[{"file":[{"date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:18:01Z","file_name":"IST-2017-782-v1+1_BudCvi15.pdf","relation":"main_file","checksum":"3e971d09eb167761aa0888ed415b0056","access_level":"open_access","creator":"system","file_size":2820207,"content_type":"application/pdf","file_id":"5319"}],"author":[{"full_name":"Budanur, Nazmi B","last_name":"Budanur","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"last_name":"Cvitanović","first_name":"Predrag","full_name":"Cvitanović, Predrag"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","has_accepted_license":"1","publisher":"Springer","language":[{"iso":"eng"}],"pubrep_id":"782","publist_id":"6136","department":[{"_id":"BjHo"}],"_id":"1211","quality_controlled":"1","citation":{"apa":"Budanur, N. B., &#38; Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-016-1672-z\">https://doi.org/10.1007/s10955-016-1672-z</a>","mla":"Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:<a href=\"https://doi.org/10.1007/s10955-016-1672-z\">10.1007/s10955-016-1672-z</a>.","short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655.","ista":"Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655.","ieee":"N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4. Springer, pp. 636–655, 2017.","ama":"Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. <i>Journal of Statistical Physics</i>. 2017;167(3-4):636-655. doi:<a href=\"https://doi.org/10.1007/s10955-016-1672-z\">10.1007/s10955-016-1672-z</a>","chicago":"Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” <i>Journal of Statistical Physics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10955-016-1672-z\">https://doi.org/10.1007/s10955-016-1672-z</a>."},"file_date_updated":"2020-07-14T12:44:39Z","type":"journal_article","scopus_import":1,"abstract":[{"text":"Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.","lang":"eng"}],"publication_status":"published","date_updated":"2021-01-12T06:49:07Z","issue":"3-4","oa":1,"month":"05","intvolume":"       167","date_published":"2017-05-01T00:00:00Z","acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","year":"2017","page":"636-655","ddc":["530"],"date_created":"2018-12-11T11:50:44Z","day":"01","status":"public","volume":167,"oa_version":"Submitted Version","doi":"10.1007/s10955-016-1672-z","publication":"Journal of Statistical Physics"},{"article_processing_charge":"No","department":[{"_id":"MaLo"}],"publist_id":"6134","language":[{"iso":"eng"}],"publisher":"Academic Press","author":[{"full_name":"Baranova, Natalia","first_name":"Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","last_name":"Baranova"},{"full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers","project":[{"grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"publication_status":"published","publication_identifier":{"issn":["0091679X"]},"citation":{"mla":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” <i>Cytokinesis</i>, edited by Arnaud  Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>.","apa":"Baranova, N. S., &#38; Loose, M. (2017). Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), <i>Cytokinesis</i> (Vol. 137, pp. 355–370). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>","chicago":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In <i>Cytokinesis</i>, edited by Arnaud  Echard, 137:355–70. Academic Press, 2017. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>.","ama":"Baranova NS, Loose M. Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. <i>Cytokinesis</i>. Vol 137. Academic Press; 2017:355-370. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>","ieee":"N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers,” in <i>Cytokinesis</i>, vol. 137, A. Echard, Ed. Academic Press, 2017, pp. 355–370.","short":"N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press, 2017, pp. 355–370.","ista":"Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol. 137, 355–370."},"type":"book_chapter","scopus_import":"1","abstract":[{"lang":"eng","text":"Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring. While superresolution microscopy experiments have helped to gain more information about the organization of the Z-ring in the dividing cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize during assembly and disassembly of the Z-ring. In this chapter, we explain how to use an in vitro reconstitution approach to investigate the self-organization of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor FtsA. We show how to perform single-molecule experiments to study the behavior of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA filament network. We describe how to analyze the dynamics of single molecules and explain why this information can help to shed light onto possible mechanism of Z-ring constriction. We believe that similar experimental approaches will be useful to study the mechanism of membrane-based polymerization of other cytoskeletal systems, not only from prokaryotic but also eukaryotic origin."}],"editor":[{"full_name":"Echard, Arnaud ","last_name":"Echard","first_name":"Arnaud "}],"_id":"1213","quality_controlled":"1","page":"355 - 370","external_id":{"isi":["000403542900022"]},"year":"2017","intvolume":"       137","month":"12","alternative_title":["Methods in Cell Biology"],"date_published":"2017-12-01T00:00:00Z","acknowledgement":"Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell).","date_updated":"2023-09-20T11:16:30Z","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/bs.mcb.2016.03.036","publication":"Cytokinesis","isi":1,"ec_funded":1,"oa_version":"None","volume":137,"date_created":"2018-12-11T11:50:45Z","status":"public","day":"01"},{"year":"2017","page":"130-137","external_id":{"pmid":["29255257"]},"date_updated":"2023-10-18T07:21:53Z","keyword":["Genetics"],"issue":"1","oa":1,"intvolume":"        50","month":"12","date_published":"2017-12-18T00:00:00Z","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","oa_version":"None","doi":"10.1038/s41588-017-0008-5","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/","open_access":"1"}],"publication":"Nature Genetics","date_created":"2023-01-16T09:18:05Z","status":"public","day":"18","pmid":1,"volume":50,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"XiFe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","author":[{"first_name":"James","last_name":"Walker","full_name":"Walker, James"},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"first_name":"Jingyi","last_name":"Zhang","full_name":"Zhang, Jingyi"},{"last_name":"Aldridge","first_name":"Billy","full_name":"Aldridge, Billy"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"first_name":"James D.","last_name":"Higgins","full_name":"Higgins, James D."},{"orcid":"0000-0002-4008-1234","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi"}],"publisher":"Nature Research","publication_status":"published","_id":"12193","quality_controlled":"1","citation":{"mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>.","apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., &#38; Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>. Nature Research, 2017. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>.","short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137.","ieee":"J. Walker <i>et al.</i>, “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” <i>Nature Genetics</i>, vol. 50, no. 1. Nature Research, pp. 130–137, 2017.","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. 2017;50(1):130-137. doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>"},"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"type":"journal_article","abstract":[{"text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.","lang":"eng"}],"scopus_import":"1"},{"publication_status":"published","quality_controlled":"1","_id":"1228","file_date_updated":"2020-07-14T12:44:39Z","type":"journal_article","abstract":[{"text":"Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD.","lang":"eng"}],"scopus_import":"1","citation":{"apa":"Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>","mla":"Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>.","ama":"Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. 2017;45(1):45-57. doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>","short":"U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.","ista":"Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57.","ieee":"U. Sauerzopf <i>et al.</i>, “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” <i>European Journal of Neuroscience</i>, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017.","chicago":"Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>."},"pubrep_id":"738","article_type":"review","language":[{"iso":"eng"}],"publist_id":"6106","department":[{"_id":"GaNo"}],"article_processing_charge":"No","file":[{"date_created":"2018-12-12T10:10:48Z","date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","checksum":"c572cf02be8fbb7020cfcfb892182e4c","relation":"main_file","access_level":"open_access","creator":"system","file_size":169145,"content_type":"application/pdf","file_id":"4838"}],"title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Ulrich","last_name":"Sauerzopf","full_name":"Sauerzopf, Ulrich"},{"full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"},{"last_name":"Niello","first_name":"Marco","full_name":"Niello, Marco"},{"full_name":"Weidenauer, Ana","last_name":"Weidenauer","first_name":"Ana"},{"first_name":"Nicole","last_name":"Praschak Rieder","full_name":"Praschak Rieder, Nicole"},{"full_name":"Sitte, Harald","last_name":"Sitte","first_name":"Harald"},{"first_name":"Matthaeus","last_name":"Willeit","full_name":"Willeit, Matthaeus"}],"publisher":"Wiley-Blackwell","has_accepted_license":"1","isi":1,"oa_version":"Published Version","doi":"10.1111/ejn.13418","publication":"European Journal of Neuroscience","day":"01","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:50:50Z","ddc":["616"],"pmid":1,"volume":45,"year":"2017","external_id":{"isi":["000392487100005"],"pmid":["27690184"]},"page":"45 - 57","issue":"1","oa":1,"date_updated":"2023-09-20T11:16:01Z","acknowledgement":"This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.","month":"01","intvolume":"        45","date_published":"2017-01-01T00:00:00Z"},{"oa":1,"title":"Scientific Computing at IST Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"full_name":"Kiss, Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","first_name":"Janos","last_name":"Kiss"}],"file":[{"date_updated":"2023-05-16T07:20:50Z","date_created":"2023-05-16T07:20:50Z","file_name":"2017_AHPC_Schloegl.pdf","success":1,"relation":"main_file","checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6","access_level":"open_access","file_size":1005486,"creator":"dernst","file_id":"12969","content_type":"application/pdf"}],"date_updated":"2023-05-16T07:22:23Z","publisher":"FSP Scientific Computing","date_published":"2017-03-03T00:00:00Z","month":"03","has_accepted_license":"1","year":"2017","language":[{"iso":"eng"}],"conference":{"end_date":"2017-03-03","start_date":"2017-03-01","name":"AHPC: Austrian HPC Meeting","location":"Grundlsee, Austria"},"department":[{"_id":"ScienComp"}],"article_processing_charge":"No","page":"28","status":"public","day":"03","_id":"12905","ddc":["000"],"date_created":"2023-05-05T12:58:53Z","type":"conference_abstract","file_date_updated":"2023-05-16T07:20:50Z","citation":{"mla":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” <i>AHPC17 – Austrian HPC Meeting 2017</i>, FSP Scientific Computing, 2017, p. 28.","apa":"Schlögl, A., &#38; Kiss, J. (2017). Scientific Computing at IST Austria. In <i>AHPC17 – Austrian HPC Meeting 2017</i> (p. 28). Grundlsee, Austria: FSP Scientific Computing.","chicago":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In <i>AHPC17 – Austrian HPC Meeting 2017</i>, 28. FSP Scientific Computing, 2017.","ista":"Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28.","ieee":"A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in <i>AHPC17 – Austrian HPC Meeting 2017</i>, Grundlsee, Austria, 2017, p. 28.","short":"A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","ama":"Schlögl A, Kiss J. Scientific Computing at IST Austria. In: <i>AHPC17 – Austrian HPC Meeting 2017</i>. FSP Scientific Computing; 2017:28."},"oa_version":"Published Version","publication":"AHPC17 – Austrian HPC Meeting 2017","publication_status":"published","main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf","open_access":"1"}]},{"date_published":"2017-03-01T00:00:00Z","intvolume":"        84","month":"03","oa":1,"date_updated":"2023-09-20T11:15:31Z","external_id":{"isi":["000388430000011"]},"page":"144 - 170","year":"2017","volume":84,"status":"public","day":"01","ddc":["004","006"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:51:12Z","publication":"Journal of Computer and System Sciences","doi":"10.1016/j.jcss.2016.09.009","oa_version":"Published Version","ec_funded":1,"isi":1,"related_material":{"record":[{"id":"2305","relation":"earlier_version","status":"public"}]},"publisher":"Elsevier","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Trading performance for stability in Markov decision processes","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Forejt, Vojtěch","first_name":"Vojtěch","last_name":"Forejt"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"}],"file":[{"file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","date_created":"2018-12-12T10:11:30Z","date_updated":"2020-07-14T12:44:42Z","file_id":"4885","content_type":"application/pdf","file_size":708657,"creator":"system","access_level":"open_access","checksum":"91271b23cf884d7c06d33bef0cd623b1","relation":"main_file"}],"department":[{"_id":"KrCh"}],"publist_id":"6009","article_processing_charge":"No","pubrep_id":"717","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints."}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:44:42Z","citation":{"mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>, vol. 84, Elsevier, 2017, pp. 144–70, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>.","apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2017). Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>.","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” <i>Journal of Computer and System Sciences</i>, vol. 84. Elsevier, pp. 144–170, 2017.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. 2017;84:144-170. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>"},"quality_controlled":"1","_id":"1294","publication_status":"published","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}]},{"publisher":"Dryad","month":"01","date_published":"2017-01-14T00:00:00Z","author":[{"full_name":"Riccio, Paul","last_name":"Riccio","first_name":"Paul"},{"last_name":"Cebrián","first_name":"Christina","full_name":"Cebrián, Christina"},{"full_name":"Zong, Hui","last_name":"Zong","first_name":"Hui"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"last_name":"Costantini","first_name":"Frank","full_name":"Costantini, Frank"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","date_updated":"2022-08-25T13:34:55Z","department":[{"_id":"SiHi"}],"article_processing_charge":"No","year":"2017","type":"research_data_reference","abstract":[{"text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.","lang":"eng"}],"citation":{"short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.” Dryad, 2017.","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis, Dryad, <a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>.","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>","chicago":"Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.pk16b\">https://doi.org/10.5061/dryad.pk16b</a>.","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., &#38; Costantini, F. (2017). Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. Dryad. <a href=\"https://doi.org/10.5061/dryad.pk16b\">https://doi.org/10.5061/dryad.pk16b</a>","mla":"Riccio, Paul, et al. <i>Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>."},"day":"14","status":"public","date_created":"2021-07-23T09:39:34Z","_id":"9707","main_file_link":[{"url":"https://doi.org/10.5061/dryad.pk16b","open_access":"1"}],"doi":"10.5061/dryad.pk16b","oa_version":"Published Version","related_material":{"record":[{"id":"9702","status":"deleted","relation":"used_in_publication"}]}},{"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1197"}]},"doi":"10.5061/dryad.1f1rc","main_file_link":[{"url":"https://doi.org/10.5061/dryad.1f1rc","open_access":"1"}],"day":"18","status":"public","_id":"9709","date_created":"2021-07-23T11:34:34Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina."}],"citation":{"mla":"Prentice, Jason, et al. <i>Data from: Error-Robust Modes of the Retinal Population Code</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., &#38; Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>.","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, <a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>."},"year":"2017","department":[{"_id":"GaTk"}],"article_processing_charge":"No","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Prentice","first_name":"Jason","full_name":"Prentice, Jason"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"first_name":"Mark","last_name":"Ioffe","full_name":"Ioffe, Mark"},{"first_name":"Adrianna","last_name":"Loback","full_name":"Loback, Adrianna"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"title":"Data from: Error-robust modes of the retinal population code","date_updated":"2023-02-21T16:34:41Z","publisher":"Dryad","month":"10","date_published":"2017-10-18T00:00:00Z"},{"year":"2017","article_processing_charge":"No","department":[{"_id":"NiBa"}],"date_updated":"2025-05-28T11:56:59Z","title":"Data for: Establishment in a new habitat by polygenic adaptation","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"date_published":"2017-12-29T00:00:00Z","month":"12","publisher":"Mendeley Data","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"564"}]},"oa_version":"Published Version","doi":"10.17632/nw68fxzjpm.1","main_file_link":[{"url":"https://doi.org/10.17632/nw68fxzjpm.1","open_access":"1"}],"_id":"9842","date_created":"2021-08-09T13:18:55Z","status":"public","day":"29","citation":{"mla":"Etheridge, Alison, and Nicholas H. Barton. <i>Data for: Establishment in a New Habitat by Polygenic Adaptation</i>. Mendeley Data, 2017, doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>.","apa":"Etheridge, A., &#38; Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>","chicago":"Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>.","ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>.","short":"A. Etheridge, N.H. Barton, (2017).","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>"},"abstract":[{"text":"Mathematica notebooks used to generate figures.","lang":"eng"}],"type":"research_data_reference"},{"doi":"10.1371/journal.pgen.1007122.s018","related_material":{"record":[{"id":"541","relation":"used_in_publication","status":"public"}]},"oa_version":"Published Version","citation":{"chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">https://doi.org/10.1371/journal.pgen.1007122.s018</a>.","ieee":"N. Nikolic <i>et al.</i>, “Source data for figures and tables.” Public Library of Science, 2017.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">10.1371/journal.pgen.1007122.s018</a>.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">10.1371/journal.pgen.1007122.s018</a>","mla":"Nikolic, Nela, et al. <i>Source Data for Figures and Tables</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">10.1371/journal.pgen.1007122.s018</a>.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Source data for figures and tables. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">https://doi.org/10.1371/journal.pgen.1007122.s018</a>"},"type":"research_data_reference","date_created":"2021-08-09T13:27:16Z","_id":"9844","day":"18","status":"public","article_processing_charge":"No","department":[{"_id":"CaGu"}],"year":"2017","month":"12","date_published":"2017-12-18T00:00:00Z","publisher":"Public Library of Science","date_updated":"2023-02-23T12:25:04Z","title":"Source data for figures and tables","author":[{"full_name":"Nikolic, Nela","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","last_name":"Nikolic"},{"full_name":"Schreiber, Frank","first_name":"Frank","last_name":"Schreiber"},{"last_name":"Dal Co","first_name":"Alma","full_name":"Dal Co, Alma"},{"last_name":"Kiviet","first_name":"Daniel","full_name":"Kiviet, Daniel"},{"last_name":"Bergmiller","orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"full_name":"Littmann, Sten","first_name":"Sten","last_name":"Littmann"},{"full_name":"Kuypers, Marcel","last_name":"Kuypers","first_name":"Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"citation":{"mla":"Nikolic, Nela, et al. <i>Mathematical Model</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">10.1371/journal.pgen.1007122.s017</a>.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">https://doi.org/10.1371/journal.pgen.1007122.s017</a>","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">https://doi.org/10.1371/journal.pgen.1007122.s017</a>.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">10.1371/journal.pgen.1007122.s017</a>","ieee":"N. 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