[{"volume":95,"day":"10","oa_version":"None","quality_controlled":"1","external_id":{"pmid":["28618504"],"isi":["000401233900007"]},"abstract":[{"lang":"eng","text":"We present a numerical study of wavy supercritical cylindrical Couette flow between counter-rotating cylinders in which the wavy pattern propagates either prograde with the inner cylinder or retrograde opposite the rotation of the inner cylinder. The wave propagation reversals from prograde to retrograde and vice versa occur at distinct values of the inner cylinder Reynolds number when the associated frequency of the wavy instability vanishes. The reversal occurs for both twofold and threefold symmetric wavy vortices. Moreover, the wave propagation reversal only occurs for sufficiently strong counter-rotation. The flow pattern reversal appears to be intrinsic in the system as either periodic boundary conditions or fixed end wall boundary conditions for different system sizes always result in the wave propagation reversal. We present a detailed bifurcation sequence and parameter space diagram with respect to retrograde behavior of wavy flows. The retrograde propagation of the instability occurs when the inner Reynolds number is about two times the outer Reynolds number. The mechanism for the retrograde propagation is associated with the inviscidly unstable region near the inner cylinder and the direction of the global average azimuthal velocity. Flow dynamics, spatio-temporal behavior, global mean angular velocity, and torque of the flow with the wavy pattern are explored."}],"article_type":"original","OA_type":"closed access","citation":{"ama":"Altmeyer S, Lueptow R. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. <i>Physical Review E</i>. 2017;95(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">10.1103/PhysRevE.95.053103</a>","chicago":"Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">https://doi.org/10.1103/PhysRevE.95.053103</a>.","short":"S. Altmeyer, R. Lueptow, Physical Review E 95 (2017).","apa":"Altmeyer, S., &#38; Lueptow, R. (2017). Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">https://doi.org/10.1103/PhysRevE.95.053103</a>","ieee":"S. Altmeyer and R. Lueptow, “Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow,” <i>Physical Review E</i>, vol. 95, no. 5. American Physical Society, 2017.","mla":"Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” <i>Physical Review E</i>, vol. 95, no. 5, 053103, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.053103\">10.1103/PhysRevE.95.053103</a>.","ista":"Altmeyer S, Lueptow R. 2017. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. 95(5), 053103."},"date_published":"2017-05-10T00:00:00Z","year":"2017","publication_status":"published","doi":"10.1103/PhysRevE.95.053103","publication_identifier":{"issn":["2470-0045"]},"publisher":"American Physical Society","article_processing_charge":"No","department":[{"_id":"BjHo"}],"month":"05","date_updated":"2025-09-10T14:26:12Z","title":"Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow","article_number":"053103","isi":1,"scopus_import":"1","date_created":"2018-12-11T11:47:50Z","status":"public","language":[{"iso":"eng"}],"publication":"Physical Review E","intvolume":"        95","pmid":1,"publist_id":"7049","_id":"673","issue":"5","corr_author":"1","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Altmeyer","full_name":"Altmeyer, Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","first_name":"Sebastian"},{"first_name":"Richard","full_name":"Lueptow, Richard","last_name":"Lueptow"}]},{"publication":"Current Biology","language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-11T11:47:51Z","scopus_import":"1","intvolume":"        27","page":"1314 - 1325","publist_id":"7050","_id":"674","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Jan","last_name":"Schwarz","full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Veronika","last_name":"Bierbaum","full_name":"Bierbaum, Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vaahtomeri, Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","first_name":"Kari"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid","last_name":"De Vries"},{"last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","first_name":"Alexander F","orcid":"0000-0002-1073-744X"},{"full_name":"Reversat, Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","first_name":"Anne","orcid":"0000-0003-0666-8928"},{"last_name":"Merrin","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609"},{"full_name":"Tarrant, Teresa","last_name":"Tarrant","first_name":"Teresa"},{"first_name":"Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","full_name":"Bollenbach, Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"type":"journal_article","corr_author":"1","issue":"9","quality_controlled":"1","external_id":{"isi":["000400741700021"]},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12"}],"day":"09","oa_version":"None","volume":27,"ec_funded":1,"abstract":[{"text":"Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo.","lang":"eng"}],"publication_status":"published","article_processing_charge":"No","publication_identifier":{"issn":["09609822"]},"publisher":"Cell Press","doi":"10.1016/j.cub.2017.04.004","year":"2017","date_published":"2017-05-09T00:00:00Z","citation":{"ista":"Schwarz J, Bierbaum V, Vaahtomeri K, Hauschild R, Brown M, de Vries I, Leithner AF, Reversat A, Merrin J, Tarrant T, Bollenbach MT, Sixt MK. 2017. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 27(9), 1314–1325.","ieee":"J. Schwarz <i>et al.</i>, “Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6,” <i>Current Biology</i>, vol. 27, no. 9. Cell Press, pp. 1314–1325, 2017.","mla":"Schwarz, Jan, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” <i>Current Biology</i>, vol. 27, no. 9, Cell Press, 2017, pp. 1314–25, doi:<a href=\"https://doi.org/10.1016/j.cub.2017.04.004\">10.1016/j.cub.2017.04.004</a>.","short":"J. Schwarz, V. Bierbaum, K. Vaahtomeri, R. Hauschild, M. Brown, I. de Vries, A.F. Leithner, A. Reversat, J. Merrin, T. Tarrant, M.T. Bollenbach, M.K. Sixt, Current Biology 27 (2017) 1314–1325.","apa":"Schwarz, J., Bierbaum, V., Vaahtomeri, K., Hauschild, R., Brown, M., de Vries, I., … Sixt, M. K. (2017). Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2017.04.004\">https://doi.org/10.1016/j.cub.2017.04.004</a>","ama":"Schwarz J, Bierbaum V, Vaahtomeri K, et al. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. <i>Current Biology</i>. 2017;27(9):1314-1325. doi:<a href=\"https://doi.org/10.1016/j.cub.2017.04.004\">10.1016/j.cub.2017.04.004</a>","chicago":"Schwarz, Jan, Veronika Bierbaum, Kari Vaahtomeri, Robert Hauschild, Markus Brown, Ingrid de Vries, Alexander F Leithner, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” <i>Current Biology</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cub.2017.04.004\">https://doi.org/10.1016/j.cub.2017.04.004</a>."},"title":"Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6","isi":1,"date_updated":"2025-09-10T14:26:47Z","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"month":"05"},{"ddc":["570"],"file":[{"creator":"system","file_id":"5171","date_updated":"2020-07-14T12:47:40Z","file_name":"IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":3005610,"date_created":"2018-12-12T10:15:48Z","checksum":"efc7287d9c6354983cb151880e9ad72a"}],"publist_id":"7046","intvolume":"        19","page":"1294 - 1303","date_created":"2018-12-11T11:47:52Z","status":"public","scopus_import":"1","publication":"Cell Reports","language":[{"iso":"eng"}],"has_accepted_license":"1","issue":"7","file_date_updated":"2020-07-14T12:47:40Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Lademann","full_name":"Lademann, Claudio","first_name":"Claudio"},{"orcid":"0000-0003-2856-3369","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","last_name":"Renkawitz"},{"full_name":"Pfander, Boris","last_name":"Pfander","first_name":"Boris"},{"full_name":"Jentsch, Stefan","last_name":"Jentsch","first_name":"Stefan"}],"type":"journal_article","oa":1,"_id":"677","abstract":[{"text":"The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR.","lang":"eng"}],"pubrep_id":"899","day":"16","volume":19,"oa_version":"Published Version","quality_controlled":"1","external_id":{"isi":["000402125100002"]},"date_updated":"2025-09-10T14:23:55Z","department":[{"_id":"MiSi"}],"month":"05","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"isi":1,"title":"The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination","date_published":"2017-05-16T00:00:00Z","year":"2017","citation":{"short":"C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303.","apa":"Lademann, C., Renkawitz, J., Pfander, B., &#38; Jentsch, S. (2017). The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">https://doi.org/10.1016/j.celrep.2017.04.051</a>","ama":"Lademann C, Renkawitz J, Pfander B, Jentsch S. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. <i>Cell Reports</i>. 2017;19(7):1294-1303. doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">10.1016/j.celrep.2017.04.051</a>","chicago":"Lademann, Claudio, Jörg Renkawitz, Boris Pfander, and Stefan Jentsch. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” <i>Cell Reports</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">https://doi.org/10.1016/j.celrep.2017.04.051</a>.","ista":"Lademann C, Renkawitz J, Pfander B, Jentsch S. 2017. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 19(7), 1294–1303.","ieee":"C. Lademann, J. Renkawitz, B. Pfander, and S. Jentsch, “The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination,” <i>Cell Reports</i>, vol. 19, no. 7. Cell Press, pp. 1294–1303, 2017.","mla":"Lademann, Claudio, et al. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” <i>Cell Reports</i>, vol. 19, no. 7, Cell Press, 2017, pp. 1294–303, doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">10.1016/j.celrep.2017.04.051</a>."},"publisher":"Cell Press","article_processing_charge":"No","publication_identifier":{"issn":["2211-1247"]},"doi":"10.1016/j.celrep.2017.04.051","publication_status":"published"},{"publication":"Nature Cell Biology","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:47:53Z","status":"public","scopus_import":"1","page":"581 - 588","intvolume":"        19","publist_id":"7040","_id":"678","author":[{"orcid":"0000-0002-8451-1195","first_name":"Nicoletta","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Petridou, Nicoletta","last_name":"Petridou"},{"full_name":"Spiro, Zoltan P","id":"426AD026-F248-11E8-B48F-1D18A9856A87","last_name":"Spiro","first_name":"Zoltan P"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","corr_author":"1","issue":"6","quality_controlled":"1","external_id":{"isi":["000402525200003"]},"project":[{"_id":"25236028-B435-11E9-9278-68D0E5697425","name":"The generation and function of anisotropic tissue tension in zebrafish epiboly","grant_number":"ALTF534-2016"}],"volume":19,"day":"31","oa_version":"None","abstract":[{"lang":"eng","text":"The seminal observation that mechanical signals can elicit changes in biochemical signalling within cells, a process commonly termed mechanosensation and mechanotransduction, has revolutionized our understanding of the role of cell mechanics in various fundamental biological processes, such as cell motility, adhesion, proliferation and differentiation. In this Review, we will discuss how the interplay and feedback between mechanical and biochemical signals control tissue morphogenesis and cell fate specification in embryonic development."}],"publication_status":"published","publisher":"Nature Publishing Group","publication_identifier":{"issn":["1465-7392"]},"article_processing_charge":"No","doi":"10.1038/ncb3524","year":"2017","date_published":"2017-05-31T00:00:00Z","citation":{"apa":"Petridou, N., Spiro, Z. P., &#38; Heisenberg, C.-P. J. (2017). Multiscale force sensing in development. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3524\">https://doi.org/10.1038/ncb3524</a>","short":"N. Petridou, Z.P. Spiro, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 581–588.","chicago":"Petridou, Nicoletta, Zoltan P Spiro, and Carl-Philipp J Heisenberg. “Multiscale Force Sensing in Development.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncb3524\">https://doi.org/10.1038/ncb3524</a>.","ama":"Petridou N, Spiro ZP, Heisenberg C-PJ. Multiscale force sensing in development. <i>Nature Cell Biology</i>. 2017;19(6):581-588. doi:<a href=\"https://doi.org/10.1038/ncb3524\">10.1038/ncb3524</a>","ista":"Petridou N, Spiro ZP, Heisenberg C-PJ. 2017. Multiscale force sensing in development. Nature Cell Biology. 19(6), 581–588.","mla":"Petridou, Nicoletta, et al. “Multiscale Force Sensing in Development.” <i>Nature Cell Biology</i>, vol. 19, no. 6, Nature Publishing Group, 2017, pp. 581–88, doi:<a href=\"https://doi.org/10.1038/ncb3524\">10.1038/ncb3524</a>.","ieee":"N. Petridou, Z. P. Spiro, and C.-P. J. Heisenberg, “Multiscale force sensing in development,” <i>Nature Cell Biology</i>, vol. 19, no. 6. Nature Publishing Group, pp. 581–588, 2017."},"title":"Multiscale force sensing in development","isi":1,"date_updated":"2025-09-10T14:23:21Z","department":[{"_id":"CaHe"}],"month":"05"},{"abstract":[{"lang":"eng","text":"In order to respond reliably to specific features of their environment, sensory neurons need to integrate multiple incoming noisy signals. Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics."}],"volume":13,"oa_version":"Published Version","day":"01","pubrep_id":"898","external_id":{"isi":["000404565400034"]},"quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-09-10T14:20:48Z","department":[{"_id":"GaTk"}],"month":"06","title":"Sensory noise predicts divisive reshaping of receptive fields","article_number":"e1005582","isi":1,"year":"2017","date_published":"2017-06-01T00:00:00Z","citation":{"chicago":"Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">https://doi.org/10.1371/journal.pcbi.1005582</a>.","ama":"Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping of receptive fields. <i>PLoS Computational Biology</i>. 2017;13(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">10.1371/journal.pcbi.1005582</a>","apa":"Chalk, M. J., Masset, P., Gutkin, B., &#38; Denève, S. (2017). Sensory noise predicts divisive reshaping of receptive fields. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">https://doi.org/10.1371/journal.pcbi.1005582</a>","short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017).","mla":"Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” <i>PLoS Computational Biology</i>, vol. 13, no. 6, e1005582, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">10.1371/journal.pcbi.1005582</a>.","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts divisive reshaping of receptive fields,” <i>PLoS Computational Biology</i>, vol. 13, no. 6. Public Library of Science, 2017.","ista":"Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582."},"publication_status":"published","publisher":"Public Library of Science","article_processing_charge":"No","publication_identifier":{"issn":["1553-734X"]},"doi":"10.1371/journal.pcbi.1005582","file":[{"file_size":14555676,"relation":"main_file","access_level":"open_access","checksum":"796a1026076af6f4405a47d985bc7b68","date_created":"2018-12-12T10:07:47Z","creator":"system","file_id":"4645","content_type":"application/pdf","file_name":"IST-2017-898-v1+1_journal.pcbi.1005582.pdf","date_updated":"2020-07-14T12:47:40Z"}],"ddc":["571"],"intvolume":"        13","publist_id":"7035","status":"public","scopus_import":"1","date_created":"2018-12-11T11:47:53Z","has_accepted_license":"1","publication":"PLoS Computational Biology","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:40Z","corr_author":"1","issue":"6","author":[{"first_name":"Matthew J","orcid":"0000-0001-7782-4436","last_name":"Chalk","full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paul","last_name":"Masset","full_name":"Masset, Paul"},{"first_name":"Boris","last_name":"Gutkin","full_name":"Gutkin, Boris"},{"full_name":"Denève, Sophie","last_name":"Denève","first_name":"Sophie"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","oa":1,"related_material":{"record":[{"id":"9855","status":"public","relation":"research_data"}]},"_id":"680"},{"ddc":["514","516"],"file":[{"date_created":"2018-12-12T10:17:12Z","checksum":"24fdde981cc513352a78dcf9b0660ae9","access_level":"open_access","file_size":710007,"relation":"main_file","file_name":"IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf","date_updated":"2020-07-14T12:47:41Z","content_type":"application/pdf","file_id":"5265","creator":"system"}],"publist_id":"7033","intvolume":"        77","date_created":"2018-12-11T11:47:54Z","scopus_import":1,"status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","corr_author":"1","file_date_updated":"2020-07-14T12:47:41Z","type":"conference","author":[{"last_name":"Lubiw","full_name":"Lubiw, Anna","first_name":"Anna"},{"orcid":"0000-0002-6660-1322","first_name":"Zuzana","full_name":"Masárová, Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová"},{"orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"later_version","status":"public","id":"5986"}]},"oa":1,"_id":"683","abstract":[{"text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.","lang":"eng"}],"conference":{"end_date":"2017-07-07","name":"SoCG: Symposium on Computational Geometry","location":"Brisbane, Australia","start_date":"2017-07-04"},"pubrep_id":"896","volume":77,"day":"01","oa_version":"Published Version","alternative_title":["LIPIcs"],"quality_controlled":"1","department":[{"_id":"UlWa"}],"month":"06","date_updated":"2025-04-15T06:53:14Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"49","title":"A proof of the orbit conjecture for flipping edge labelled triangulations","citation":{"short":"A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","apa":"Lubiw, A., Masárová, Z., &#38; Wagner, U. (2017). A proof of the orbit conjecture for flipping edge labelled triangulations (Vol. 77). Presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">https://doi.org/10.4230/LIPIcs.SoCG.2017.49</a>","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">10.4230/LIPIcs.SoCG.2017.49</a>","chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">https://doi.org/10.4230/LIPIcs.SoCG.2017.49</a>.","ista":"Lubiw A, Masárová Z, Wagner U. 2017. A proof of the orbit conjecture for flipping edge labelled triangulations. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 77, 49.","ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge labelled triangulations,” presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia, 2017, vol. 77.","mla":"Lubiw, Anna, et al. <i>A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations</i>. Vol. 77, 49, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">10.4230/LIPIcs.SoCG.2017.49</a>."},"date_published":"2017-06-01T00:00:00Z","year":"2017","doi":"10.4230/LIPIcs.SoCG.2017.49","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published"},{"issue":"2","corr_author":"1","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Nir","last_name":"Piterman","full_name":"Piterman, Nir"}],"oa":1,"arxiv":1,"_id":"684","publist_id":"7026","page":"420 - 452","intvolume":"        82","date_created":"2018-12-11T11:47:54Z","scopus_import":"1","status":"public","language":[{"iso":"eng"}],"publication":"Journal of Symbolic Logic","department":[{"_id":"KrCh"}],"month":"06","date_updated":"2025-09-10T14:18:30Z","isi":1,"title":"Obligation blackwell games and p-automata","citation":{"mla":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” <i>Journal of Symbolic Logic</i>, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:<a href=\"https://doi.org/10.1017/jsl.2016.71\">10.1017/jsl.2016.71</a>.","ieee":"K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” <i>Journal of Symbolic Logic</i>, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017.","ista":"Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” <i>Journal of Symbolic Logic</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jsl.2016.71\">https://doi.org/10.1017/jsl.2016.71</a>.","ama":"Chatterjee K, Piterman N. Obligation blackwell games and p-automata. <i>Journal of Symbolic Logic</i>. 2017;82(2):420-452. doi:<a href=\"https://doi.org/10.1017/jsl.2016.71\">10.1017/jsl.2016.71</a>","apa":"Chatterjee, K., &#38; Piterman, N. (2017). Obligation blackwell games and p-automata. <i>Journal of Symbolic Logic</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jsl.2016.71\">https://doi.org/10.1017/jsl.2016.71</a>","short":"K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452."},"date_published":"2017-06-01T00:00:00Z","year":"2017","doi":"10.1017/jsl.2016.71","publication_identifier":{"issn":["0022-4812"],"eissn":["1943-5886"]},"article_processing_charge":"No","publisher":"Cambridge University Press","publication_status":"published","abstract":[{"text":"We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1206.5174","open_access":"1"}],"volume":82,"day":"01","oa_version":"Submitted Version","quality_controlled":"1","external_id":{"arxiv":["1206.5174"],"isi":["000403796700002"]}},{"arxiv":1,"publisher":"International Conference on Learning Representations","publication_status":"published","_id":"6841","citation":{"ista":"Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations.","mla":"Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>, International Conference on Learning Representations, 2017.","ieee":"G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>, Toulon, France, 2017.","apa":"Martius, G. S., &#38; Lampert, C. (2017). Extrapolation and learning equations. In <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>. Toulon, France: International Conference on Learning Representations.","short":"G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","chicago":"Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>. International Conference on Learning Representations, 2017.","ama":"Martius GS, Lampert C. Extrapolation and learning equations. In: <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>. International Conference on Learning Representations; 2017."},"date_published":"2017-02-21T00:00:00Z","oa":1,"year":"2017","type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","last_name":"Martius"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert"}],"title":"Extrapolation and learning equations","month":"02","department":[{"_id":"ChLa"}],"date_updated":"2021-01-12T08:09:17Z","language":[{"iso":"eng"}],"publication":"5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings","project":[{"name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036"}],"external_id":{"arxiv":["1610.02995"]},"quality_controlled":"1","ec_funded":1,"status":"public","date_created":"2019-09-01T22:01:00Z","scopus_import":1,"day":"21","oa_version":"Preprint","conference":{"start_date":"2017-04-24","location":"Toulon, France","name":"ICLR: International Conference on Learning Representations","end_date":"2017-04-26"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02995"}],"abstract":[{"lang":"eng","text":"In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified."}]},{"citation":{"ama":"Davison B. The critical CoHA of a quiver with potential. <i>Quarterly Journal of Mathematics</i>. 2017;68(2):635-703. doi:<a href=\"https://doi.org/10.1093/qmath/haw053\">10.1093/qmath/haw053</a>","chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” <i>Quarterly Journal of Mathematics</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/qmath/haw053\">https://doi.org/10.1093/qmath/haw053</a>.","short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703.","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. <i>Quarterly Journal of Mathematics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/qmath/haw053\">https://doi.org/10.1093/qmath/haw053</a>","ieee":"B. Davison, “The critical CoHA of a quiver with potential,” <i>Quarterly Journal of Mathematics</i>, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017.","mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” <i>Quarterly Journal of Mathematics</i>, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:<a href=\"https://doi.org/10.1093/qmath/haw053\">10.1093/qmath/haw053</a>.","ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703."},"date_published":"2017-06-01T00:00:00Z","year":"2017","publication_status":"published","doi":"10.1093/qmath/haw053","article_processing_charge":"No","publication_identifier":{"issn":["0033-5606"]},"publisher":"Oxford University Press","department":[{"_id":"TaHa"}],"month":"06","date_updated":"2025-09-10T14:15:30Z","title":"The critical CoHA of a quiver with potential","isi":1,"oa_version":"Submitted Version","volume":68,"day":"01","ec_funded":1,"project":[{"name":"Arithmetic and physics of Higgs moduli spaces","_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"320593"}],"quality_controlled":"1","external_id":{"arxiv":["1311.7172"],"isi":["000404545300015"]},"abstract":[{"lang":"eng","text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.7172"}],"oa":1,"_id":"687","arxiv":1,"issue":"2","corr_author":"1","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Davison","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87","full_name":"Davison, Ben","orcid":"0000-0002-8944-4390","first_name":"Ben"}],"scopus_import":"1","date_created":"2018-12-11T11:47:55Z","status":"public","language":[{"iso":"eng"}],"publication":"Quarterly Journal of Mathematics","page":"635 - 703","intvolume":"        68","publist_id":"7022"},{"citation":{"ieee":"H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916.","mla":"Edelsbrunner, Herbert, and Hubert Wagner. <i>Topological Data Analysis with Bregman Divergences</i>. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">10.4230/LIPIcs.SoCG.2017.39</a>.","ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916.","ama":"Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">10.4230/LIPIcs.SoCG.2017.39</a>","chicago":"Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">https://doi.org/10.4230/LIPIcs.SoCG.2017.39</a>.","short":"H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916.","apa":"Edelsbrunner, H., &#38; Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">https://doi.org/10.4230/LIPIcs.SoCG.2017.39</a>"},"date_published":"2017-06-01T00:00:00Z","year":"2017","publication_status":"published","doi":"10.4230/LIPIcs.SoCG.2017.39","article_processing_charge":"No","publication_identifier":{"issn":["1868-8969"]},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"HeEd"},{"_id":"UlWa"}],"month":"06","date_updated":"2025-07-10T11:53:56Z","title":"Topological data analysis with Bregman divergences","day":"01","oa_version":"Published Version","volume":77,"pubrep_id":"895","quality_controlled":"1","alternative_title":["LIPIcs"],"abstract":[{"text":"We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. ","lang":"eng"}],"conference":{"end_date":"2017-07-07","name":"Symposium on Computational Geometry, SoCG","start_date":"2017-07-04","location":"Brisbane, Australia"},"oa":1,"_id":"688","file_date_updated":"2020-07-14T12:47:42Z","corr_author":"1","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"first_name":"Hubert","last_name":"Wagner","full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"status":"public","date_created":"2018-12-11T11:47:56Z","scopus_import":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"checksum":"067ab0cb3f962bae6c3af6bf0094e0f3","date_created":"2018-12-12T10:11:03Z","relation":"main_file","file_size":990546,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:42Z","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf","creator":"system","file_id":"4856"}],"ddc":["514","516"],"page":"391-3916","intvolume":"        77","publist_id":"7021"},{"abstract":[{"lang":"eng","text":"Rett syndrome modeling in monkey mirrors the human disorder."}],"quality_controlled":"1","day":"07","volume":9,"oa_version":"None","article_number":"eaan8196","title":"Rett syndrome modeling goes simian","month":"06","department":[{"_id":"GaNo"}],"date_updated":"2025-07-10T11:54:00Z","doi":"10.1126/scitranslmed.aan8196","article_processing_charge":"No","publication_identifier":{"issn":["1946-6234"]},"publisher":"American Association for the Advancement of Science","publication_status":"published","citation":{"mla":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” <i>Science Translational Medicine</i>, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">10.1126/scitranslmed.aan8196</a>.","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” <i>Science Translational Medicine</i>, vol. 9, no. 393. American Association for the Advancement of Science, 2017.","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196.","chicago":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">https://doi.org/10.1126/scitranslmed.aan8196</a>.","ama":"Novarino G. Rett syndrome modeling goes simian. <i>Science Translational Medicine</i>. 2017;9(393). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">10.1126/scitranslmed.aan8196</a>","apa":"Novarino, G. (2017). Rett syndrome modeling goes simian. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">https://doi.org/10.1126/scitranslmed.aan8196</a>","short":"G. Novarino, Science Translational Medicine 9 (2017)."},"year":"2017","date_published":"2017-06-07T00:00:00Z","publist_id":"7019","intvolume":"         9","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","scopus_import":"1","date_created":"2018-12-11T11:47:56Z","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"issue":"393","corr_author":"1","_id":"689"},{"_id":"693","oa":1,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Miki, Takafumi","last_name":"Miki","first_name":"Takafumi"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315"},{"first_name":"Gerardo","full_name":"Malagon, Gerardo","last_name":"Malagon"},{"first_name":"Laura","last_name":"Gomez","full_name":"Gomez, Laura"},{"first_name":"Katsuhiko","last_name":"Tabuchi","full_name":"Tabuchi, Katsuhiko"},{"first_name":"Masahiko","full_name":"Watanabe, Masahiko","last_name":"Watanabe"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"first_name":"Alain","last_name":"Marty","full_name":"Marty, Alain"}],"issue":"26","corr_author":"1","file_date_updated":"2020-07-14T12:47:44Z","language":[{"iso":"eng"}],"publication":"PNAS","has_accepted_license":"1","date_created":"2018-12-11T11:47:57Z","status":"public","scopus_import":"1","publist_id":"7013","intvolume":"       114","pmid":1,"page":"E5246 - E5255","ddc":["570"],"file":[{"content_type":"application/pdf","file_name":"2017_PNAS_Miki.pdf","date_updated":"2020-07-14T12:47:44Z","file_id":"7223","creator":"kschuh","checksum":"2ab75d554f3df4a34d20fa8040589b7e","date_created":"2020-01-03T13:27:29Z","relation":"main_file","file_size":2721544,"access_level":"open_access"}],"doi":"10.1073/pnas.1704470114","article_processing_charge":"Yes (in subscription journal)","publisher":"National Academy of Sciences","publication_identifier":{"issn":["0027-8424"]},"publication_status":"published","citation":{"apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. 2017;114(26):E5246-E5255. doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>.","ieee":"T. Miki <i>et al.</i>, “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” <i>PNAS</i>, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017."},"year":"2017","date_published":"2017-06-27T00:00:00Z","isi":1,"title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","month":"06","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"date_updated":"2025-09-10T14:00:03Z","quality_controlled":"1","external_id":{"isi":["000404108400028"],"pmid":["28607047"]},"day":"27","oa_version":"Published Version","volume":114,"abstract":[{"lang":"eng","text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. "}]},{"article_type":"original","abstract":[{"lang":"eng","text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells."}],"external_id":{"isi":["000405612200009"],"pmid":["28515231"]},"quality_controlled":"1","day":"01","oa_version":"Published Version","volume":130,"isi":1,"title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","date_updated":"2025-09-10T11:13:35Z","month":"07","department":[{"_id":"MiSi"}],"publisher":"Company of Biologists","article_processing_charge":"No","publication_identifier":{"issn":["0021-9533"]},"doi":"10.1242/jcs.200899","publication_status":"published","date_published":"2017-07-01T00:00:00Z","year":"2017","citation":{"apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., &#38; Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. 2017;130(13):2172-2184. doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>.","ieee":"A. Veß <i>et al.</i>, “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” <i>Journal of Cell Science</i>, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017."},"publist_id":"7008","page":"2172 - 2184","pmid":1,"intvolume":"       130","ddc":["570"],"file":[{"access_level":"open_access","file_size":10847596,"relation":"main_file","date_created":"2019-10-24T09:43:56Z","checksum":"42c81a0a4fc3128883b391c3af3f74bc","creator":"dernst","file_id":"6966","file_name":"2017_CellScience_Vess.pdf","date_updated":"2020-07-14T12:47:45Z","content_type":"application/pdf"}],"publication":"Journal of Cell Science","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","scopus_import":"1","date_created":"2018-12-11T11:47:58Z","author":[{"first_name":"Astrid","last_name":"Veß","full_name":"Veß, Astrid"},{"last_name":"Blache","full_name":"Blache, Ulrich","first_name":"Ulrich"},{"first_name":"Laura","last_name":"Leitner","full_name":"Leitner, Laura"},{"first_name":"Angela","last_name":"Kurz","full_name":"Kurz, Angela"},{"first_name":"Anja","last_name":"Ehrenpfordt","full_name":"Ehrenpfordt, Anja"},{"first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"first_name":"Guido","last_name":"Posern","full_name":"Posern, Guido"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","issue":"13","file_date_updated":"2020-07-14T12:47:45Z","_id":"694","oa":1},{"quality_controlled":"1","project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"alternative_title":["LIPIcs"],"oa_version":"Published Version","day":"01","volume":80,"ec_funded":1,"pubrep_id":"893","conference":{"start_date":"2017-07-10","location":"Warsaw, Poland","end_date":"2017-07-14","name":"ICALP: Automata, Languages and Programming"},"abstract":[{"text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. ","lang":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1868-8969"]},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"No","doi":"10.4230/LIPIcs.ICALP.2017.39","year":"2017","date_published":"2017-07-01T00:00:00Z","citation":{"ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: Automata, Languages and Programming, LIPIcs, vol. 80, 39.","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: Automata, Languages and Programming, Warsaw, Poland, 2017, vol. 80.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. <i>Non Uniform Attacks against Pseudoentropy</i>. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>.","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","apa":"Pietrzak, K. Z., &#38; Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: Automata, Languages and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>","ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>."},"title":"Non uniform attacks against pseudoentropy","article_number":"39","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-07-10T11:54:07Z","month":"07","department":[{"_id":"KrPi"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2018-12-11T11:47:59Z","status":"public","intvolume":"        80","publist_id":"7003","file":[{"file_id":"4701","creator":"system","content_type":"application/pdf","file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","date_updated":"2020-07-14T12:47:46Z","relation":"main_file","file_size":601004,"access_level":"open_access","checksum":"e95618a001692f1af2d68f5fde43bc1f","date_created":"2018-12-12T10:08:40Z"}],"ddc":["005"],"_id":"697","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Skórski","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"}],"type":"conference","file_date_updated":"2020-07-14T12:47:46Z","corr_author":"1"},{"publication":"Molecular Biology of the Cell","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","date_created":"2018-12-11T11:47:59Z","scopus_import":"1","publist_id":"7001","intvolume":"        28","page":"1997 - 2009","ddc":["519"],"file":[{"file_id":"4844","creator":"system","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","date_updated":"2020-07-14T12:47:46Z","content_type":"application/pdf","access_level":"open_access","file_size":1086097,"relation":"main_file","date_created":"2018-12-12T10:10:53Z","checksum":"de01dac9e30970cfa6ae902480a4e04d"}],"_id":"698","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Wang, Yejun","last_name":"Wang","first_name":"Yejun"},{"first_name":"Mallika","full_name":"Nagarajan, Mallika","last_name":"Nagarajan"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216"},{"first_name":"Gv","full_name":"Shivashankar, Gv","last_name":"Shivashankar"}],"type":"journal_article","issue":"14","file_date_updated":"2020-07-14T12:47:46Z","quality_controlled":"1","external_id":{"isi":["000406471600019"]},"project":[{"grant_number":"Y 903-N35","call_identifier":"FWF","_id":"2530CA10-B435-11E9-9278-68D0E5697425","name":"Gaussian Graphical Models: Theory and Applications"}],"pubrep_id":"892","day":"07","oa_version":"Published Version","volume":28,"abstract":[{"lang":"eng","text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. "}],"publisher":"American Society for Cell Biology","publication_identifier":{"issn":["1059-1524"]},"article_processing_charge":"No","doi":"10.1091/mbc.E16-12-0825","publication_status":"published","date_published":"2017-07-07T00:00:00Z","year":"2017","citation":{"apa":"Wang, Y., Nagarajan, M., Uhler, C., &#38; Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>","short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2017. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>.","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. 2017;28(14):1997-2009. doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>.","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017."},"isi":1,"title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","date_updated":"2025-09-10T11:09:13Z","department":[{"_id":"CaUh"}],"month":"07","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"}},{"type":"journal_article","author":[{"first_name":"Carl","full_name":"Veller, Carl","last_name":"Veller"},{"first_name":"Laura","last_name":"Hayward","full_name":"Hayward, Laura"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"27","_id":"699","oa":1,"page":"E5396 - E5405","pmid":1,"intvolume":"       114","publist_id":"7002","language":[{"iso":"eng"}],"publication":"PNAS","scopus_import":"1","date_created":"2018-12-11T11:48:00Z","status":"public","title":"The red queen and king in finite populations","isi":1,"department":[{"_id":"KrCh"}],"month":"07","date_updated":"2025-09-10T11:11:07Z","publication_status":"published","doi":"10.1073/pnas.1702020114","article_processing_charge":"No","publication_identifier":{"issn":["0027-8424"]},"publisher":"National Academy of Sciences","citation":{"apa":"Veller, C., Hayward, L., Nowak, M., &#38; Hilbe, C. (2017). The red queen and king in finite populations. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>.","ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. <i>PNAS</i>. 2017;114(27):E5396-E5405. doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” <i>PNAS</i>, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>.","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” <i>PNAS</i>, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017."},"year":"2017","date_published":"2017-07-03T00:00:00Z","abstract":[{"text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ","lang":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/","open_access":"1"}],"quality_controlled":"1","external_id":{"pmid":["28630336"],"isi":["000404576100017"]},"day":"03","volume":114,"oa_version":"Submitted Version"},{"isi":1,"article_number":"012404","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","date_updated":"2025-09-10T11:08:33Z","department":[{"_id":"JoFi"}],"month":"07","publication_identifier":{"issn":["2470-0045"]},"publisher":"American Institute of Physics","article_processing_charge":"No","doi":"10.1103/PhysRevE.96.012404","publication_status":"published","year":"2017","date_published":"2017-07-12T00:00:00Z","citation":{"chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>.","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., &#38; Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon,  Physical Review E Statistical Nonlinear and Soft Matter Physics  96 (2017).","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>.","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1. American Institute of Physics, 2017.","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404."},"abstract":[{"text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1612.07061","open_access":"1"}],"quality_controlled":"1","external_id":{"arxiv":["1612.07061"],"isi":["000405367200012"]},"project":[{"grant_number":"707438","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"ec_funded":1,"day":"12","volume":96,"oa_version":"Submitted Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","first_name":"Shabir","orcid":"0000-0003-0415-1423"},{"full_name":"Salari, Vahid","last_name":"Salari","first_name":"Vahid"},{"first_name":"Jack","last_name":"Tuszynski","full_name":"Tuszynski, Jack"},{"last_name":"Cifra","full_name":"Cifra, Michal","first_name":"Michal"},{"first_name":"Christoph","full_name":"Simon, Christoph","last_name":"Simon"}],"type":"journal_article","issue":"1","arxiv":1,"_id":"700","oa":1,"publist_id":"6997","intvolume":"        96","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-11T11:48:00Z","scopus_import":"1"},{"publist_id":"6996","intvolume":"        24","page":"1-44","ddc":["500"],"file":[{"file_id":"5077","creator":"system","content_type":"application/pdf","file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf","date_updated":"2020-07-14T12:47:47Z","file_size":544042,"relation":"main_file","access_level":"open_access","checksum":"a431e573e31df13bc0f66de3061006ec","date_created":"2018-12-12T10:14:25Z"}],"language":[{"iso":"eng"}],"publication":"The Electronic Journal of Combinatorics","has_accepted_license":"1","date_created":"2018-12-11T11:48:00Z","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"},{"last_name":"Patakova","full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3975-1683","first_name":"Zuzana"}],"issue":"3","corr_author":"1","file_date_updated":"2020-07-14T12:47:47Z","_id":"701","oa":1,"abstract":[{"text":"A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2.","lang":"eng"}],"quality_controlled":"1","pubrep_id":"984","volume":24,"day":"14","oa_version":"Submitted Version","title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","month":"07","department":[{"_id":"UlWa"}],"date_updated":"2025-07-10T11:54:09Z","article_processing_charge":"No","publisher":"International Press","publication_identifier":{"issn":["1077-8926"]},"publication_status":"published","citation":{"ama":"Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. <i>The Electronic Journal of Combinatorics</i>. 2017;24(3):1-44.","chicago":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” <i>The Electronic Journal of Combinatorics</i>. International Press, 2017.","short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44.","apa":"Kynčl, J., &#38; Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. <i>The Electronic Journal of Combinatorics</i>. International Press.","ieee":"J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” <i>The Electronic Journal of Combinatorics</i>, vol. 24, no. 3. International Press, pp. 1–44, 2017.","mla":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” <i>The Electronic Journal of Combinatorics</i>, vol. 24, no. 3, International Press, 2017, pp. 1–44.","ista":"Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44."},"date_published":"2017-07-14T00:00:00Z","year":"2017"},{"department":[{"_id":"GaNo"}],"month":"07","date_updated":"2025-07-10T11:54:10Z","title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","citation":{"ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. 2017;9(399):eaao0972. doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>","chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>.","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>","ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” <i>Science Translational Medicine</i>, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>.","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972."},"date_published":"2017-07-19T00:00:00Z","year":"2017","doi":"10.1126/scitranslmed.aao0972","publisher":"American Association for the Advancement of Science","article_processing_charge":"No","publication_identifier":{"issn":["1946-6234"]},"publication_status":"published","abstract":[{"text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n","lang":"eng"}],"volume":9,"day":"19","oa_version":"None","quality_controlled":"1","issue":"399","corr_author":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"}],"_id":"702","publist_id":"6993","intvolume":"         9","page":"eaao0972","status":"public","date_created":"2018-12-11T11:48:01Z","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Science Translational Medicine"},{"external_id":{"isi":["000409224300003"]},"quality_controlled":"1","day":"01","volume":22,"oa_version":"None","abstract":[{"text":"A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse.","lang":"eng"}],"article_processing_charge":"No","publisher":"Wiley-Blackwell","publication_identifier":{"issn":["1356-9597"]},"doi":"10.1111/gtc.12508","publication_status":"published","date_published":"2017-08-01T00:00:00Z","year":"2017","citation":{"short":"X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722.","apa":"Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. <i>Genes to Cells</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/gtc.12508\">https://doi.org/10.1111/gtc.12508</a>","ama":"Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. <i>Genes to Cells</i>. 2017;22(8):715-722. doi:<a href=\"https://doi.org/10.1111/gtc.12508\">10.1111/gtc.12508</a>","chicago":"Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” <i>Genes to Cells</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/gtc.12508\">https://doi.org/10.1111/gtc.12508</a>.","ista":"Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722.","ieee":"X. Geng <i>et al.</i>, “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” <i>Genes to Cells</i>, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017.","mla":"Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” <i>Genes to Cells</i>, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:<a href=\"https://doi.org/10.1111/gtc.12508\">10.1111/gtc.12508</a>."},"isi":1,"title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","date_updated":"2025-09-10T11:06:14Z","department":[{"_id":"PeJo"}],"month":"08","publication":"Genes to Cells","language":[{"iso":"eng"}],"scopus_import":"1","status":"public","date_created":"2018-12-11T11:48:02Z","publist_id":"6987","intvolume":"        22","page":"715 - 722","_id":"706","author":[{"id":"3395256A-F248-11E8-B48F-1D18A9856A87","full_name":"Geng, Xiaoqi","last_name":"Geng","first_name":"Xiaoqi"},{"first_name":"Tomohiko","last_name":"Maruo","full_name":"Maruo, Tomohiko"},{"first_name":"Kenji","full_name":"Mandai, Kenji","last_name":"Mandai"},{"first_name":"Irwan","full_name":"Supriyanto, Irwan","last_name":"Supriyanto"},{"first_name":"Muneaki","last_name":"Miyata","full_name":"Miyata, Muneaki"},{"last_name":"Sakakibara","full_name":"Sakakibara, Shotaro","first_name":"Shotaro"},{"first_name":"Akira","last_name":"Mizoguchi","full_name":"Mizoguchi, Akira"},{"first_name":"Yoshimi","last_name":"Takai","full_name":"Takai, Yoshimi"},{"last_name":"Mori","full_name":"Mori, Masahiro","first_name":"Masahiro"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","issue":"8"}]