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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","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","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."},"oa":1,"date_published":"2023-05-19T00:00:00Z","doi":"10.15479/AT:ISTA:12817","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"type":"research_data","file_date_updated":"2023-05-18T19:51:52Z","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."}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","_id":"12817","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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. 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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."}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","type":"research_data","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12675"}]},"contributor":[{"first_name":"Mélanie","contributor_type":"researcher","last_name":"Berbon"},{"contributor_type":"researcher","last_name":"Vallet","first_name":"Alicia"},{"contributor_type":"researcher","last_name":"Grelard","first_name":"Axelle"},{"last_name":"Morvan","contributor_type":"researcher","first_name":"Estelle"},{"first_name":"Benjamin","contributor_type":"researcher","last_name":"Bardiaux"},{"contributor_type":"researcher","last_name":"Lichtenecker","first_name":"Roman"},{"first_name":"Matthias","last_name":"Ernst","contributor_type":"researcher"},{"first_name":"Antoine","contributor_type":"researcher","last_name":"Loquet"},{"last_name":"Schanda","contributor_type":"contact_person","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Becker","contributor_type":"researcher","first_name":"Lea Marie","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"}],"author":[{"full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","first_name":"Lea Marie","last_name":"Becker"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"}],"file":[{"creator":"lbecker","file_size":87018103,"content_type":"application/zip","file_name":"Research_Data.zip","access_level":"open_access","date_created":"2023-03-23T10:03:16Z","date_updated":"2023-03-24T09:34:20Z","checksum":"fd9a28620a81a82991fb70f4fd6591d9","file_id":"12743","relation":"main_file"},{"date_updated":"2023-03-24T09:42:03Z","date_created":"2023-03-24T07:13:55Z","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","file_id":"12755","relation":"main_file","creator":"dernst","content_type":"text/plain","file_size":747,"file_name":"README.txt","access_level":"open_access"}],"oa_version":"Published Version","date_created":"2023-02-03T08:08:02Z","date_updated":"2024-02-21T12:14:06Z","_id":"12497","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"status":"public","title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","ddc":["572"]},{"date_created":"2023-06-07T07:15:12Z","date_updated":"2024-02-21T12:18:19Z","related_material":{"link":[{"url":"https://pub.ista.ac.at/group_danzl/data/CATS/","description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. 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We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file_date_updated":"2023-08-04T13:19:47Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"doi":"10.15479/AT:ISTA:13126","project":[{"grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in 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Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"type":"research_data","date_published":"2023-08-04T00:00:00Z","citation":{"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","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.","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi: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).","mla":"Danzl, Johann G. 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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). ","article_processing_charge":"No","has_accepted_license":"1","day":"26","date_published":"2023-07-26T00:00:00Z","citation":{"ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:10.15479/AT:ISTA:13116","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.","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.","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.","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).","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."},"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. 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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.","lang":"eng"}],"file_date_updated":"2023-11-30T14:16:59Z","type":"research_data","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14613"}]},"contributor":[{"contributor_type":"researcher","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"author":[{"orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","last_name":"Lasne","first_name":"Clementine","full_name":"Lasne, Clementine"},{"full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"}],"oa_version":"Published Version","file":[{"file_name":"panorpaX.zip","access_level":"open_access","creator":"clasne","file_size":404968272,"content_type":"application/zip","file_id":"14625","relation":"main_file","date_updated":"2023-11-28T13:15:26Z","date_created":"2023-11-28T13:15:26Z","success":1,"checksum":"cd0f13322b5156819ecaebd2bc8e7d12"},{"file_name":"panorpa_readme.txt","access_level":"open_access","creator":"clasne","file_size":2625,"content_type":"text/plain","file_id":"14634","relation":"main_file","date_updated":"2023-11-30T14:16:59Z","date_created":"2023-11-30T14:16:59Z","success":1,"checksum":"9ff600416577687a737cb3c96dfcb26c"}],"date_created":"2023-11-27T16:39:19Z","date_updated":"2024-02-21T12:18:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14614","year":"2023","department":[{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"status":"public","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","has_accepted_license":"1","article_processing_charge":"No","month":"12","day":"01","keyword":["Panorpa","scorpionfly","genome","transcriptome"],"doi":"10.15479/AT:ISTA:14614","date_published":"2023-12-01T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"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.","short":"C. Lasne, M.N. Elkrewi, (2023).","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.","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","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.","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.","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"}},{"file_date_updated":"2024-02-06T07:21:43Z","abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles at the presynaptic active zone (AZ). Strikingly, tonic and phasic release exhibit distinct coupling distances and are selectively affected by deletion of synaptoporin (SPO) and Ca2+-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. Double pre-embedding immunolabeling confirmed the co-localization of CAPS2 and SPO inside the same terminal. The cytosolic protein CAPS2 showed a synaptic vesicle (SV)-associated distribution similar to the vesicular transmembrane protein SPO. A newly developed “Flash and Freeze-fracture” method revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to a persistent RRP increase. Thus, we discovered structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"type":"research_data","date_created":"2023-06-29T13:16:42Z","date_updated":"2024-03-12T13:44:18Z","oa_version":"Published Version","file":[{"creator":"shigemot","file_size":542873672,"content_type":"application/x-zip-compressed","description":"After review an updated version of the data is provided","file_name":"Raw data for Koppensteiner et al.zip","access_level":"closed","date_created":"2023-06-29T13:11:22Z","date_updated":"2023-11-17T14:30:44Z","checksum":"ed59170869ba621f89f7c1894092192f","file_id":"13174","title":"Outdated Version","relation":"main_file"},{"creator":"patrickd","file_size":915079,"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","access_level":"open_access","file_name":"11-17-23 Updated Koppensteiner et al. raw data.xlsx","success":1,"checksum":"c07860eb82b4d367245f1b589fe5c250","date_updated":"2023-11-17T14:13:02Z","date_created":"2023-11-17T14:13:02Z","file_id":"14550","relation":"main_file"},{"content_type":"application/x-zip-compressed","file_size":544868924,"creator":"dernst","access_level":"open_access","file_name":"EM_Images.zip","checksum":"abf84b1699edac4349dc3a92d466fb7b","success":1,"date_updated":"2024-02-06T07:21:43Z","date_created":"2024-02-06T07:21:43Z","relation":"main_file","file_id":"14942"}],"author":[{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"}],"related_material":{"record":[{"id":"15084","relation":"used_in_publication","status":"public"}]},"status":"public","title":"Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals","ddc":["571"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"RySh"}],"year":"2023","_id":"13173","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"29","month":"07","article_processing_charge":"No","has_accepted_license":"1","keyword":["medial habenula","GABAB receptor","vesicle release","Flash and Freeze","Flash and Freeze-fracture"],"date_published":"2023-07-29T00:00:00Z","doi":"10.15479/AT:ISTA:13173","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"citation":{"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.","short":"R. Shigemoto, (2023).","mla":"Shigemoto, Ryuichi. Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13173.","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","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.","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.","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"}},{"keyword":["Bacterial cell division","in vitro reconstitution","FtsZ","FtsN","FtsA"],"day":"05","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10934.","short":"P. Radler, (2022).","mla":"Radler, Philipp. In Vitro Reconstitution of Escherichia Coli Divisome Activation. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10934.","ieee":"P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022.","apa":"Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. 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"}],"type":"research_data","file":[{"file_name":"Data_Code.zip","access_level":"open_access","content_type":"application/x-zip-compressed","file_size":13260571,"creator":"larathoo","relation":"main_file","file_id":"11326","date_updated":"2022-04-22T09:39:03Z","date_created":"2022-04-22T09:39:03Z","checksum":"96c1b86cdf25481f2a52972fcc45ca7f","success":1}],"oa_version":"Published Version","date_updated":"2024-02-21T12:41:09Z","date_created":"2022-04-22T09:42:24Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11411"},{"status":"public","relation":"earlier_version","id":"9192"},{"id":"8254","status":"public","relation":"earlier_version"}]},"contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Arathoon","first_name":"Louise S"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","first_name":"Carina","last_name":"Baskett","contributor_type":"project_member"},{"last_name":"Field","contributor_type":"project_member","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","contributor_type":"project_member","first_name":"Melinda"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","contributor_type":"project_member","last_name":"Barton"}],"author":[{"first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy"},{"full_name":"Arathoon, Louise S","first_name":"Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","first_name":"Carina","last_name":"Baskett","full_name":"Baskett, Carina"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11321","year":"2022"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"short":"M.N. Elkrewi, (2022).","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.","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.","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","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.","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_published":"2022-08-05T00:00:00Z","doi":"10.15479/AT:ISTA:11653","day":"05","month":"08","article_processing_charge":"No","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11653","year":"2022","status":"public","ddc":["570"],"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"author":[{"first_name":"Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"}],"contributor":[{"last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","first_name":"Andrea"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"last_name":"Sax","first_name":"Luca"},{"last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hontoria ","first_name":"Francisco"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12248"}]},"date_created":"2022-07-26T11:01:47Z","date_updated":"2024-02-21T12:35:53Z","file":[{"checksum":"5f1d7c6d7ab5375ed2564521432bed0c","date_updated":"2022-08-08T22:30:04Z","date_created":"2022-07-26T12:37:52Z","relation":"main_file","file_id":"11655","embargo":"2022-08-07","title":"Supplementary Datasets","content_type":"application/x-zip-compressed","file_size":2209382998,"creator":"melkrewi","access_level":"open_access","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","file_name":"Data.zip"}],"oa_version":"Published Version","type":"research_data","file_date_updated":"2022-08-08T22:30:04Z","abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}]},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ama":"Katsaros G. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. 2021. doi: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.","apa":"Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9291","ieee":"G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium.” Institute of Science and Technology Austria, 2021.","mla":"Katsaros, Georgios. Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9291.","short":"G. Katsaros, (2021).","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."},"date_published":"2021-03-29T00:00:00Z","doi":"10.15479/AT:ISTA:9291","has_accepted_license":"1","article_processing_charge":"No","day":"29","month":"03","_id":"9291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["530"],"title":"Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium","author":[{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip","content_type":"application/x-zip-compressed","file_size":10616071,"creator":"gkatsaro","relation":"main_file","file_id":"9292","checksum":"635df3c08fc13c3dac008cd421aefbe4","success":1,"date_created":"2021-03-27T13:46:17Z","date_updated":"2021-03-27T13:46:17Z"},{"relation":"main_file","file_id":"9302","checksum":"12b3ca69ae7509a346711baae0b02a75","success":1,"date_updated":"2021-04-01T07:52:56Z","date_created":"2021-04-01T07:52:56Z","access_level":"open_access","file_name":"README.txt","file_size":470,"content_type":"text/plain","creator":"dernst"}],"date_created":"2021-03-27T13:47:49Z","date_updated":"2024-02-21T12:37:14Z","type":"research_data","file_date_updated":"2021-04-01T07:52:56Z","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"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/"},{"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"citation":{"chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","short":"A.P. Higginbotham, (2021).","mla":"Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology Austria, 2021.","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021.","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021."},"date_published":"2021-01-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9636","year":"2021","publisher":"Institute of Science and Technology Austria","department":[{"_id":"AnHi"}],"title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10029"}]},"author":[{"orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"}],"oa_version":"Submitted Version","file":[{"content_type":"application/zip","file_size":3345244,"creator":"ahigginb","file_name":"figures_data.zip","access_level":"open_access","date_updated":"2021-07-07T20:37:28Z","date_created":"2021-07-07T20:37:28Z","checksum":"18e90687ec7bbd75f8bfea4d8293fb30","success":1,"relation":"main_file","file_id":"9637"}],"date_created":"2021-07-07T20:43:10Z","date_updated":"2024-02-21T12:36:52Z","type":"research_data","file_date_updated":"2021-07-07T20:37:28Z"},{"doi":"10.15479/AT:ISTA:9323","date_published":"2021-04-14T00:00:00Z","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:10.15479/AT:ISTA:9323","ista":"Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar Ge’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9323.","apa":"Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar Ge.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9323","ieee":"D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’” Institute of Science and Technology Austria, 2021.","mla":"Jirovec, Daniel. Research Data for “A Singlet-Triplet Hole Spin Qubit Planar Ge.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9323.","short":"D. Jirovec, (2021).","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."},"month":"04","day":"14","article_processing_charge":"No","has_accepted_license":"1","date_created":"2021-04-14T09:50:22Z","date_updated":"2024-02-21T12:39:15Z","file":[{"creator":"djirovec","file_size":221832287,"content_type":"application/x-zip-compressed","access_level":"open_access","file_name":"DataRepositorySTqubit.zip","success":1,"checksum":"c569d2a2ce1694445cdbca19cf8ae023","date_created":"2021-04-14T09:48:47Z","date_updated":"2021-04-14T09:48:47Z","file_id":"9324","relation":"main_file"},{"relation":"main_file","file_id":"9325","checksum":"845bdf87430718ad6aff47eda7b5fc92","success":1,"date_created":"2021-04-14T09:49:30Z","date_updated":"2021-04-14T09:49:30Z","access_level":"open_access","file_name":"ReadMe","content_type":"application/octet-stream","file_size":4323,"creator":"djirovec"}],"oa_version":"Published Version","author":[{"full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","first_name":"Daniel","last_name":"Jirovec"}],"related_material":{"record":[{"id":"8909","relation":"used_in_publication","status":"public"}]},"contributor":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Jirovec","contributor_type":"project_member"}],"status":"public","ddc":["530"],"title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"year":"2021","_id":"9323","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"This .zip File contains the data for figures presented in the main text and supplementary material of \"A singlet triplet hole spin qubit in planar Ge\" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python."}],"file_date_updated":"2021-04-14T09:49:30Z","type":"research_data"},{"has_accepted_license":"1","article_processing_charge":"No","doi":"10.15479/AT:ISTA:9389","date_published":"2021-01-01T00:00:00Z","acknowledged_ssus":[{"_id":"NanoFab"}],"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.","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).","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.","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.","apa":"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. https://doi.org/10.15479/AT:ISTA:9389","ama":"Valentini M. 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Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:10.15479/AT:ISTA:8834","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8834","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","ista":"Katsaros G. 2020. Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8834.","short":"G. Katsaros, (2020).","mla":"Katsaros, Georgios. Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2020, doi: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."},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1},{"type":"research_data","abstract":[{"lang":"eng","text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology."}],"file_date_updated":"2020-07-14T12:48:09Z","status":"public","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8097","year":"2020","date_updated":"2024-02-21T12:40:51Z","date_created":"2020-07-06T20:40:19Z","file":[{"relation":"main_file","file_id":"8098","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","date_updated":"2020-07-14T12:48:09Z","date_created":"2020-07-06T20:38:27Z","access_level":"open_access","file_name":"natComm_2020_scripts.zip","file_size":255770756,"content_type":"application/zip","creator":"bkavcic"}],"oa_version":"Published Version","author":[{"last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor"}],"contributor":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","contributor_type":"research_group","last_name":"Tkačik","first_name":"Gašper"},{"contributor_type":"research_group","last_name":"Bollenbach","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"month":"07","day":"15","has_accepted_license":"1","article_processing_charge":"No","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"B. Kavcic, (2020).","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.","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.","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","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.","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","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."},"acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2020-07-15T00:00:00Z","doi":"10.15479/AT:ISTA:8097"},{"type":"research_data","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"file_date_updated":"2020-08-18T08:03:23Z","_id":"8254","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"status":"public","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Arathoon, Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","first_name":"Louise S","last_name":"Arathoon"}],"contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","last_name":"Arathoon","contributor_type":"data_collector"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Surendranadh","first_name":"Parvathy"},{"last_name":"Barton","contributor_type":"project_member","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","contributor_type":"project_member","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"contributor_type":"project_member","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Baskett","first_name":"Carina"}],"related_material":{"record":[{"id":"11321","relation":"later_version","status":"public"},{"status":"public","relation":"later_version","id":"9192"}]},"date_created":"2020-08-12T12:49:23Z","date_updated":"2024-02-21T12:41:09Z","oa_version":"Published Version","file":[{"date_updated":"2020-08-18T08:03:23Z","date_created":"2020-08-18T08:03:23Z","success":1,"checksum":"4f1382ed4384751b6013398c11557bf6","file_id":"8280","relation":"main_file","creator":"dernst","content_type":"application/x-zip-compressed","file_size":5778420,"file_name":"Data_Rcode_MathematicaNB.zip","access_level":"open_access"}],"month":"08","day":"18","has_accepted_license":"1","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.","mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254.","short":"L.S. Arathoon, (2020).","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.","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254"},"doi":"10.15479/AT:ISTA:8254","date_published":"2020-08-18T00:00:00Z"},{"keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"month":"12","day":"10","has_accepted_license":"1","article_processing_charge":"No","citation":{"short":"B. Kavcic, (2020).","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","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.","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","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."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"date_published":"2020-12-10T00:00:00Z","doi":"10.15479/AT:ISTA:8930","type":"research_data","file_date_updated":"2020-12-09T15:00:19Z","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."}],"year":"2020","_id":"8930","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"author":[{"full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X"}],"contributor":[{"contributor_type":"supervisor","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","contributor_type":"supervisor","first_name":"Tobias"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8997"}]},"date_updated":"2024-02-21T12:41:42Z","date_created":"2020-12-09T15:04:02Z","file":[{"file_id":"8932","relation":"main_file","date_updated":"2020-12-09T15:00:19Z","date_created":"2020-12-09T15:00:19Z","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","file_name":"PLoSCompBiol2020_datarep.zip","access_level":"open_access","creator":"bkavcic","file_size":315494370,"content_type":"application/zip"}],"oa_version":"Published Version"},{"doi":"10.15479/AT:ISTA:8951","date_published":"2020-12-21T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"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.","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","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","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","short":"A.A. Nagy-Staron, (2020)."},"day":"21","month":"12","article_processing_charge":"No","has_accepted_license":"1","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"author":[{"full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron","first_name":"Anna A","orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"}],"contributor":[{"last_name":"Nagy-Staron","contributor_type":"project_member","first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Tomasek","first_name":"Kathrin"},{"first_name":"Caroline","contributor_type":"project_member","last_name":"Caruso Carter"},{"first_name":"Elisabeth","last_name":"Sonnleitner","contributor_type":"project_member"},{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","contributor_type":"project_member","last_name":"Kavcic"},{"first_name":"Tiago","contributor_type":"project_member","last_name":"Paixão"},{"contributor_type":"project_manager","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9283"}]},"date_updated":"2024-02-21T12:41:57Z","date_created":"2020-12-20T10:00:26Z","oa_version":"Published Version","file":[{"checksum":"f57862aeee1690c7effd2b1117d40ed1","success":1,"date_created":"2020-12-20T09:52:52Z","date_updated":"2020-12-20T09:52:52Z","relation":"main_file","file_id":"8952","content_type":"text/plain","file_size":523,"creator":"bkavcic","access_level":"open_access","file_name":"readme.txt"},{"date_updated":"2020-12-20T22:01:44Z","date_created":"2020-12-20T22:01:44Z","success":1,"checksum":"f2c6d5232ec6d551b6993991e8689e9f","file_id":"8954","relation":"main_file","creator":"bkavcic","file_size":379228,"content_type":"application/octet-stream","file_name":"GRNs Research depository.gb","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8951","year":"2020","status":"public","ddc":["570"],"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","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."}],"file_date_updated":"2020-12-20T22:01:44Z","type":"research_data"},{"citation":{"chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.","short":"R. Grah, (2020).","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383.","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.","apa":"Grah, R. (2020). 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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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:57Z"},{"type":"research_data","file_date_updated":"2021-03-10T07:31:50Z","_id":"9222","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"status":"public","title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7541"}]},"contributor":[{"contributor_type":"research_group","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-21T12:42:13Z","date_created":"2021-03-05T18:00:47Z","file":[{"access_level":"open_access","file_name":"DOI_SiteControlledHWs.zip","content_type":"application/x-zip-compressed","file_size":13317557,"creator":"gkatsaro","relation":"main_file","file_id":"9223","checksum":"41b66e195ed3dbd73077feee77b05652","date_updated":"2021-03-05T17:50:45Z","date_created":"2021-03-05T17:50:45Z"},{"file_name":"Readme.txt","access_level":"open_access","creator":"dernst","content_type":"text/plain","file_size":3515,"file_id":"9233","relation":"main_file","date_updated":"2021-03-10T07:31:50Z","date_created":"2021-03-10T07:31:50Z","success":1,"checksum":"a1dc5f710ba4b3bb7f248195ba754ab2"}],"oa_version":"Published Version","month":"03","day":"16","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Katsaros G. 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All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\r\n"}],"file_date_updated":"2020-07-14T12:48:02Z","project":[{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"},{"name":"Towards scalable hut wire quantum devices","call_identifier":"FWF","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"}],"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Katsaros, Georgios. “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.","short":"G. Katsaros, (2020).","mla":"Katsaros, Georgios. 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Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563.","short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","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.","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."},"date_published":"2020-10-19T00:00:00Z","doi":"10.15479/AT:ISTA:8563"},{"file_date_updated":"2023-12-01T10:39:59Z","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. 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However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. 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","lang":"eng"}],"_id":"5584","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"title":"Nonlinear decoding of a complex movie from the mammalian retina","ddc":["570"],"status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"292"}]},"author":[{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"last_name":"Botella-Soler","first_name":"Vicente","full_name":"Botella-Soler, Vicente"},{"full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","first_name":"Georg S"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"file":[{"checksum":"6808748837b9afbbbabc2a356ca2b88a","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:24Z","relation":"main_file","file_id":"5590","content_type":"application/octet-stream","file_size":1142543971,"creator":"system","access_level":"open_access","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat"},{"access_level":"open_access","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","content_type":"application/pdf","file_size":702336,"creator":"system","relation":"main_file","file_id":"5591","checksum":"d6d6cd07743038fe3a12352983fcf9dd","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:25Z"},{"creator":"system","content_type":"application/octet-stream","file_size":432,"file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","access_level":"open_access","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:26Z","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","file_id":"5592","relation":"main_file"},{"access_level":"open_access","file_name":"IST-2018-98-v1+4_README.txt","creator":"system","file_size":986,"content_type":"text/plain","file_id":"5593","relation":"main_file","checksum":"2a83b011012e21e934b4596285b1a183","date_created":"2018-12-12T13:02:26Z","date_updated":"2020-07-14T12:47:07Z"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:26Z","date_created":"2018-12-12T12:31:39Z"},{"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109","ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109","ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, 10.15479/AT:ISTA:109.","short":"B. Vicoso, (2018).","mla":"Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018). Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109.","chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109."},"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"date_published":"2018-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:109","keyword":["schistosoma","Z-chromosome","gene expression"],"article_processing_charge":"No","has_accepted_license":"1","day":"24","month":"07","year":"2018","_id":"5586","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"status":"public","title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)","contributor":[{"first_name":"Marion A","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"}],"related_material":{"record":[{"id":"131","status":"public","relation":"research_paper"}]},"author":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"file":[{"file_id":"5601","relation":"main_file","checksum":"e60b484bd6f55c08eb66a189cb72c923","date_updated":"2020-07-14T12:47:08Z","date_created":"2018-12-12T13:02:35Z","access_level":"open_access","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","creator":"system","file_size":11918144,"content_type":"application/zip"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:12Z","date_created":"2018-12-12T12:31:40Z","type":"research_data","datarep_id":"109","abstract":[{"text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018).","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:08Z"},{"date_created":"2018-12-12T12:31:39Z","date_updated":"2024-02-21T13:45:01Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","creator":"system","file_size":122048,"content_type":"text/csv","file_id":"5606","relation":"main_file","checksum":"fc6aab51439f2622ba6df8632e66fd4f","date_created":"2018-12-12T13:02:41Z","date_updated":"2020-07-14T12:47:07Z"},{"file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","access_level":"open_access","creator":"system","file_size":235980,"content_type":"text/csv","file_id":"5607","relation":"main_file","date_created":"2018-12-12T13:02:42Z","date_updated":"2020-07-14T12:47:07Z","checksum":"92347586ae4f8a6eb7c04354797bf314"},{"file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","access_level":"open_access","content_type":"text/csv","file_size":311712,"creator":"system","relation":"main_file","file_id":"5608","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:43Z","checksum":"3300813645a54e6c5c39f41917228354"},{"content_type":"application/zip","file_size":342090,"creator":"system","file_name":"IST-2018-95-v1+4_faps_scripts.zip","access_level":"open_access","date_created":"2018-12-12T13:02:44Z","date_updated":"2020-07-14T12:47:07Z","checksum":"e739fc473567fd8f39438b445fc46147","relation":"main_file","file_id":"5609"}],"author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas"}],"related_material":{"record":[{"id":"286","relation":"research_paper","status":"public"}]},"contributor":[{"last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"title":"Data and Python scripts supporting Python package FAPS","status":"public","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","_id":"5583","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","file_date_updated":"2020-07-14T12:47:07Z","abstract":[{"lang":"eng","text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone."}],"datarep_id":"95","type":"research_data","date_published":"2018-02-12T00:00:00Z","doi":"10.15479/AT:ISTA:95","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95.","short":"T. Ellis, (2018).","mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95."},"month":"02","day":"12","article_processing_charge":"No","has_accepted_license":"1"},{"doi":"10.15479/AT:ISTA:74","date_published":"2018-02-07T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.","short":"T. Bergmiller, N. Nikolic, (2018).","mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74.","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74"},"month":"02","day":"07","has_accepted_license":"1","article_processing_charge":"No","keyword":["microscopy","microfluidics"],"date_updated":"2024-02-21T13:44:45Z","date_created":"2018-12-12T12:31:35Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-74-v1+2_15-11-05.zip","creator":"system","file_size":3558703796,"content_type":"application/zip","file_id":"5637","relation":"main_file","checksum":"61ebb92213cfffeba3ddbaff984b81af","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:39Z"},{"date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:55Z","checksum":"bf26649af310ef6892d68576515cde6d","file_id":"5638","relation":"main_file","creator":"system","file_size":1830422606,"content_type":"application/zip","file_name":"IST-2018-74-v1+3_15-07-31.zip","access_level":"open_access"},{"date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:05:11Z","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","relation":"main_file","file_id":"5639","file_size":2140849248,"content_type":"application/zip","creator":"system","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","access_level":"open_access"}],"author":[{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"438"}]},"status":"public","ddc":["579"],"title":"Time-lapse microscopy data","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","year":"2018","_id":"5569","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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."}],"file_date_updated":"2020-07-14T12:47:04Z","publist_id":"7385","datarep_id":"74","type":"research_data"},{"month":"09","day":"21","article_processing_charge":"No","has_accepted_license":"1","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"doi":"10.15479/AT:ISTA:62","date_published":"2018-09-21T00:00:00Z","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62","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","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.","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.","short":"D. De Martino, G. Tkačik, (2018).","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.","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."},"oa":1,"file_date_updated":"2020-07-14T12:47:08Z","abstract":[{"lang":"eng","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)."}],"ec_funded":1,"datarep_id":"111","type":"research_data","date_created":"2018-12-12T12:31:41Z","date_updated":"2024-02-21T13:45:39Z","file":[{"date_created":"2018-12-12T13:05:13Z","date_updated":"2020-07-14T12:47:08Z","checksum":"97992e3e8cf8544ec985a48971708726","relation":"main_file","file_id":"5641","file_size":14376,"content_type":"application/zip","creator":"system","file_name":"IST-2018-111-v1+1_CODES.zip","access_level":"open_access"}],"oa_version":"Published Version","author":[{"full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"161"}]},"status":"public","ddc":["530"],"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5587","year":"2018"}]