","author":[{"last_name":"Nardin","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"}],"article_processing_charge":"No","title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","file_date_updated":"2020-07-14T12:47:18Z","department":[{"_id":"JoCs"}],"date_updated":"2024-02-21T12:46:04Z","citation":{"ieee":"M. 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Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74."},"file_date_updated":"2020-07-14T12:47:04Z","title":"Time-lapse microscopy data","department":[{"_id":"CaGu"}],"author":[{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"}],"publist_id":"7385","article_processing_charge":"No","_id":"5569","status":"public","keyword":["microscopy","microfluidics"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5637","checksum":"61ebb92213cfffeba3ddbaff984b81af","creator":"system","date_updated":"2020-07-14T12:47:04Z","file_size":3558703796,"date_created":"2018-12-12T13:04:39Z","file_name":"IST-2018-74-v1+2_15-11-05.zip"},{"creator":"system","file_size":1830422606,"date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2018-74-v1+3_15-07-31.zip","date_created":"2018-12-12T13:04:55Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5638","checksum":"bf26649af310ef6892d68576515cde6d"},{"date_updated":"2020-07-14T12:47:04Z","file_size":2140849248,"creator":"system","date_created":"2018-12-12T13:05:11Z","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","file_id":"5639","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd"}],"day":"07","has_accepted_license":"1","year":"2018","datarep_id":"74","date_published":"2018-02-07T00:00:00Z","doi":"10.15479/AT:ISTA:74","related_material":{"record":[{"relation":"research_paper","id":"438","status":"public"}]},"date_created":"2018-12-12T12:31:35Z","oa_version":"Published Version","abstract":[{"text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic.","lang":"eng"}],"month":"02","publisher":"Institute of Science and Technology Austria","oa":1},{"date_created":"2018-12-12T12:31:41Z","ec_funded":1,"doi":"10.15479/AT:ISTA:62","related_material":{"record":[{"id":"161","status":"public","relation":"research_paper"}]},"date_published":"2018-09-21T00:00:00Z","year":"2018","datarep_id":"111","has_accepted_license":"1","file":[{"creator":"system","date_updated":"2020-07-14T12:47:08Z","file_size":14376,"date_created":"2018-12-12T13:05:13Z","file_name":"IST-2018-111-v1+1_CODES.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"97992e3e8cf8544ec985a48971708726","file_id":"5641"}],"day":"21","oa":1,"publisher":"Institute of Science and Technology Austria","month":"09","abstract":[{"text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","last_name":"De Martino"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GaTk"}],"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","file_date_updated":"2020-07-14T12:47:08Z","citation":{"ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:62.","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62.","short":"D. De Martino, G. Tkačik, (2018).","ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","apa":"De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:62","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62","mla":"De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62."},"date_updated":"2024-02-21T13:45:39Z","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"status":"public","_id":"5587"},{"file":[{"creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":369837892,"date_created":"2018-12-19T14:19:52Z","file_name":"FileS1.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_id":"5758"},{"content_type":"application/zip","access_level":"open_access","relation":"main_file","file_id":"5759","checksum":"3592e467b4d8206650860b612d6e12f3","date_updated":"2020-07-14T12:47:11Z","file_size":84856909,"creator":"cfraisse","date_created":"2018-12-19T14:19:49Z","file_name":"FileS2.zip"},{"file_size":881133,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS3.txt","date_created":"2018-12-19T14:19:49Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","checksum":"c37ac5d5437c457338afc128c1240655","file_id":"5760"},{"file_id":"5761","checksum":"943dfd14da61817441e33e3e3cb8cdb9","relation":"main_file","access_level":"open_access","content_type":"text/plain","file_name":"FileS4.txt","date_created":"2018-12-19T14:19:49Z","creator":"cfraisse","file_size":883742,"date_updated":"2020-07-14T12:47:11Z"},{"relation":"main_file","access_level":"open_access","content_type":"text/plain","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","file_id":"5762","creator":"cfraisse","file_size":2495437,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS5.txt","date_created":"2018-12-19T14:19:49Z"},{"date_created":"2018-12-19T14:19:50Z","file_name":"FileS6.txt","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":15913457,"file_id":"5763","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","access_level":"open_access","relation":"main_file","content_type":"text/plain"},{"date_created":"2018-12-19T14:19:50Z","file_name":"FileS7.txt","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":2584120,"checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_id":"5764","access_level":"open_access","relation":"main_file","content_type":"text/plain"},{"creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":2446059,"date_created":"2018-12-19T14:19:50Z","file_name":"FileS8.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","file_id":"5765"},{"content_type":"text/plain","access_level":"open_access","relation":"main_file","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","file_id":"5766","date_updated":"2020-07-14T12:47:11Z","file_size":100737,"creator":"cfraisse","date_created":"2018-12-19T14:19:50Z","file_name":"FileS9.txt"}],"day":"19","has_accepted_license":"1","year":"2018","related_material":{"record":[{"relation":"research_paper","id":"6089","status":"public"}]},"doi":"10.15479/at:ista:/5757","date_published":"2018-12-19T00:00:00Z","date_created":"2018-12-19T14:22:35Z","ec_funded":1,"contributor":[{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants."}],"month":"12","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","short":"C. Fraisse, (2018).","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757."},"date_updated":"2024-02-21T13:59:18Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:11Z","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"}],"article_processing_charge":"No","_id":"5757","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"status":"public","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"type":"research_data"},{"status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"},{"grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"5585","file_date_updated":"2020-07-14T12:47:07Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","author":[{"first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia","last_name":"Igler"},{"last_name":"Lagator","full_name":"Lagator, Mato","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"date_updated":"2024-03-27T23:30:48Z","citation":{"ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 10.15479/AT:ISTA:108.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","mla":"Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:108."},"month":"07","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Mean repression values and standard error of the mean are given for all operator mutant libraries."}],"date_published":"2018-07-20T00:00:00Z","doi":"10.15479/AT:ISTA:108","related_material":{"record":[{"status":"public","id":"67","relation":"research_paper"},{"status":"public","id":"6371","relation":"research_paper"}]},"date_created":"2018-12-12T12:31:40Z","ec_funded":1,"file":[{"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","access_level":"open_access","relation":"main_file","checksum":"1435781526c77413802adee0d4583cce","file_id":"5611","date_updated":"2020-07-14T12:47:07Z","file_size":16507,"creator":"system","date_created":"2018-12-12T13:02:45Z","file_name":"IST-2018-108-v1+1_data_figures.xlsx"}],"day":"20","has_accepted_license":"1","datarep_id":"108","year":"2018"},{"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","keyword":["multi-electrode recording","retinal ganglion cells"],"_id":"5562","author":[{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Dario","full_name":"Amodei, Dario","last_name":"Amodei"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"last_name":"Berry","full_name":"Berry, Michael","first_name":"Michael"}],"article_processing_charge":"No","title":"Multi-electrode array recording from salamander retinal ganglion cells","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:03Z","date_updated":"2024-02-21T13:46:14Z","citation":{"ista":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:61.","chicago":"Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.","ama":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61","apa":"Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:61","short":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).","ieee":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017.","mla":"Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:61."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","abstract":[{"lang":"eng","text":"This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408."}],"oa_version":"Published Version","related_material":{"record":[{"id":"2257","status":"public","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:61","date_published":"2017-02-27T00:00:00Z","date_created":"2018-12-12T12:31:33Z","has_accepted_license":"1","year":"2017","datarep_id":"61","day":"27","file":[{"creator":"system","date_updated":"2020-07-14T12:47:03Z","file_size":1336936,"date_created":"2018-12-12T13:03:04Z","file_name":"IST-2017-61-v1+1_bint_fishmovie32_100.mat","access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","checksum":"e620eff260646f57b479a69492c8b765","file_id":"5622"},{"content_type":"application/zip","relation":"main_file","access_level":"open_access","file_id":"5623","checksum":"de83f9b81ea0aae3cddfc3ed982e0759","file_size":1897543,"date_updated":"2020-07-14T12:47:03Z","creator":"system","file_name":"IST-2017-61-v1+2_bint_fishmovie32_100.zip","date_created":"2018-12-12T13:03:05Z"}]},{"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","keyword":["graph matching","feature matching","QAP","MAP-inference"],"status":"public","_id":"5561","article_processing_charge":"No","author":[{"full_name":"Kainmueller, Dagmar","last_name":"Kainmueller","first_name":"Dagmar"},{"first_name":"Florian","full_name":"Jug, Florian","last_name":"Jug"},{"last_name":"Rother","full_name":"Rother, Carsten","first_name":"Carsten"},{"first_name":"Gene","full_name":"Meyers, Gene","last_name":"Meyers"}],"department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:47:03Z","title":"Graph matching problems for annotating C. 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Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in \"Feature Correspondence via Graph Matching: Models and Global Optimization.\" by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. 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Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel, Institute of Science and Technology Austria, 10.15479/AT:ISTA:66.","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:66.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:66","ama":"von Wangenheim D, Hauschild R, Friml J. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. 2017. doi:10.15479/AT:ISTA:66","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel.” Institute of Science and Technology Austria, 2017.","short":"D. von Wangenheim, R. Hauschild, J. Friml, (2017).","mla":"von Wangenheim, Daniel, et al. Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel. 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Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. \r\nThe Video is licensed under a CC BY NC ND license. ","lang":"eng"}]},{"abstract":[{"text":"Current minimal version of TipTracker","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"07","has_accepted_license":"1","year":"2017","datarep_id":"69","day":"21","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5636","checksum":"a976000e6715106724a271cc9422be4a","creator":"system","file_size":1587986,"date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2017-69-v1+2_TipTrackerZeissLSM700.zip","date_created":"2018-12-12T13:04:12Z"}],"date_published":"2017-07-21T00:00:00Z","doi":"10.15479/AT:ISTA:69","related_material":{"record":[{"id":"946","status":"public","relation":"research_paper"}]},"date_created":"2018-12-12T12:31:34Z","_id":"5566","type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"status":"public","keyword":["tool","tracking","confocal microscopy"],"citation":{"ista":"Hauschild R. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots, Institute of Science and Technology Austria, 10.15479/AT:ISTA:69.","chicago":"Hauschild, Robert. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:69.","short":"R. Hauschild, (2017).","ieee":"R. Hauschild, “Live tracking of moving samples in confocal microscopy for vertically grown roots.” Institute of Science and Technology Austria, 2017.","apa":"Hauschild, R. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:69","ama":"Hauschild R. Live tracking of moving samples in confocal microscopy for vertically grown roots. 2017. doi:10.15479/AT:ISTA:69","mla":"Hauschild, Robert. Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:69."},"date_updated":"2024-02-21T13:49:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"author":[{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"Bio"}],"title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","file_date_updated":"2020-07-14T12:47:04Z"},{"article_processing_charge":"No","author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"}],"publist_id":"5828","department":[{"_id":"NiBa"}],"title":"Flower colour data and phylogeny (NEXUS) files","file_date_updated":"2020-07-14T12:47:00Z","citation":{"ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, 10.15479/AT:ISTA:34.","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:34.","apa":"Ellis, T., & Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:34","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:10.15479/AT:ISTA:34","short":"T. Ellis, D. Field, (2016).","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas, and David Field. Flower Colour Data and Phylogeny (NEXUS) Files. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:34."},"date_updated":"2024-02-21T13:49:54Z","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","status":"public","_id":"5550","date_created":"2018-12-12T12:31:29Z","related_material":{"record":[{"status":"public","id":"1382","relation":"research_paper"}]},"date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:34","datarep_id":"34","year":"2016","has_accepted_license":"1","file":[{"file_id":"5594","checksum":"950f85b80427d357bfeff09608ba02e9","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:02:27Z","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","date_updated":"2020-07-14T12:47:00Z","file_size":4468543,"creator":"system"}],"day":"19","oa":1,"publisher":"Institute of Science and Technology Austria","month":"02","abstract":[{"text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"oa_version":"Published Version"},{"oa_version":"Published Version","abstract":[{"text":"This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.","lang":"eng"}],"month":"07","oa":1,"publisher":"Institute of Science and Technology Austria","file":[{"file_name":"IST-2016-44-v1+1_migrationAnalyzer.zip","date_created":"2018-12-12T13:03:03Z","creator":"system","file_size":20692,"date_updated":"2020-07-14T12:47:02Z","checksum":"9f96cddbcd4ed689f48712ffe234d5e5","file_id":"5621","relation":"main_file","access_level":"open_access","content_type":"application/zip"}],"day":"08","year":"2016","datarep_id":"44","has_accepted_license":"1","date_created":"2018-12-12T12:31:31Z","doi":"10.15479/AT:ISTA:44","date_published":"2016-07-08T00:00:00Z","_id":"5555","keyword":["cell migration","wide field microscopy","FIJI"],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"ama":"Hauschild R. Fiji script to determine average speed and direction of migration of cells. 2016. doi:10.15479/AT:ISTA:44","apa":"Hauschild, R. (2016). Fiji script to determine average speed and direction of migration of cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:44","short":"R. Hauschild, (2016).","ieee":"R. Hauschild, “Fiji script to determine average speed and direction of migration of cells.” Institute of Science and Technology Austria, 2016.","mla":"Hauschild, Robert. Fiji Script to Determine Average Speed and Direction of Migration of Cells. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:44.","ista":"Hauschild R. 2016. Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:44.","chicago":"Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction of Migration of Cells.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:44."},"date_updated":"2024-02-21T13:50:06Z","file_date_updated":"2020-07-14T12:47:02Z","department":[{"_id":"Bio"}],"title":"Fiji script to determine average speed and direction of migration of cells","article_processing_charge":"No","author":[{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}]},{"month":"09","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5.","lang":"eng"}],"date_created":"2018-12-12T12:31:31Z","contributor":[{"contributor_type":"data_collector","first_name":"Jan","last_name":"Kuske"}],"date_published":"2016-09-20T00:00:00Z","doi":"10.15479/AT:ISTA:46","file":[{"file_id":"5645","checksum":"aa5a16a0dc888da7186fb8fc45e88439","access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2018-12-12T13:05:19Z","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","creator":"system","date_updated":"2020-07-14T12:47:02Z","file_size":36058401}],"day":"20","year":"2016","datarep_id":"46","has_accepted_license":"1","keyword":["discrete tomography"],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"5557","title":"Synthetic discrete tomography problems","department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:47:02Z","article_processing_charge":"No","author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","full_name":"Swoboda, Paul","last_name":"Swoboda"}],"ddc":["006"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:46.","ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, 10.15479/AT:ISTA:46.","mla":"Swoboda, Paul. Synthetic Discrete Tomography Problems. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:46.","short":"P. Swoboda, (2016).","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:10.15479/AT:ISTA:46","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:46"},"date_updated":"2024-02-21T13:50:21Z"},{"title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","file_date_updated":"2020-07-14T12:47:01Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","last_name":"Ellis"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"date_updated":"2024-02-21T13:51:14Z","citation":{"apa":"Field, D., & Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:37","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37","short":"D. Field, T. Ellis, (2016).","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","mla":"Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:37.","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, 10.15479/AT:ISTA:37.","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:37."},"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"5553","date_created":"2018-12-12T12:31:30Z","contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_manager","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"doi":"10.15479/AT:ISTA:37","date_published":"2016-02-19T00:00:00Z","related_material":{"record":[{"status":"public","id":"1398","relation":"research_paper"}]},"file":[{"content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"4ae751b1fa4897fa216241f975a57313","file_id":"5620","date_updated":"2020-07-14T12:47:01Z","file_size":132808,"creator":"system","date_created":"2018-12-12T13:03:02Z","file_name":"IST-2016-37-v1+1_paternity_archive.zip"}],"day":"19","datarep_id":"37","year":"2016","has_accepted_license":"1","month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org."}]},{"year":"2016","datarep_id":"35","has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:47:01Z","file_size":32775,"creator":"system","date_created":"2018-12-12T13:05:12Z","file_name":"IST-2016-35-v1+1_array_data.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","file_id":"5640"}],"day":"19","contributor":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"date_created":"2018-12-12T12:31:29Z","date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:35","related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"abstract":[{"lang":"eng","text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid."}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"02","date_updated":"2024-02-21T13:51:27Z","citation":{"chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:35.","mla":"Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.","short":"T. Ellis, (2016).","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"file_date_updated":"2020-07-14T12:47:01Z","department":[{"_id":"NiBa"}],"title":"Data on pollinator observations and offpsring phenotypes","_id":"5551","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","status":"public"},{"_id":"5552","status":"public","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:51:40Z","citation":{"chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:36.","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, 10.15479/AT:ISTA:36.","mla":"Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:36.","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","short":"T. Ellis, (2016).","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:36"},"title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","file_date_updated":"2020-07-14T12:47:01Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","file":[{"file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","date_created":"2018-12-12T13:03:07Z","file_size":44905,"date_updated":"2020-07-14T12:47:01Z","creator":"system","checksum":"cbc61b523d4d475a04a737d50dc470ef","file_id":"5625","content_type":"application/zip","relation":"main_file","access_level":"open_access"}],"day":"19","datarep_id":"36","year":"2016","has_accepted_license":"1","date_created":"2018-12-12T12:31:30Z","contributor":[{"last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"date_published":"2016-02-19T00:00:00Z","related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:36"},{"_id":"5554","status":"public","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:50:34Z","citation":{"ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","short":"M. Tugrul, (2016).","mla":"Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43."},"file_date_updated":"2020-07-14T12:47:01Z","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"author":[{"last_name":"Tugrul","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.","lang":"eng"}],"month":"05","publisher":"Institute of Science and Technology Austria","oa":1,"day":"12","file":[{"checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","file_id":"5626","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:03:08Z","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","date_updated":"2020-07-14T12:47:01Z","file_size":1123495,"creator":"system"}],"has_accepted_license":"1","year":"2016","datarep_id":"43","date_published":"2016-05-12T00:00:00Z","doi":"10.15479/AT:ISTA:43","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1131"}]},"contributor":[{"last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Magdalena"},{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Fabienne","last_name":"Jesse"}],"date_created":"2018-12-12T12:31:30Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"citation":{"chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48.","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 10.15479/AT:ISTA:48.","mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.","ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:10.15479/AT:ISTA:48","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","short":"M. 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Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","mla":"Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28."},"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"contributor":[{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"1603","relation":"popular_science"}]},"file":[{"date_updated":"2020-07-14T12:47:00Z","file_size":49557109,"creator":"system","date_created":"2018-12-12T13:02:31Z","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"b8bcb43c0893023cda66c1b69c16ac62","file_id":"5597"}],"datarep_id":"28","month":"08","oa_version":"Published Version","abstract":[{"text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication.","lang":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:00Z","ddc":["004"],"date_updated":"2024-02-21T13:52:07Z","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"5549"}]