[{"publication_identifier":{"issn":["13697412"]},"citation":{"mla":"Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:<a href=\"https://doi.org/10.1111/rssb.12217\">10.1111/rssb.12217</a>.","apa":"Zwiernik, P., Uhler, C., &#38; Richards, D. (2017). Maximum likelihood estimation for linear Gaussian covariance models. <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/rssb.12217\">https://doi.org/10.1111/rssb.12217</a>","chicago":"Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/rssb.12217\">https://doi.org/10.1111/rssb.12217</a>.","ama":"Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear Gaussian covariance models. <i>Journal of the Royal Statistical Society Series B: Statistical Methodology</i>. 2017;79(4):1269-1292. doi:<a href=\"https://doi.org/10.1111/rssb.12217\">10.1111/rssb.12217</a>","short":"P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society. Series B: Statistical Methodology 79 (2017) 1269–1292.","ista":"Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. 79(4), 1269–1292.","ieee":"P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for linear Gaussian covariance models,” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292, 2017."},"scopus_import":"1","abstract":[{"text":"We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ&gt;1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd.","lang":"eng"}],"type":"journal_article","_id":"1208","quality_controlled":"1","project":[{"name":"Gaussian Graphical Models: Theory and Applications","_id":"2530CA10-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y 903-N35"}],"publication_status":"published","publisher":"Wiley-Blackwell","title":"Maximum likelihood estimation for linear Gaussian covariance models","author":[{"first_name":"Piotr","last_name":"Zwiernik","full_name":"Zwiernik, Piotr"},{"last_name":"Uhler","orcid":"0000-0002-7008-0216","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline"},{"first_name":"Donald","last_name":"Richards","full_name":"Richards, Donald"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","publist_id":"6142","department":[{"_id":"CaUh"}],"language":[{"iso":"eng"}],"volume":79,"date_created":"2018-12-11T11:50:43Z","day":"01","status":"public","publication":"Journal of the Royal Statistical Society. Series B: Statistical Methodology","doi":"10.1111/rssb.12217","main_file_link":[{"url":"https://arxiv.org/abs/1408.5604","open_access":"1"}],"oa_version":"Submitted Version","isi":1,"date_published":"2017-09-01T00:00:00Z","month":"09","intvolume":"        79","date_updated":"2023-09-20T11:17:21Z","oa":1,"issue":"4","page":"1269 - 1292","external_id":{"isi":["000411712300012"]},"year":"2017"},{"publication_status":"published","citation":{"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>.","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>","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.","short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 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.","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>.","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>"},"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"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:39Z","type":"journal_article","_id":"1211","quality_controlled":"1","department":[{"_id":"BjHo"}],"publist_id":"6136","language":[{"iso":"eng"}],"pubrep_id":"782","has_accepted_license":"1","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cvitanović","first_name":"Predrag","full_name":"Cvitanović, Predrag"}],"title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","file":[{"access_level":"open_access","relation":"main_file","checksum":"3e971d09eb167761aa0888ed415b0056","file_size":2820207,"creator":"system","file_id":"5319","content_type":"application/pdf","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:18:01Z","file_name":"IST-2017-782-v1+1_BudCvi15.pdf"}],"publication":"Journal of Statistical Physics","doi":"10.1007/s10955-016-1672-z","oa_version":"Submitted Version","volume":167,"date_created":"2018-12-11T11:50:44Z","ddc":["530"],"day":"01","status":"public","page":"636-655","year":"2017","date_published":"2017-05-01T00:00:00Z","month":"05","intvolume":"       167","acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","date_updated":"2021-01-12T06:49:07Z","oa":1,"issue":"3-4"},{"year":"2017","page":"355 - 370","external_id":{"isi":["000403542900022"]},"date_updated":"2023-09-20T11:16:30Z","acknowledged_ssus":[{"_id":"Bio"}],"intvolume":"       137","month":"12","date_published":"2017-12-01T00:00:00Z","alternative_title":["Methods in Cell Biology"],"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).","isi":1,"oa_version":"None","ec_funded":1,"doi":"10.1016/bs.mcb.2016.03.036","publication":"Cytokinesis","date_created":"2018-12-11T11:50:45Z","status":"public","day":"01","volume":137,"language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"6134","department":[{"_id":"MaLo"}],"author":[{"first_name":"Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers","publisher":"Academic Press","project":[{"grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publication_status":"published","editor":[{"full_name":"Echard, Arnaud ","last_name":"Echard","first_name":"Arnaud "}],"_id":"1213","quality_controlled":"1","publication_identifier":{"issn":["0091679X"]},"citation":{"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>","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>.","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.","short":"N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press, 2017, pp. 355–370.","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.","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>","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>."},"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."}]},{"date_created":"2023-01-16T09:18:05Z","day":"18","status":"public","volume":50,"pmid":1,"oa_version":"None","publication":"Nature Genetics","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/"}],"doi":"10.1038/s41588-017-0008-5","keyword":["Genetics"],"date_updated":"2023-10-18T07:21:53Z","oa":1,"issue":"1","date_published":"2017-12-18T00:00:00Z","month":"12","intvolume":"        50","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.","year":"2017","external_id":{"pmid":["29255257"]},"page":"130-137","_id":"12193","quality_controlled":"1","citation":{"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>","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.","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.","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>.","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>","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>."},"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"abstract":[{"lang":"eng","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."}],"scopus_import":"1","type":"journal_article","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","author":[{"full_name":"Walker, James","first_name":"James","last_name":"Walker"},{"last_name":"Gao","first_name":"Hongbo","full_name":"Gao, Hongbo"},{"full_name":"Zhang, Jingyi","last_name":"Zhang","first_name":"Jingyi"},{"full_name":"Aldridge, Billy","last_name":"Aldridge","first_name":"Billy"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"last_name":"Higgins","first_name":"James D.","full_name":"Higgins, James D."},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}],"publisher":"Nature Research","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"XiFe"}]},{"oa_version":"Published Version","isi":1,"publication":"European Journal of Neuroscience","doi":"10.1111/ejn.13418","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"],"day":"01","status":"public","volume":45,"pmid":1,"year":"2017","external_id":{"isi":["000392487100005"],"pmid":["27690184"]},"page":"45 - 57","date_updated":"2023-09-20T11:16:01Z","oa":1,"issue":"1","date_published":"2017-01-01T00:00:00Z","intvolume":"        45","month":"01","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.","publication_status":"published","_id":"1228","quality_controlled":"1","citation":{"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.","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>","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>.","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>."},"abstract":[{"lang":"eng","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."}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:44:39Z","language":[{"iso":"eng"}],"article_type":"review","pubrep_id":"738","article_processing_charge":"No","department":[{"_id":"GaNo"}],"publist_id":"6106","author":[{"last_name":"Sauerzopf","first_name":"Ulrich","full_name":"Sauerzopf, Ulrich"},{"full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco"},{"full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178"},{"full_name":"Niello, Marco","last_name":"Niello","first_name":"Marco"},{"first_name":"Ana","last_name":"Weidenauer","full_name":"Weidenauer, Ana"},{"first_name":"Nicole","last_name":"Praschak Rieder","full_name":"Praschak Rieder, Nicole"},{"full_name":"Sitte, Harald","last_name":"Sitte","first_name":"Harald"},{"full_name":"Willeit, Matthaeus","first_name":"Matthaeus","last_name":"Willeit"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","file":[{"relation":"main_file","access_level":"open_access","checksum":"c572cf02be8fbb7020cfcfb892182e4c","content_type":"application/pdf","file_id":"4838","file_size":169145,"creator":"system","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:10:48Z","file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf"}],"has_accepted_license":"1","publisher":"Wiley-Blackwell"},{"oa_version":"Preprint","publication":"Nature Physics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.03530"}],"doi":"10.1038/nphys4194","date_created":"2018-12-11T11:44:45Z","day":"24","status":"public","volume":13,"year":"2017","external_id":{"arxiv":["1705.03530"]},"page":"1095 - 1099","date_updated":"2021-01-12T06:49:14Z","oa":1,"issue":"11","date_published":"2017-07-24T00:00:00Z","month":"07","intvolume":"        13","acknowledgement":"A.S. acknowledges funding from the Delta Institute for Theoretical Physics and the hospitality of the IBS Center for Theoretical Physics of Complex Systems, Daejeon, South Korea. We acknowledge funding from the Netherlands Organisation for Scientific Research through grants VICI No. NWO-680-47-609 (M.v.H. and S.R.W.), VENI No. NWO-680-47-445 (C.C.) and VENI No. NWO-680-47-453 (S.R.W.).","publication_status":"published","_id":"123","quality_controlled":"1","citation":{"mla":"Waitukaitis, Scott R., et al. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” <i>Nature Physics</i>, vol. 13, no. 11, Nature Publishing Group, 2017, pp. 1095–99, doi:<a href=\"https://doi.org/10.1038/nphys4194\">10.1038/nphys4194</a>.","apa":"Waitukaitis, S. R., Zuiderwijk, A., Souslov, A., Coulais, C., &#38; Van Hecke, M. (2017). Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys4194\">https://doi.org/10.1038/nphys4194</a>","chicago":"Waitukaitis, Scott R, Antal Zuiderwijk, Anton Souslov, Corentin Coulais, and Martin Van Hecke. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” <i>Nature Physics</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/nphys4194\">https://doi.org/10.1038/nphys4194</a>.","ama":"Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. <i>Nature Physics</i>. 2017;13(11):1095-1099. doi:<a href=\"https://doi.org/10.1038/nphys4194\">10.1038/nphys4194</a>","short":"S.R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, M. Van Hecke, Nature Physics 13 (2017) 1095–1099.","ieee":"S. R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, and M. Van Hecke, “Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing,” <i>Nature Physics</i>, vol. 13, no. 11. Nature Publishing Group, pp. 1095–1099, 2017.","ista":"Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. 2017. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. 13(11), 1095–1099."},"extern":"1","abstract":[{"lang":"eng","text":"The Leidenfrost effect occurs when an object near a hot surface vaporizes rapidly enough to lift itself up and hover. Although well understood for liquids and stiff sublimable solids, nothing is known about the effect with materials whose stiffness lies between these extremes. Here we introduce a new phenomenon that occurs with vaporizable soft solids - the elastic Leidenfrost effect. By dropping hydrogel spheres onto hot surfaces we find that, rather than hovering, they energetically bounce several times their diameter for minutes at a time. With high-speed video during a single impact, we uncover high-frequency microscopic gap dynamics at the sphere/substrate interface. We show how these otherwise-hidden agitations constitute work cycles that harvest mechanical energy from the vapour and sustain the bouncing. Our findings suggest a new strategy for injecting mechanical energy into a widely used class of soft materials, with potential relevance to fields such as active matter, soft robotics and microfluidics."}],"arxiv":1,"type":"journal_article","language":[{"iso":"eng"}],"publist_id":"7931","author":[{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R"},{"first_name":"Antal","last_name":"Zuiderwijk","full_name":"Zuiderwijk, Antal"},{"full_name":"Souslov, Anton","last_name":"Souslov","first_name":"Anton"},{"last_name":"Coulais","first_name":"Corentin","full_name":"Coulais, Corentin"},{"first_name":"Martin","last_name":"Van Hecke","full_name":"Van Hecke, Martin"}],"title":"Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group"},{"oa":1,"date_updated":"2023-02-20T07:57:24Z","intvolume":"     10328","month":"05","date_published":"2017-05-24T00:00:00Z","alternative_title":["LNCS"],"year":"2017","conference":{"name":"IPCO: Integer Programming and Combinatorial Optimization","start_date":"2017-06-26","end_date":"2017-06-28","location":"Waterloo, ON, Canada"},"page":"86-98","external_id":{"arxiv":["1611.00198"]},"day":"24","status":"public","date_created":"2023-02-20T07:52:31Z","volume":10328,"oa_version":"Preprint","doi":"10.1007/978-3-319-59250-3_8","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.00198"}],"publication":"19th International Conference on Integer Programming and Combinatorial Optimization","author":[{"last_name":"Bhattacharya","first_name":"Sayan","full_name":"Bhattacharya, Sayan"},{"last_name":"Chakrabarty","first_name":"Deeparnab","full_name":"Chakrabarty, Deeparnab"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530"}],"title":"Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","_id":"12571","type":"conference","arxiv":1,"scopus_import":"1","abstract":[{"text":"We consider the problems of maintaining approximate maximum matching and minimum vertex cover in a dynamic graph. Starting with the seminal work of Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. Very recently, extending the framework of Baswana, Gupta and Sen [FOCS 2011], Solomon [FOCS 2016] gave a randomized 2-approximation dynamic algorithm for this problem that has amortized update time of O(1) with high probability. We consider the natural open question of derandomizing this result. We present a new deterministic fully dynamic algorithm that maintains a O(1)-approximate minimum vertex cover and maximum fractional matching, with an amortized update time of O(1). Previously, the best deterministic algorithm for this problem was due to Bhattacharya, Henzinger and Italiano [SODA 2015]; it had an approximation ratio of (2+ϵ) and an amortized update time of O(logn/ϵ2). Our result can be generalized to give a fully dynamic O(f3)-approximation algorithm with O(f2) amortized update time for the hypergraph vertex cover and fractional matching problems, where every hyperedge has at most f vertices.","lang":"eng"}],"publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["9783319592497"],"eisbn":["9783319592503"]},"extern":"1","citation":{"ieee":"S. Bhattacharya, D. Chakrabarty, and M. H. Henzinger, “Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time,” in <i>19th International Conference on Integer Programming and Combinatorial Optimization</i>, Waterloo, ON, Canada, 2017, vol. 10328, pp. 86–98.","ista":"Bhattacharya S, Chakrabarty D, Henzinger MH. 2017. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. 19th International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 10328, 86–98.","short":"S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, in:, 19th International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2017, pp. 86–98.","ama":"Bhattacharya S, Chakrabarty D, Henzinger MH. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In: <i>19th International Conference on Integer Programming and Combinatorial Optimization</i>. Vol 10328. Springer Nature; 2017:86-98. doi:<a href=\"https://doi.org/10.1007/978-3-319-59250-3_8\">10.1007/978-3-319-59250-3_8</a>","chicago":"Bhattacharya, Sayan, Deeparnab Chakrabarty, and Monika H Henzinger. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” In <i>19th International Conference on Integer Programming and Combinatorial Optimization</i>, 10328:86–98. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-59250-3_8\">https://doi.org/10.1007/978-3-319-59250-3_8</a>.","apa":"Bhattacharya, S., Chakrabarty, D., &#38; Henzinger, M. H. (2017). Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In <i>19th International Conference on Integer Programming and Combinatorial Optimization</i> (Vol. 10328, pp. 86–98). Waterloo, ON, Canada: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-59250-3_8\">https://doi.org/10.1007/978-3-319-59250-3_8</a>","mla":"Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” <i>19th International Conference on Integer Programming and Combinatorial Optimization</i>, vol. 10328, Springer Nature, 2017, pp. 86–98, doi:<a href=\"https://doi.org/10.1007/978-3-319-59250-3_8\">10.1007/978-3-319-59250-3_8</a>."},"publication_status":"published"},{"publisher":"Cambridge University Press","author":[{"last_name":"SHAW","first_name":"THOMAS E.","full_name":"SHAW, THOMAS E."},{"full_name":"BROCK, BEN W.","last_name":"BROCK","first_name":"BEN W."},{"full_name":"AYALA, ÁLVARO","first_name":"ÁLVARO","last_name":"AYALA"},{"last_name":"RUTTER","first_name":"NICK","full_name":"RUTTER, NICK"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","abstract":[{"text":"The spatio-temporal distribution of air temperature over mountain glaciers can demonstrate complex patterns, yet it is often represented simplistically using linear vertical temperature gradients (VTGs) extrapolated from off-glacier locations. We analyse a network of centreline and lateral air temperature observations at Tsanteleina Glacier, Italy, during summer 2015. On average, VTGs are steep (&lt;−0.0065 °C m<jats:sup>−1</jats:sup>), but they are shallow under warm ambient conditions when the correlation between air temperature and elevation becomes weaker. Published along-flowline temperature distribution methods explain centreline observations well, including warming on the lower glacier tongue, but cannot estimate lateral temperature variability. Application of temperature distribution methods improves simulation of melt rates (RMSE) in an energy-balance model by up to 36% compared to the environmental lapse rate extrapolated from an off-glacier station. However, results suggest that model parameters are not easily transferable to glaciers with a small fetch without recalibration. Such methods have potential to improve estimates of temperature across a glacier, but their parameter transferability should be further linked to the glacier and atmospheric characteristics. Furthermore, ‘cold spots’, which can be &gt;2°C cooler than expected for their elevation, whose occurrence is not predicted by the temperature distribution models, are identified at one-quarter of the measurement sites.","lang":"eng"}],"publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"extern":"1","citation":{"mla":"SHAW, THOMAS E., et al. “Centreline and Cross-Glacier Air Temperature Variability on an Alpine Glacier: Assessing Temperature Distribution Methods and Their Influence on Melt Model Calculations.” <i>Journal of Glaciology</i>, vol. 63, no. 242, Cambridge University Press, 2017, pp. 973–88, doi:<a href=\"https://doi.org/10.1017/jog.2017.65\">10.1017/jog.2017.65</a>.","apa":"SHAW, T. E., BROCK, B. W., AYALA, Á., RUTTER, N., &#38; Pellicciotti, F. (2017). Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations. <i>Journal of Glaciology</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jog.2017.65\">https://doi.org/10.1017/jog.2017.65</a>","chicago":"SHAW, THOMAS E., BEN W. BROCK, ÁLVARO AYALA, NICK RUTTER, and Francesca Pellicciotti. “Centreline and Cross-Glacier Air Temperature Variability on an Alpine Glacier: Assessing Temperature Distribution Methods and Their Influence on Melt Model Calculations.” <i>Journal of Glaciology</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jog.2017.65\">https://doi.org/10.1017/jog.2017.65</a>.","ama":"SHAW TE, BROCK BW, AYALA Á, RUTTER N, Pellicciotti F. Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations. <i>Journal of Glaciology</i>. 2017;63(242):973-988. doi:<a href=\"https://doi.org/10.1017/jog.2017.65\">10.1017/jog.2017.65</a>","ista":"SHAW TE, BROCK BW, AYALA Á, RUTTER N, Pellicciotti F. 2017. Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations. Journal of Glaciology. 63(242), 973–988.","short":"T.E. SHAW, B.W. BROCK, Á. AYALA, N. RUTTER, F. Pellicciotti, Journal of Glaciology 63 (2017) 973–988.","ieee":"T. E. SHAW, B. W. BROCK, Á. AYALA, N. RUTTER, and F. Pellicciotti, “Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations,” <i>Journal of Glaciology</i>, vol. 63, no. 242. Cambridge University Press, pp. 973–988, 2017."},"quality_controlled":"1","_id":"12608","publication_status":"published","intvolume":"        63","month":"12","date_published":"2017-12-01T00:00:00Z","issue":"242","oa":1,"date_updated":"2023-02-28T11:30:34Z","keyword":["Earth-Surface Processes"],"page":"973-988","year":"2017","volume":63,"day":"01","status":"public","date_created":"2023-02-20T08:13:47Z","doi":"10.1017/jog.2017.65","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/jog.2017.65"}],"publication":"Journal of Glaciology","oa_version":"Published Version"},{"year":"2017","page":"803-822","date_updated":"2023-02-28T11:28:19Z","keyword":["Earth-Surface Processes"],"issue":"241","oa":1,"month":"10","intvolume":"        63","date_published":"2017-10-01T00:00:00Z","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1017/jog.2017.46","open_access":"1"}],"doi":"10.1017/jog.2017.46","publication":"Journal of Glaciology","date_created":"2023-02-20T08:13:53Z","day":"01","status":"public","volume":63,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile","author":[{"full_name":"AYALA, A.","last_name":"AYALA","first_name":"A."},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"full_name":"PELEG, N.","last_name":"PELEG","first_name":"N."},{"first_name":"P.","last_name":"BURLANDO","full_name":"BURLANDO, P."}],"publisher":"Cambridge University Press","publication_status":"published","_id":"12609","quality_controlled":"1","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"citation":{"ama":"AYALA A, Pellicciotti F, PELEG N, BURLANDO P. Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile. <i>Journal of Glaciology</i>. 2017;63(241):803-822. doi:<a href=\"https://doi.org/10.1017/jog.2017.46\">10.1017/jog.2017.46</a>","ieee":"A. AYALA, F. Pellicciotti, N. PELEG, and P. BURLANDO, “Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile,” <i>Journal of Glaciology</i>, vol. 63, no. 241. Cambridge University Press, pp. 803–822, 2017.","ista":"AYALA A, Pellicciotti F, PELEG N, BURLANDO P. 2017. Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile. Journal of Glaciology. 63(241), 803–822.","short":"A. AYALA, F. Pellicciotti, N. PELEG, P. BURLANDO, Journal of Glaciology 63 (2017) 803–822.","chicago":"AYALA, A., Francesca Pellicciotti, N. PELEG, and P. BURLANDO. “Melt and Surface Sublimation across a Glacier in a Dry Environment: Distributed Energy-Balance Modelling of Juncal Norte Glacier, Chile.” <i>Journal of Glaciology</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jog.2017.46\">https://doi.org/10.1017/jog.2017.46</a>.","apa":"AYALA, A., Pellicciotti, F., PELEG, N., &#38; BURLANDO, P. (2017). Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile. <i>Journal of Glaciology</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jog.2017.46\">https://doi.org/10.1017/jog.2017.46</a>","mla":"AYALA, A., et al. “Melt and Surface Sublimation across a Glacier in a Dry Environment: Distributed Energy-Balance Modelling of Juncal Norte Glacier, Chile.” <i>Journal of Glaciology</i>, vol. 63, no. 241, Cambridge University Press, 2017, pp. 803–22, doi:<a href=\"https://doi.org/10.1017/jog.2017.46\">10.1017/jog.2017.46</a>."},"extern":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Previous estimates of melt and surface sublimation on glaciers of the subtropical semiarid Andes (29–34°S) have been obtained at few specific locations, but it is not clear how ablation components vary across the entire extent of a glacier in this dry environment. Here, we simulate the distributed energy and mass balance of Juncal Norte Glacier (33°S) during a 2-month summer period. Forcing fields of near-surface air temperature and wind speed are generated using two methods accounting for the main physical processes that shape their spatial variations. Simulated meteorological variables and ablation agree well with observations on the glacier tongue and reveal complex patterns of energy and mass fluxes. Ablation decreases from 70 mm w.e. d<jats:sup>−1</jats:sup> at the low-albedo glacier terminus (~3000 m), where almost 100% of total ablation corresponds to melt, to &lt;5 mm w.e. d<jats:sup>−1</jats:sup> at wind-exposed, strong-radiated sites above 5500 m, where surface sublimation represents &gt;75% of total ablation. Our simulations provide the first glacier-scale estimates of ablation components on a glacier in the study region and better reproduce the observed and expected spatial variations of melt and surface sublimation, in comparison with more simple assumptions, such as linear gradients and uniform wind speeds."}],"scopus_import":"1"},{"doi":"10.3389/feart.2017.00069","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3389/feart.2017.00069"}],"publication":"Frontiers in Earth Science","oa_version":"Published Version","volume":5,"day":"21","status":"public","date_created":"2023-02-20T08:14:04Z","year":"2017","article_number":"69","intvolume":"         5","month":"09","date_published":"2017-09-21T00:00:00Z","oa":1,"date_updated":"2023-02-28T11:13:23Z","keyword":["General Earth and Planetary Sciences"],"publication_status":"published","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"The hydrological systems of heavily-downwasted debris-covered glaciers differ from those of clean-ice glaciers due to the hummocky surface and debris mantle of such glaciers, leading to a relatively limited understanding of drainage pathways. Supraglacial ponds represent sinks within the discontinuous supraglacial drainage system, and occasionally drain englacially. To assess pond dynamics, we made pond water level measurements on Lirung Glacier, Nepal, during May and October of 2013 and 2014. Simultaneously, aerial, satellite, and terrestrial orthoimages and digital elevation models were obtained, providing snapshots of the ponds and their surroundings. We performed a DEM-based analysis of the glacier's closed surface catchments to identify surface drainage pathways and englacial drainage points, and compared this to field observations of surface and near-surface water flow. The total ponded area was higher in the pre-monsoon than post-monsoon, with individual ponds filling and draining seasonally associated with the surface exposure of englacial conduit segments. We recorded four pond drainage events, all of which occurred gradually (duration of weeks), observed diurnal fluctuations indicative of varying water supply and outflow discharge, and we documented instances of interaction between distant ponds. The DEM drainage analysis identified numerous sinks >3 m in depth across the glacier surface, few of which exhibited ponds (23%), while the field survey highlighted instances of surface water only explicable via englacial routes. Taken together, our observations provide evidence for widespread supraglacial-englacial connectivity of meltwater drainage paths. Results suggest that successive englacial conduit collapse events, themselves likely driven by supraglacial pond drainage, cause the glacier surface drainage system to evolve into a configuration following relict englacial conduit systems. Within this system, ponds form in depressions of reduced drainage efficiency and link the supraglacial and englacial drainage networks."}],"citation":{"apa":"Miles, E. S., Steiner, J., Willis, I., Buri, P., Immerzeel, W. W., Chesnokova, A., &#38; Pellicciotti, F. (2017). Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal. <i>Frontiers in Earth Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/feart.2017.00069\">https://doi.org/10.3389/feart.2017.00069</a>","mla":"Miles, Evan S., et al. “Pond Dynamics and Supraglacial-Englacial Connectivity on Debris-Covered Lirung Glacier, Nepal.” <i>Frontiers in Earth Science</i>, vol. 5, 69, Frontiers Media, 2017, doi:<a href=\"https://doi.org/10.3389/feart.2017.00069\">10.3389/feart.2017.00069</a>.","ama":"Miles ES, Steiner J, Willis I, et al. Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal. <i>Frontiers in Earth Science</i>. 2017;5. doi:<a href=\"https://doi.org/10.3389/feart.2017.00069\">10.3389/feart.2017.00069</a>","ieee":"E. S. Miles <i>et al.</i>, “Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal,” <i>Frontiers in Earth Science</i>, vol. 5. Frontiers Media, 2017.","short":"E.S. Miles, J. Steiner, I. Willis, P. Buri, W.W. Immerzeel, A. Chesnokova, F. Pellicciotti, Frontiers in Earth Science 5 (2017).","ista":"Miles ES, Steiner J, Willis I, Buri P, Immerzeel WW, Chesnokova A, Pellicciotti F. 2017. Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal. Frontiers in Earth Science. 5, 69.","chicago":"Miles, Evan S., Jakob Steiner, Ian Willis, Pascal Buri, Walter W. Immerzeel, Anna Chesnokova, and Francesca Pellicciotti. “Pond Dynamics and Supraglacial-Englacial Connectivity on Debris-Covered Lirung Glacier, Nepal.” <i>Frontiers in Earth Science</i>. Frontiers Media, 2017. <a href=\"https://doi.org/10.3389/feart.2017.00069\">https://doi.org/10.3389/feart.2017.00069</a>."},"extern":"1","publication_identifier":{"issn":["2296-6463"]},"quality_controlled":"1","_id":"12610","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Frontiers Media","title":"Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Miles","first_name":"Evan S.","full_name":"Miles, Evan S."},{"first_name":"Jakob","last_name":"Steiner","full_name":"Steiner, Jakob"},{"full_name":"Willis, Ian","first_name":"Ian","last_name":"Willis"},{"first_name":"Pascal","last_name":"Buri","full_name":"Buri, Pascal"},{"last_name":"Immerzeel","first_name":"Walter W.","full_name":"Immerzeel, Walter W."},{"full_name":"Chesnokova, Anna","last_name":"Chesnokova","first_name":"Anna"},{"full_name":"Pellicciotti, Francesca","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti"}]},{"issue":"7","keyword":["Water Science and Technology"],"date_updated":"2023-02-24T11:41:55Z","date_published":"2017-07-10T00:00:00Z","intvolume":"        53","month":"07","year":"2017","page":"5601-5625","day":"10","status":"public","date_created":"2023-02-20T08:14:10Z","volume":53,"oa_version":"None","publication":"Water Resources Research","doi":"10.1002/2016wr020126","title":"Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions","author":[{"first_name":"A.","last_name":"Ayala","full_name":"Ayala, A."},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"},{"last_name":"MacDonell","first_name":"S.","full_name":"MacDonell, S."},{"last_name":"McPhee","first_name":"J.","full_name":"McPhee, J."},{"full_name":"Burlando, P.","first_name":"P.","last_name":"Burlando"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Geophysical Union","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","_id":"12611","scopus_import":"1","abstract":[{"text":"We investigate the energy balance and ablation regimes of glaciers in high-elevation, dry environments using glaciometeorological data collected on six glaciers in the semiarid Andes of North-Central Chile (29–34°S, 3127–5324 m). We use a point-scale physically based energy balance (EB) model and an enhanced Temperature-Index (ETI) model that calculates melt rates only as a function of air temperature and net shortwave radiation. At all sites, the largest energy inputs are net shortwave and incoming longwave radiation, which are controlled by surface albedo and elevation, respectively. Turbulent fluxes cancel each other out at the lower sites, but as elevation increases, cold, dry and wind-exposed conditions increase the magnitude of negative latent heat fluxes, associated with large surface sublimation rates. In midsummer (January), ablation rates vary from 67.9 mm w.e. d−1 at the lowest site (∼100% corresponding to melt), to 2.3 mm w.e. d−1 at the highest site (>85% corresponding to surface sublimation). At low-elevation, low-albedo, melt-dominated sites, the ETI model correctly reproduces melt using a large range of possible parameters, but both the performance and parameter transferability decrease with elevation for two main reasons: (i) the air temperature threshold approach for melt onset does not capture the diurnal variability of melt in cold and strong irradiated environments and (ii) energy losses decrease the correlation between melt and net shortwave radiation. We summarize our results by means of an elevation profile of ablation components that can be used as reference in future studies of glacier ablation in the semiarid Andes.","lang":"eng"}],"type":"journal_article","extern":"1","citation":{"mla":"Ayala, A., et al. “Patterns of Glacier Ablation across North-Central Chile: Identifying the Limits of Empirical Melt Models under Sublimation-Favorable Conditions.” <i>Water Resources Research</i>, vol. 53, no. 7, American Geophysical Union, 2017, pp. 5601–25, doi:<a href=\"https://doi.org/10.1002/2016wr020126\">10.1002/2016wr020126</a>.","apa":"Ayala, A., Pellicciotti, F., MacDonell, S., McPhee, J., &#38; Burlando, P. (2017). Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2016wr020126\">https://doi.org/10.1002/2016wr020126</a>","chicago":"Ayala, A., Francesca Pellicciotti, S. MacDonell, J. McPhee, and P. Burlando. “Patterns of Glacier Ablation across North-Central Chile: Identifying the Limits of Empirical Melt Models under Sublimation-Favorable Conditions.” <i>Water Resources Research</i>. American Geophysical Union, 2017. <a href=\"https://doi.org/10.1002/2016wr020126\">https://doi.org/10.1002/2016wr020126</a>.","ieee":"A. Ayala, F. Pellicciotti, S. MacDonell, J. McPhee, and P. Burlando, “Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions,” <i>Water Resources Research</i>, vol. 53, no. 7. American Geophysical Union, pp. 5601–5625, 2017.","ista":"Ayala A, Pellicciotti F, MacDonell S, McPhee J, Burlando P. 2017. Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions. Water Resources Research. 53(7), 5601–5625.","short":"A. Ayala, F. Pellicciotti, S. MacDonell, J. McPhee, P. Burlando, Water Resources Research 53 (2017) 5601–5625.","ama":"Ayala A, Pellicciotti F, MacDonell S, McPhee J, Burlando P. Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions. <i>Water Resources Research</i>. 2017;53(7):5601-5625. doi:<a href=\"https://doi.org/10.1002/2016wr020126\">10.1002/2016wr020126</a>"},"publication_identifier":{"issn":["0043-1397"]},"publication_status":"published"},{"doi":"10.1017/jog.2016.120","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/jog.2016.120"}],"publication":"Journal of Glaciology","oa_version":"Published Version","volume":63,"date_created":"2023-02-20T08:14:16Z","day":"01","status":"public","page":"88-105","year":"2017","intvolume":"        63","month":"02","date_published":"2017-02-01T00:00:00Z","date_updated":"2023-02-24T11:38:31Z","keyword":["Earth-Surface Processes"],"issue":"237","oa":1,"publication_status":"published","citation":{"ama":"MILES ES, WILLIS IC, ARNOLD NS, STEINER J, Pellicciotti F. Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013. <i>Journal of Glaciology</i>. 2017;63(237):88-105. doi:<a href=\"https://doi.org/10.1017/jog.2016.120\">10.1017/jog.2016.120</a>","ista":"MILES ES, WILLIS IC, ARNOLD NS, STEINER J, Pellicciotti F. 2017. Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013. Journal of Glaciology. 63(237), 88–105.","short":"E.S. MILES, I.C. WILLIS, N.S. ARNOLD, J. STEINER, F. Pellicciotti, Journal of Glaciology 63 (2017) 88–105.","ieee":"E. S. MILES, I. C. WILLIS, N. S. ARNOLD, J. STEINER, and F. Pellicciotti, “Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013,” <i>Journal of Glaciology</i>, vol. 63, no. 237. Cambridge University Press, pp. 88–105, 2017.","chicago":"MILES, EVAN S., IAN C. WILLIS, NEIL S. ARNOLD, JAKOB STEINER, and Francesca Pellicciotti. “Spatial, Seasonal and Interannual Variability of Supraglacial Ponds in the Langtang Valley of Nepal, 1999–2013.” <i>Journal of Glaciology</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jog.2016.120\">https://doi.org/10.1017/jog.2016.120</a>.","apa":"MILES, E. S., WILLIS, I. C., ARNOLD, N. S., STEINER, J., &#38; Pellicciotti, F. (2017). Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013. <i>Journal of Glaciology</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jog.2016.120\">https://doi.org/10.1017/jog.2016.120</a>","mla":"MILES, EVAN S., et al. “Spatial, Seasonal and Interannual Variability of Supraglacial Ponds in the Langtang Valley of Nepal, 1999–2013.” <i>Journal of Glaciology</i>, vol. 63, no. 237, Cambridge University Press, 2017, pp. 88–105, doi:<a href=\"https://doi.org/10.1017/jog.2016.120\">10.1017/jog.2016.120</a>."},"extern":"1","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"type":"journal_article","scopus_import":"1","abstract":[{"text":"Supraglacial ponds play a key role in absorbing atmospheric energy and directing it to the ice of debris-covered glaciers, but the spatial and temporal distribution of these features is not well documented. We analyse 172 Landsat TM/ETM+ scenes for the period 1999–2013 to identify thawed supraglacial ponds for the debris-covered tongues of five glaciers in the Langtang Valley of Nepal. We apply an advanced atmospheric correction routine (Landcor/6S) and use band ratio and image morphological techniques to identify ponds and validate our results with 2.5 m Cartosat-1 observations. We then characterize the spatial, seasonal and interannual patterns of ponds. We find high variability in pond incidence between glaciers (May–October means of 0.08–1.69% of debris area), with ponds most frequent in zones of low surface gradient and velocity. The ponds show pronounced seasonality, appearing in the pre-monsoon as snow melts, peaking at the monsoon onset at 2% of debris-covered area, then declining in the post-monsoon as ponds drain or freeze. Ponds are highly recurrent and persistent, with 40.5% of pond locations occurring for multiple years. Rather than a trend in pond cover over the study period, we find high interannual variability for each glacier after controlling for seasonality.","lang":"eng"}],"_id":"12612","quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","publisher":"Cambridge University Press","title":"Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013","author":[{"full_name":"MILES, EVAN S.","last_name":"MILES","first_name":"EVAN S."},{"last_name":"WILLIS","first_name":"IAN C.","full_name":"WILLIS, IAN C."},{"first_name":"NEIL S.","last_name":"ARNOLD","full_name":"ARNOLD, NEIL S."},{"last_name":"STEINER","first_name":"JAKOB","full_name":"STEINER, JAKOB"},{"last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"page":"28","article_processing_charge":"No","conference":{"start_date":"2017-03-01","end_date":"2017-03-03","name":"AHPC: Austrian HPC Meeting","location":"Grundlsee, Austria"},"department":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"year":"2017","month":"03","has_accepted_license":"1","date_published":"2017-03-03T00:00:00Z","publisher":"FSP Scientific Computing","date_updated":"2023-05-16T07:22:23Z","file":[{"content_type":"application/pdf","file_id":"12969","creator":"dernst","file_size":1005486,"checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6","relation":"main_file","access_level":"open_access","success":1,"file_name":"2017_AHPC_Schloegl.pdf","date_updated":"2023-05-16T07:20:50Z","date_created":"2023-05-16T07:20:50Z"}],"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","orcid":"0000-0002-5621-8100","last_name":"Schlögl","full_name":"Schlögl, Alois"},{"last_name":"Kiss","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","first_name":"Janos","full_name":"Kiss, Janos"}],"main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf","open_access":"1"}],"publication_status":"published","publication":"AHPC17 – Austrian HPC Meeting 2017","oa_version":"Published Version","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."},"type":"conference_abstract","file_date_updated":"2023-05-16T07:20:50Z","_id":"12905","ddc":["000"],"date_created":"2023-05-05T12:58:53Z","day":"03","status":"public"},{"year":"2017","page":"144 - 170","external_id":{"isi":["000388430000011"]},"oa":1,"date_updated":"2023-09-20T11:15:31Z","date_published":"2017-03-01T00:00:00Z","month":"03","intvolume":"        84","ec_funded":1,"oa_version":"Published Version","isi":1,"related_material":{"record":[{"id":"2305","relation":"earlier_version","status":"public"}]},"publication":"Journal of Computer and System Sciences","doi":"10.1016/j.jcss.2016.09.009","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","volume":84,"pubrep_id":"717","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publist_id":"6009","article_processing_charge":"No","title":"Trading performance for stability in Markov decision processes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"last_name":"Kučera","first_name":"Antonín","full_name":"Kučera, Antonín"}],"file":[{"date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:11:30Z","file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","checksum":"91271b23cf884d7c06d33bef0cd623b1","relation":"main_file","access_level":"open_access","file_id":"4885","content_type":"application/pdf","file_size":708657,"creator":"system"}],"publisher":"Elsevier","has_accepted_license":"1","publication_status":"published","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","_id":"1294","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:44:42Z","citation":{"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>","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>.","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>","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.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170.","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.","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>."}},{"abstract":[{"lang":"eng","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."}],"type":"research_data_reference","citation":{"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>.","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>","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>.","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>.","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.","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>"},"day":"14","status":"public","date_created":"2021-07-23T09:39:34Z","_id":"9707","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.pk16b"}],"doi":"10.5061/dryad.pk16b","oa_version":"Published Version","related_material":{"record":[{"status":"deleted","relation":"used_in_publication","id":"9702"}]},"publisher":"Dryad","date_published":"2017-01-14T00:00:00Z","month":"01","title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","author":[{"full_name":"Riccio, Paul","first_name":"Paul","last_name":"Riccio"},{"full_name":"Cebrián, Christina","first_name":"Christina","last_name":"Cebrián"},{"first_name":"Hui","last_name":"Zong","full_name":"Zong, Hui"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Costantini","first_name":"Frank","full_name":"Costantini, Frank"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"date_updated":"2022-08-25T13:34:55Z","department":[{"_id":"SiHi"}],"article_processing_charge":"No","year":"2017"},{"citation":{"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>","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>.","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>","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>.","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).","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>."},"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."}],"date_created":"2021-07-23T11:34:34Z","_id":"9709","status":"public","day":"18","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.1f1rc"}],"doi":"10.5061/dryad.1f1rc","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1197"}]},"oa_version":"Published Version","month":"10","date_published":"2017-10-18T00:00:00Z","publisher":"Dryad","date_updated":"2023-02-21T16:34:41Z","title":"Data from: Error-robust modes of the retinal population code","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Jason","last_name":"Prentice","full_name":"Prentice, Jason"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"last_name":"Ioffe","first_name":"Mark","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"},{"last_name":"Berry","first_name":"Michael","full_name":"Berry, Michael"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"year":"2017"},{"status":"public","day":"29","_id":"9842","date_created":"2021-08-09T13:18:55Z","type":"research_data_reference","abstract":[{"text":"Mathematica notebooks used to generate figures.","lang":"eng"}],"citation":{"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>","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>.","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>","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>."},"oa_version":"Published Version","related_material":{"record":[{"id":"564","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"url":"https://doi.org/10.17632/nw68fxzjpm.1","open_access":"1"}],"doi":"10.17632/nw68fxzjpm.1","oa":1,"title":"Data for: Establishment in a new habitat by polygenic adaptation","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"date_updated":"2025-05-28T11:56:59Z","publisher":"Mendeley Data","month":"12","date_published":"2017-12-29T00:00:00Z","year":"2017","department":[{"_id":"NiBa"}],"article_processing_charge":"No"},{"type":"research_data_reference","citation":{"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>","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>.","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>","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","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>."},"day":"18","status":"public","date_created":"2021-08-09T13:27:16Z","_id":"9844","doi":"10.1371/journal.pgen.1007122.s018","oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"541"}]},"publisher":"Public Library of Science","month":"12","date_published":"2017-12-18T00:00:00Z","author":[{"full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic"},{"last_name":"Schreiber","first_name":"Frank","full_name":"Schreiber, Frank"},{"last_name":"Dal Co","first_name":"Alma","full_name":"Dal Co, Alma"},{"full_name":"Kiviet, Daniel","first_name":"Daniel","last_name":"Kiviet"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"first_name":"Sten","last_name":"Littmann","full_name":"Littmann, Sten"},{"last_name":"Kuypers","first_name":"Marcel","full_name":"Kuypers, Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"title":"Source data for figures and tables","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T12:25:04Z","department":[{"_id":"CaGu"}],"article_processing_charge":"No","year":"2017"},{"year":"2017","article_processing_charge":"No","department":[{"_id":"CaGu"}],"date_updated":"2023-02-23T12:25:04Z","author":[{"full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic"},{"first_name":"Frank","last_name":"Schreiber","full_name":"Schreiber, Frank"},{"full_name":"Dal Co, Alma","first_name":"Alma","last_name":"Dal Co"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Littmann, Sten","first_name":"Sten","last_name":"Littmann"},{"full_name":"Kuypers, Marcel","last_name":"Kuypers","first_name":"Marcel"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"}],"title":"Mathematical model","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2017-12-18T00:00:00Z","month":"12","publisher":"Public Library of Science","related_material":{"record":[{"id":"541","relation":"used_in_publication","status":"public"}]},"oa_version":"None","doi":"10.1371/journal.pgen.1007122.s017","date_created":"2021-08-09T13:31:51Z","_id":"9845","day":"18","status":"public","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>.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Mathematical model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">10.1371/journal.pgen.1007122.s017</a>.","ieee":"N. Nikolic <i>et al.</i>, “Mathematical model.” Public Library of Science, 2017.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. 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