[{"publication":"Annals of Statistics","status":"public","_id":"6748","month":"12","year":"2020","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Analysis of a two-layer neural network via displacement convexity","fulldoi":"https://doi.org/10.1214/20-AOS1945","doi":"10.1214/20-AOS1945","publisher":"Institute of Mathematical Statistics","publication_identifier":{"eissn":["1941-7330"],"issn":["1932-6157"]},"day":"11","abstract":[{"text":"Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.\r\nHere we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge.","lang":"eng"}],"author":[{"full_name":"Javanmard, Adel","first_name":"Adel","last_name":"Javanmard"},{"last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"last_name":"Montanari","first_name":"Andrea","full_name":"Montanari, Andrea"}],"isi":1,"type":"journal_article","date_published":"2020-12-11T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-07-31T09:39:42Z","arxiv":1,"intvolume":"        48","quality_controlled":"1","article_type":"original","date_updated":"2024-10-21T06:02:33Z","publication_status":"published","department":[{"_id":"MaMo"}],"volume":48,"page":"3619-3642","citation":{"ieee":"A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural network via displacement convexity,” <i>Annals of Statistics</i>, vol. 48, no. 6. Institute of Mathematical Statistics, pp. 3619–3642, 2020.","short":"A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.","ama":"Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network via displacement convexity. <i>Annals of Statistics</i>. 2020;48(6):3619-3642. doi:<a href=\"https://doi.org/10.1214/20-AOS1945\">10.1214/20-AOS1945</a>","ista":"Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 48(6), 3619–3642.","apa":"Javanmard, A., Mondelli, M., &#38; Montanari, A. (2020). Analysis of a two-layer neural network via displacement convexity. <i>Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/20-AOS1945\">https://doi.org/10.1214/20-AOS1945</a>","mla":"Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” <i>Annals of Statistics</i>, vol. 48, no. 6, Institute of Mathematical Statistics, 2020, pp. 3619–42, doi:<a href=\"https://doi.org/10.1214/20-AOS1945\">10.1214/20-AOS1945</a>.","chicago":"Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” <i>Annals of Statistics</i>. Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/20-AOS1945\">https://doi.org/10.1214/20-AOS1945</a>."},"external_id":{"arxiv":["1901.01375"],"isi":["000598369200021"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.01375"}],"issue":"6"},{"external_id":{"isi":["000512219400004"]},"citation":{"chicago":"Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation Games.” <i>Theoretical Computer Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.tcs.2019.06.031\">https://doi.org/10.1016/j.tcs.2019.06.031</a>.","short":"G. Avni, T.A. Henzinger, O. Kupferman, Theoretical Computer Science 807 (2020) 42–55.","ieee":"G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” <i>Theoretical Computer Science</i>, vol. 807. Elsevier, pp. 42–55, 2020.","apa":"Avni, G., Henzinger, T. A., &#38; Kupferman, O. (2020). Dynamic resource allocation games. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2019.06.031\">https://doi.org/10.1016/j.tcs.2019.06.031</a>","mla":"Avni, Guy, et al. “Dynamic Resource Allocation Games.” <i>Theoretical Computer Science</i>, vol. 807, Elsevier, 2020, pp. 42–55, doi:<a href=\"https://doi.org/10.1016/j.tcs.2019.06.031\">10.1016/j.tcs.2019.06.031</a>.","ista":"Avni G, Henzinger TA, Kupferman O. 2020. Dynamic resource allocation games. Theoretical Computer Science. 807, 42–55.","ama":"Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. <i>Theoretical Computer Science</i>. 2020;807:42-55. doi:<a href=\"https://doi.org/10.1016/j.tcs.2019.06.031\">10.1016/j.tcs.2019.06.031</a>"},"page":"42-55","project":[{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","call_identifier":"FWF"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"}],"volume":807,"department":[{"_id":"ToHe"}],"publication_status":"published","date_updated":"2026-04-16T09:35:15Z","article_type":"original","file":[{"success":1,"content_type":"application/pdf","file_name":"2020_TheoreticalCS_Avni.pdf","file_id":"8639","relation":"main_file","checksum":"e86635417f45eb2cd75778f91382f737","date_updated":"2020-10-09T06:31:22Z","access_level":"open_access","file_size":1413001,"creator":"dernst","date_created":"2020-10-09T06:31:22Z"}],"quality_controlled":"1","intvolume":"       807","date_created":"2019-08-04T21:59:20Z","oa_version":"Submitted Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"date_published":"2020-02-06T00:00:00Z","has_accepted_license":"1","type":"journal_article","isi":1,"author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","orcid":"0000-0001-5588-8287","last_name":"Avni"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1341"}]},"abstract":[{"lang":"eng","text":"In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability."}],"day":"06","publication_identifier":{"issn":["0304-3975"]},"publisher":"Elsevier","file_date_updated":"2020-10-09T06:31:22Z","doi":"10.1016/j.tcs.2019.06.031","ddc":["000"],"fulldoi":"https://doi.org/10.1016/j.tcs.2019.06.031","title":"Dynamic resource allocation games","scopus_import":"1","oa":1,"article_processing_charge":"No","year":"2020","status":"public","_id":"6761","month":"02","publication":"Theoretical Computer Science"},{"isi":1,"abstract":[{"lang":"eng","text":"Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses."}],"author":[{"orcid":"0000-0001-9439-3148","first_name":"Federico","full_name":"Stella, Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","last_name":"Stella"},{"first_name":"Eugenio","full_name":"Urdapilleta, Eugenio","last_name":"Urdapilleta"},{"last_name":"Luo","full_name":"Luo, Yifan","first_name":"Yifan"},{"first_name":"Alessandro","full_name":"Treves, Alessandro","last_name":"Treves"}],"pmid":1,"file_date_updated":"2020-07-14T12:47:40Z","doi":"10.1002/hipo.23144","publisher":"Wiley","fulldoi":"https://doi.org/10.1002/hipo.23144","ddc":["570"],"day":"01","publication_identifier":{"issn":["1050-9631"],"eissn":["1098-1063"]},"month":"04","_id":"6796","status":"public","year":"2020","publication":"Hippocampus","scopus_import":"1","title":"Partial coherence and frustration in self-organizing spherical grids","article_processing_charge":"No","oa":1,"citation":{"ama":"Stella F, Urdapilleta E, Luo Y, Treves A. Partial coherence and frustration in self-organizing spherical grids. <i>Hippocampus</i>. 2020;30(4):302-313. doi:<a href=\"https://doi.org/10.1002/hipo.23144\">10.1002/hipo.23144</a>","ista":"Stella F, Urdapilleta E, Luo Y, Treves A. 2020. Partial coherence and frustration in self-organizing spherical grids. Hippocampus. 30(4), 302–313.","mla":"Stella, Federico, et al. “Partial Coherence and Frustration in Self-Organizing Spherical Grids.” <i>Hippocampus</i>, vol. 30, no. 4, Wiley, 2020, pp. 302–13, doi:<a href=\"https://doi.org/10.1002/hipo.23144\">10.1002/hipo.23144</a>.","apa":"Stella, F., Urdapilleta, E., Luo, Y., &#38; Treves, A. (2020). Partial coherence and frustration in self-organizing spherical grids. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.23144\">https://doi.org/10.1002/hipo.23144</a>","ieee":"F. Stella, E. Urdapilleta, Y. Luo, and A. Treves, “Partial coherence and frustration in self-organizing spherical grids,” <i>Hippocampus</i>, vol. 30, no. 4. Wiley, pp. 302–313, 2020.","short":"F. Stella, E. Urdapilleta, Y. Luo, A. Treves, Hippocampus 30 (2020) 302–313.","chicago":"Stella, Federico, Eugenio Urdapilleta, Yifan Luo, and Alessandro Treves. “Partial Coherence and Frustration in Self-Organizing Spherical Grids.” <i>Hippocampus</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/hipo.23144\">https://doi.org/10.1002/hipo.23144</a>."},"page":"302-313","external_id":{"pmid":["31339190"],"isi":["000477299600001"]},"issue":"4","volume":30,"article_type":"original","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)"},"file":[{"access_level":"open_access","date_created":"2019-08-12T07:53:33Z","creator":"dernst","file_size":2370658,"file_name":"2019_Hippocampus_Stella.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:40Z","relation":"main_file","checksum":"7b54d22bfbfc0d1188a9ea24d985bfb2","file_id":"6800"}],"department":[{"_id":"JoCs"}],"publication_status":"published","date_updated":"2025-05-22T11:13:25Z","date_published":"2020-04-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","quality_controlled":"1","intvolume":"        30","language":[{"iso":"eng"}],"user_id":"9947682f-b9fa-11ee-9c4a-b3ffaafe6614","oa_version":"Published Version","date_created":"2019-08-11T21:59:24Z"},{"article_type":"original","date_updated":"2025-04-14T09:39:25Z","department":[{"_id":"JoDa"}],"publication_status":"published","type":"journal_article","date_published":"2020-03-01T00:00:00Z","oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-08-12T16:36:32Z","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       174","external_id":{"isi":["000525860400005"],"pmid":["31344404"]},"citation":{"chicago":"Jahr, Wiebke, Philipp Velicky, and Johann G Danzl. “Strategies to Maximize Performance in STimulated Emission Depletion (STED) Nanoscopy of Biological Specimens.” <i>Methods</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.ymeth.2019.07.019\">https://doi.org/10.1016/j.ymeth.2019.07.019</a>.","ista":"Jahr W, Velicky P, Danzl JG. 2020. Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. Methods. 174(3), 27–41.","ama":"Jahr W, Velicky P, Danzl JG. Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. <i>Methods</i>. 2020;174(3):27-41. doi:<a href=\"https://doi.org/10.1016/j.ymeth.2019.07.019\">10.1016/j.ymeth.2019.07.019</a>","apa":"Jahr, W., Velicky, P., &#38; Danzl, J. G. (2020). Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. <i>Methods</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ymeth.2019.07.019\">https://doi.org/10.1016/j.ymeth.2019.07.019</a>","mla":"Jahr, Wiebke, et al. “Strategies to Maximize Performance in STimulated Emission Depletion (STED) Nanoscopy of Biological Specimens.” <i>Methods</i>, vol. 174, no. 3, Elsevier, 2020, pp. 27–41, doi:<a href=\"https://doi.org/10.1016/j.ymeth.2019.07.019\">10.1016/j.ymeth.2019.07.019</a>.","ieee":"W. Jahr, P. Velicky, and J. G. Danzl, “Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens,” <i>Methods</i>, vol. 174, no. 3. Elsevier, pp. 27–41, 2020.","short":"W. Jahr, P. Velicky, J.G. Danzl, Methods 174 (2020) 27–41."},"page":"27-41","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100895/","open_access":"1"}],"issue":"3","volume":174,"project":[{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1016/j.ymeth.2019.07.019","publisher":"Elsevier","doi":"10.1016/j.ymeth.2019.07.019","publication_identifier":{"issn":["1046-2023"]},"day":"01","publication":"Methods","year":"2020","status":"public","_id":"6808","month":"03","oa":1,"article_processing_charge":"No","title":"Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens","scopus_import":"1","isi":1,"abstract":[{"lang":"eng","text":"Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions."}],"pmid":1,"author":[{"last_name":"Jahr","first_name":"Wiebke","full_name":"Jahr, Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velicky","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0002-2340-7431"},{"last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G"}]},{"ec_funded":1,"external_id":{"isi":["000536053300012"],"arxiv":["1812.03086"]},"citation":{"chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” <i>Communications in Mathematical Physics</i>. Springer, 2020. <a href=\"https://doi.org/10.1007/s00220-019-03555-9\">https://doi.org/10.1007/s00220-019-03555-9</a>.","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. <i>Communications in Mathematical Physics</i>. 2020;376:1311-1395. doi:<a href=\"https://doi.org/10.1007/s00220-019-03555-9\">10.1007/s00220-019-03555-9</a>","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 376, 1311–1395.","mla":"Boccato, Chiara, et al. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” <i>Communications in Mathematical Physics</i>, vol. 376, Springer, 2020, pp. 1311–95, doi:<a href=\"https://doi.org/10.1007/s00220-019-03555-9\">10.1007/s00220-019-03555-9</a>.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., &#38; Schlein, B. (2020). Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-019-03555-9\">https://doi.org/10.1007/s00220-019-03555-9</a>","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime,” <i>Communications in Mathematical Physics</i>, vol. 376. Springer, pp. 1311–1395, 2020.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Communications in Mathematical Physics 376 (2020) 1311–1395."},"page":"1311-1395","main_file_link":[{"url":"https://arxiv.org/abs/1812.03086","open_access":"1"}],"volume":376,"acknowledgement":"We would like to thank P. T. Nam and R. Seiringer for several useful discussions and\r\nfor suggesting us to use the localization techniques from [9]. C. Boccato has received funding from the\r\nEuropean Research Council (ERC) under the programme Horizon 2020 (Grant Agreement 694227). B. Schlein gratefully acknowledges support from the NCCR SwissMAP and from the Swiss National Foundation of Science (Grant No. 200020_1726230) through the SNF Grant “Dynamical and energetic properties of Bose–Einstein condensates”.","project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-04-14T07:27:00Z","department":[{"_id":"RoSe"}],"publication_status":"published","article_type":"original","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_created":"2019-09-24T17:30:59Z","language":[{"iso":"eng"}],"arxiv":1,"intvolume":"       376","quality_controlled":"1","type":"journal_article","date_published":"2020-06-01T00:00:00Z","isi":1,"author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","full_name":"Boccato, Chiara","first_name":"Chiara","last_name":"Boccato"},{"first_name":"Christian","full_name":"Brennecke, Christian","last_name":"Brennecke"},{"last_name":"Cenatiempo","first_name":"Serena","full_name":"Cenatiempo, Serena"},{"last_name":"Schlein","full_name":"Schlein, Benjamin","first_name":"Benjamin"}],"abstract":[{"text":"We consider systems of bosons trapped in a box, in the Gross–Pitaevskii regime. We show that low-energy states exhibit complete Bose–Einstein condensation with an optimal bound on the number of orthogonal excitations. This extends recent results obtained in Boccato et al. (Commun Math Phys 359(3):975–1026, 2018), removing the assumption of small interaction potential.","lang":"eng"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"day":"01","fulldoi":"https://doi.org/10.1007/s00220-019-03555-9","publisher":"Springer","doi":"10.1007/s00220-019-03555-9","oa":1,"article_processing_charge":"No","title":"Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime","scopus_import":"1","publication":"Communications in Mathematical Physics","year":"2020","_id":"6906","status":"public","month":"06"},{"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11263-019-01262-5"}],"record":[{"relation":"earlier_version","id":"6482","status":"public"}]},"abstract":[{"lang":"eng","text":"We study the problem of automatically detecting if a given multi-class classifier operates outside of its specifications (out-of-specs), i.e. on input data from a different distribution than what it was trained for. This is an important problem to solve on the road towards creating reliable computer vision systems for real-world applications, because the quality of a classifier’s predictions cannot be guaranteed if it operates out-of-specs. Previously proposed methods for out-of-specs detection make decisions on the level of single inputs. This, however, is insufficient to achieve low false positive rate and high false negative rates at the same time. In this work, we describe a new procedure named KS(conf), based on statistical reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied to the set of predicted confidence values for batches of samples. Working with batches instead of single samples allows increasing the true positive rate without negatively affecting the false positive rate, thereby overcoming a crucial limitation of single sample tests. We show by extensive experiments using a variety of convolutional network architectures and datasets that KS(conf) reliably detects out-of-specs situations even under conditions where other tests fail. It furthermore has a number of properties that make it an excellent candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with any classifier that outputs confidence scores, and requires no a priori knowledge about how the data distribution could change."}],"author":[{"last_name":"Sun","full_name":"Sun, Rémy","first_name":"Rémy"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"corr_author":"1","isi":1,"_id":"6944","month":"04","status":"public","year":"2020","publication":"International Journal of Computer Vision","scopus_import":"1","title":"KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications","article_processing_charge":"Yes (via OA deal)","oa":1,"doi":"10.1007/s11263-019-01232-x","file_date_updated":"2020-07-14T12:47:45Z","publisher":"Springer Nature","ddc":["004"],"fulldoi":"https://doi.org/10.1007/s11263-019-01232-x","day":"01","publication_identifier":{"eissn":["1573-1405"],"issn":["0920-5691"]},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"volume":128,"page":"970-995","citation":{"chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” <i>International Journal of Computer Vision</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11263-019-01232-x\">https://doi.org/10.1007/s11263-019-01232-x</a>.","ista":"Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 128(4), 970–995.","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. <i>International Journal of Computer Vision</i>. 2020;128(4):970-995. doi:<a href=\"https://doi.org/10.1007/s11263-019-01232-x\">10.1007/s11263-019-01232-x</a>","apa":"Sun, R., &#38; Lampert, C. (2020). KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. <i>International Journal of Computer Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11263-019-01232-x\">https://doi.org/10.1007/s11263-019-01232-x</a>","mla":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” <i>International Journal of Computer Vision</i>, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:<a href=\"https://doi.org/10.1007/s11263-019-01232-x\">10.1007/s11263-019-01232-x</a>.","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications,” <i>International Journal of Computer Vision</i>, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020.","short":"R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995."},"external_id":{"isi":["000494406800001"]},"ec_funded":1,"issue":"4","date_published":"2020-04-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","quality_controlled":"1","intvolume":"       128","language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2019-10-14T09:14:28Z","article_type":"original","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)"},"file":[{"access_level":"open_access","date_created":"2019-11-26T10:30:02Z","file_size":1715072,"creator":"dernst","content_type":"application/pdf","file_name":"2019_IJCV_Sun.pdf","date_updated":"2020-07-14T12:47:45Z","file_id":"7110","checksum":"155e63edf664dcacb3bdc1c2223e606f","relation":"main_file"}],"department":[{"_id":"ChLa"}],"publication_status":"published","date_updated":"2025-04-15T07:10:25Z"},{"publication_status":"published","department":[{"_id":"JiFr"}],"date_updated":"2025-04-14T07:45:04Z","article_type":"original","file":[{"access_level":"open_access","file_size":717345,"creator":"dernst","date_created":"2020-11-18T16:42:48Z","success":1,"content_type":"application/pdf","file_name":"2020_NewPhytologist_Zhang.pdf","file_id":"8772","relation":"main_file","checksum":"cd42ffdb381fd52812b9583d4d407139","date_updated":"2020-11-18T16:42:48Z"}],"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)"},"intvolume":"       225","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-11-12T11:41:32Z","oa_version":"Published Version","language":[{"iso":"eng"}],"date_published":"2020-02-01T00:00:00Z","has_accepted_license":"1","type":"journal_article","ec_funded":1,"issue":"3","external_id":{"isi":["000489638800001"],"pmid":["31603260"]},"page":"1049-1052","citation":{"short":"Y. Zhang, J. Friml, New Phytologist 225 (2020) 1049–1052.","ieee":"Y. Zhang and J. Friml, “Auxin guides roots to avoid obstacles during gravitropic growth,” <i>New Phytologist</i>, vol. 225, no. 3. Wiley, pp. 1049–1052, 2020.","apa":"Zhang, Y., &#38; Friml, J. (2020). Auxin guides roots to avoid obstacles during gravitropic growth. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16203\">https://doi.org/10.1111/nph.16203</a>","mla":"Zhang, Yuzhou, and Jiří Friml. “Auxin Guides Roots to Avoid Obstacles during Gravitropic Growth.” <i>New Phytologist</i>, vol. 225, no. 3, Wiley, 2020, pp. 1049–52, doi:<a href=\"https://doi.org/10.1111/nph.16203\">10.1111/nph.16203</a>.","ista":"Zhang Y, Friml J. 2020. Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. 225(3), 1049–1052.","ama":"Zhang Y, Friml J. Auxin guides roots to avoid obstacles during gravitropic growth. <i>New Phytologist</i>. 2020;225(3):1049-1052. doi:<a href=\"https://doi.org/10.1111/nph.16203\">10.1111/nph.16203</a>","chicago":"Zhang, Yuzhou, and Jiří Friml. “Auxin Guides Roots to Avoid Obstacles during Gravitropic Growth.” <i>New Phytologist</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/nph.16203\">https://doi.org/10.1111/nph.16203</a>."},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"volume":225,"day":"01","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"publisher":"Wiley","file_date_updated":"2020-11-18T16:42:48Z","doi":"10.1111/nph.16203","fulldoi":"https://doi.org/10.1111/nph.16203","ddc":["580"],"title":"Auxin guides roots to avoid obstacles during gravitropic growth","scopus_import":"1","oa":1,"article_processing_charge":"Yes (via OA deal)","year":"2020","_id":"6997","status":"public","month":"02","publication":"New Phytologist","corr_author":"1","isi":1,"author":[{"last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","first_name":"Yuzhou"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"pmid":1},{"status":"public","_id":"7004","month":"06","year":"2020","publication":"Communications in Mathematical Physics","scopus_import":"1","title":"Cohomological Hall algebras, vertex algebras and instantons","article_processing_charge":"No","oa":1,"doi":"10.1007/s00220-019-03575-5","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1007/s00220-019-03575-5","day":"01","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"abstract":[{"lang":"eng","text":"We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds."}],"author":[{"last_name":"Rapcak","full_name":"Rapcak, Miroslav","first_name":"Miroslav"},{"first_name":"Yan","full_name":"Soibelman, Yan","last_name":"Soibelman"},{"last_name":"Yang","first_name":"Yaping","full_name":"Yang, Yaping"},{"first_name":"Gufang","full_name":"Zhao, Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","last_name":"Zhao"}],"isi":1,"date_published":"2020-06-01T00:00:00Z","type":"journal_article","quality_controlled":"1","intvolume":"       376","arxiv":1,"language":[{"iso":"eng"}],"date_created":"2019-11-12T14:01:27Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","article_type":"original","department":[{"_id":"TaHa"}],"publication_status":"published","date_updated":"2025-04-14T09:12:46Z","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"volume":376,"main_file_link":[{"url":"https://arxiv.org/abs/1810.10402","open_access":"1"}],"citation":{"mla":"Rapcak, Miroslav, et al. “Cohomological Hall Algebras, Vertex Algebras and Instantons.” <i>Communications in Mathematical Physics</i>, vol. 376, Springer Nature, 2020, pp. 1803–73, doi:<a href=\"https://doi.org/10.1007/s00220-019-03575-5\">10.1007/s00220-019-03575-5</a>.","apa":"Rapcak, M., Soibelman, Y., Yang, Y., &#38; Zhao, G. (2020). Cohomological Hall algebras, vertex algebras and instantons. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03575-5\">https://doi.org/10.1007/s00220-019-03575-5</a>","ista":"Rapcak M, Soibelman Y, Yang Y, Zhao G. 2020. Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. 376, 1803–1873.","ama":"Rapcak M, Soibelman Y, Yang Y, Zhao G. Cohomological Hall algebras, vertex algebras and instantons. <i>Communications in Mathematical Physics</i>. 2020;376:1803-1873. doi:<a href=\"https://doi.org/10.1007/s00220-019-03575-5\">10.1007/s00220-019-03575-5</a>","short":"M. Rapcak, Y. Soibelman, Y. Yang, G. Zhao, Communications in Mathematical Physics 376 (2020) 1803–1873.","ieee":"M. Rapcak, Y. Soibelman, Y. Yang, and G. Zhao, “Cohomological Hall algebras, vertex algebras and instantons,” <i>Communications in Mathematical Physics</i>, vol. 376. Springer Nature, pp. 1803–1873, 2020.","chicago":"Rapcak, Miroslav, Yan Soibelman, Yaping Yang, and Gufang Zhao. “Cohomological Hall Algebras, Vertex Algebras and Instantons.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00220-019-03575-5\">https://doi.org/10.1007/s00220-019-03575-5</a>."},"page":"1803-1873","external_id":{"arxiv":["1810.10402"],"isi":["000536255500004"]},"ec_funded":1},{"volume":57,"acknowledgement":"This work was supported by National Eye Institute grants R01 EY012223 (RWN), R01 EY030123 (RWN), T32 EY027721 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), and a Vision Science Core grant P30 EY016665 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), an unrestricted funding grant from Research to Prevent Blindness (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), the Frederick A. Davis Endowment (RWN), and the Mr. and Mrs. George Taylor Foundation (RWN).","issue":"2","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035206/"}],"external_id":{"pmid":["31673950"],"isi":["000493754200001"]},"citation":{"chicago":"Donahue, RJ, Margaret E Maes, JA Grosser, and RW Nickells. “BAX-Depleted Retinal Ganglion Cells Survive and Become Quiescent Following Optic Nerve Damage.” <i>Molecular Neurobiology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s12035-019-01783-7\">https://doi.org/10.1007/s12035-019-01783-7</a>.","short":"R. Donahue, M.E. Maes, J. Grosser, R. Nickells, Molecular Neurobiology 57 (2020) 1070–1084.","ieee":"R. Donahue, M. E. Maes, J. Grosser, and R. Nickells, “BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage,” <i>Molecular Neurobiology</i>, vol. 57, no. 2. Springer Nature, pp. 1070–1084, 2020.","apa":"Donahue, R., Maes, M. E., Grosser, J., &#38; Nickells, R. (2020). BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. <i>Molecular Neurobiology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12035-019-01783-7\">https://doi.org/10.1007/s12035-019-01783-7</a>","mla":"Donahue, RJ, et al. “BAX-Depleted Retinal Ganglion Cells Survive and Become Quiescent Following Optic Nerve Damage.” <i>Molecular Neurobiology</i>, vol. 57, no. 2, Springer Nature, 2020, pp. 1070–1084, doi:<a href=\"https://doi.org/10.1007/s12035-019-01783-7\">10.1007/s12035-019-01783-7</a>.","ista":"Donahue R, Maes ME, Grosser J, Nickells R. 2020. BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. 57(2), 1070–1084.","ama":"Donahue R, Maes ME, Grosser J, Nickells R. BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. <i>Molecular Neurobiology</i>. 2020;57(2):1070–1084. doi:<a href=\"https://doi.org/10.1007/s12035-019-01783-7\">10.1007/s12035-019-01783-7</a>"},"page":"1070–1084","quality_controlled":"1","intvolume":"        57","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","date_created":"2019-11-18T14:18:39Z","language":[{"iso":"eng"}],"date_published":"2020-02-01T00:00:00Z","type":"journal_article","department":[{"_id":"SaSi"}],"publication_status":"published","date_updated":"2023-08-17T14:05:48Z","article_type":"original","author":[{"first_name":"RJ","full_name":"Donahue, RJ","last_name":"Donahue"},{"last_name":"Maes","first_name":"Margaret E","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grosser, JA","first_name":"JA","last_name":"Grosser"},{"last_name":"Nickells","first_name":"RW","full_name":"Nickells, RW"}],"pmid":1,"abstract":[{"lang":"eng","text":"Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality."}],"isi":1,"title":"BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage","scopus_import":"1","oa":1,"article_processing_charge":"No","year":"2020","_id":"7033","status":"public","month":"02","publication":"Molecular Neurobiology","day":"01","publication_identifier":{"issn":["0893-7648"],"eissn":["1559-1182"]},"publisher":"Springer Nature","doi":"10.1007/s12035-019-01783-7","fulldoi":"https://doi.org/10.1007/s12035-019-01783-7"},{"article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Scaling limits of discrete optimal transport","publication":"SIAM Journal on Mathematical Analysis","_id":"71","month":"10","status":"public","year":"2020","publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"day":"01","fulldoi":"https://doi.org/10.1137/19M1243440","doi":"10.1137/19M1243440","publisher":"Society for Industrial and Applied Mathematics","author":[{"full_name":"Gladbach, Peter","first_name":"Peter","last_name":"Gladbach"},{"last_name":"Kopfer","first_name":"Eva","full_name":"Kopfer, Eva"},{"first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","last_name":"Maas"}],"abstract":[{"lang":"eng","text":"We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric 𝕎2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of 𝕎2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric."}],"isi":1,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_created":"2018-12-11T11:44:28Z","intvolume":"        52","arxiv":1,"quality_controlled":"1","type":"journal_article","date_published":"2020-10-01T00:00:00Z","date_updated":"2025-07-10T11:54:14Z","publication_status":"published","department":[{"_id":"JaMa"}],"article_type":"original","volume":52,"publist_id":"7983","issue":"3","page":"2759-2802","citation":{"ieee":"P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 3. Society for Industrial and Applied Mathematics, pp. 2759–2802, 2020.","short":"P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802.","ista":"Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802.","ama":"Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport. <i>SIAM Journal on Mathematical Analysis</i>. 2020;52(3):2759-2802. doi:<a href=\"https://doi.org/10.1137/19M1243440\">10.1137/19M1243440</a>","apa":"Gladbach, P., Kopfer, E., &#38; Maas, J. (2020). Scaling limits of discrete optimal transport. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/19M1243440\">https://doi.org/10.1137/19M1243440</a>","mla":"Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:<a href=\"https://doi.org/10.1137/19M1243440\">10.1137/19M1243440</a>.","chicago":"Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2020. <a href=\"https://doi.org/10.1137/19M1243440\">https://doi.org/10.1137/19M1243440</a>."},"external_id":{"arxiv":["1809.01092"],"isi":["000546975100017"]},"main_file_link":[{"url":"https://arxiv.org/abs/1809.01092","open_access":"1"}]},{"quality_controlled":"1","intvolume":"        53","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-12-02T12:05:26Z","oa_version":"None","date_published":"2020-02-01T00:00:00Z","type":"journal_article","department":[{"_id":"JiFr"}],"publication_status":"published","date_updated":"2026-04-07T14:18:57Z","article_type":"original","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"}],"volume":53,"acknowledgement":"Research in J.F. laboratory is funded by the European Union's Horizon 2020 program (ERC grant agreement n° 742985); C.L. is supported by the Austrian Science Fund (FWF grant P 31493).","ec_funded":1,"issue":"2","citation":{"chicago":"Gallei, Michelle C, Christian Luschnig, and Jiří Friml. “Auxin Signalling in Growth: Schrödinger’s Cat out of the Bag.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.pbi.2019.10.003\">https://doi.org/10.1016/j.pbi.2019.10.003</a>.","ama":"Gallei MC, Luschnig C, Friml J. Auxin signalling in growth: Schrödinger’s cat out of the bag. <i>Current Opinion in Plant Biology</i>. 2020;53(2):43-49. doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.10.003\">10.1016/j.pbi.2019.10.003</a>","ista":"Gallei MC, Luschnig C, Friml J. 2020. Auxin signalling in growth: Schrödinger’s cat out of the bag. Current Opinion in Plant Biology. 53(2), 43–49.","apa":"Gallei, M. C., Luschnig, C., &#38; Friml, J. (2020). Auxin signalling in growth: Schrödinger’s cat out of the bag. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2019.10.003\">https://doi.org/10.1016/j.pbi.2019.10.003</a>","mla":"Gallei, Michelle C., et al. “Auxin Signalling in Growth: Schrödinger’s Cat out of the Bag.” <i>Current Opinion in Plant Biology</i>, vol. 53, no. 2, Elsevier, 2020, pp. 43–49, doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.10.003\">10.1016/j.pbi.2019.10.003</a>.","ieee":"M. C. Gallei, C. Luschnig, and J. Friml, “Auxin signalling in growth: Schrödinger’s cat out of the bag,” <i>Current Opinion in Plant Biology</i>, vol. 53, no. 2. Elsevier, pp. 43–49, 2020.","short":"M.C. Gallei, C. Luschnig, J. Friml, Current Opinion in Plant Biology 53 (2020) 43–49."},"page":"43-49","external_id":{"isi":["000521120600007"],"pmid":["31760231"]},"scopus_import":"1","title":"Auxin signalling in growth: Schrödinger's cat out of the bag","article_processing_charge":"No","_id":"7142","month":"02","status":"public","year":"2020","publication":"Current Opinion in Plant Biology","day":"01","publication_identifier":{"issn":["1369-5266"],"eissn":["1879-0356"]},"doi":"10.1016/j.pbi.2019.10.003","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.pbi.2019.10.003","author":[{"last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","first_name":"Michelle C","orcid":"0000-0003-1286-7368"},{"first_name":"Christian","full_name":"Luschnig, Christian","last_name":"Luschnig"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"}],"pmid":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"}]},"abstract":[{"text":"The phytohormone auxin acts as an amazingly versatile coordinator of plant growth and development. With its morphogen-like properties, auxin controls sites and timing of differentiation and/or growth responses both, in quantitative and qualitative terms. Specificity in the auxin response depends largely on distinct modes of signal transmission, by which individual cells perceive and convert auxin signals into a remarkable diversity of responses. The best understood, or so-called canonical mechanism of auxin perception ultimately results in variable adjustments of the cellular transcriptome, via a short, nuclear signal transduction pathway. Additional findings that accumulated over decades implied that an additional, presumably, cell surface-based auxin perception mechanism mediates very rapid cellular responses and decisively contributes to the cell's overall hormonal response. Recent investigations into both, nuclear and cell surface auxin signalling challenged this assumed partition of roles for different auxin signalling pathways and revealed an unexpected complexity in transcriptional and non-transcriptional cellular responses mediated by auxin.","lang":"eng"}],"isi":1,"corr_author":"1"},{"fulldoi":"https://doi.org/10.1002/cne.24792","ddc":["571","599"],"doi":"10.1002/cne.24792","publisher":"Wiley","publication_identifier":{"issn":["0021-9967"],"eissn":["1096-9861"]},"day":"01","publication":"Journal of Comparative Neurology","month":"04","_id":"7148","status":"public","year":"2020","article_processing_charge":"No","scopus_import":"1","title":"Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain","isi":1,"abstract":[{"lang":"eng","text":"In the cerebellum, GluD2 is exclusively expressed in Purkinje cells, where it regulates synapse formation and regeneration, synaptic plasticity, and motor learning. Delayed cognitive development in humans with GluD2 gene mutations suggests extracerebellar functions of GluD2. However, extracerebellar expression of GluD2 and its relationship with that of GluD1 are poorly understood. GluD2 mRNA and protein were widely detected, with relatively high levels observed in the olfactory glomerular layer, medial prefrontal cortex, cingulate cortex, retrosplenial granular cortex, olfactory tubercle, subiculum, striatum, lateral septum, anterodorsal thalamic nucleus, and arcuate hypothalamic nucleus. These regions were also enriched for GluD1, and many individual neurons coexpressed the two GluDs. In the retrosplenial granular cortex, GluD1 and GluD2 were selectively expressed at PSD‐95‐expressing glutamatergic synapses, and their coexpression on the same synapses was shown by SDS‐digested freeze‐fracture replica labeling. Biochemically, GluD1 and GluD2 formed coimmunoprecipitable complex formation in HEK293T cells and in the cerebral cortex and hippocampus. We further estimated the relative protein amount by quantitative immunoblotting using GluA2/GluD2 and GluA2/GluD1 chimeric proteins as standards for titration of GluD1 and GluD2 antibodies. Intriguingly, the relative amount of GluD2 was almost comparable to that of GluD1 in the postsynaptic density fraction prepared from the cerebral cortex and hippocampus. In contrast, GluD2 was overwhelmingly predominant in the cerebellum. Thus, we have determined the relative extracerebellar expression of GluD1 and GluD2 at regional, neuronal, and synaptic levels. These data provide a molecular–anatomical basis for possible competitive and cooperative interactions of GluD family members at synapses in various brain regions."}],"pmid":1,"author":[{"last_name":"Nakamoto","full_name":"Nakamoto, Chihiro","first_name":"Chihiro"},{"last_name":"Konno","first_name":"Kohtarou","full_name":"Konno, Kohtarou"},{"first_name":"Taisuke","full_name":"Miyazaki, Taisuke","last_name":"Miyazaki"},{"last_name":"Nakatsukasa","first_name":"Ena","full_name":"Nakatsukasa, Ena"},{"last_name":"Natsume","first_name":"Rie","full_name":"Natsume, Rie"},{"last_name":"Abe","first_name":"Manabu","full_name":"Abe, Manabu"},{"last_name":"Kawamura","full_name":"Kawamura, Meiko","first_name":"Meiko"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"first_name":"Miwako","full_name":"Yamasaki, Miwako","last_name":"Yamasaki"},{"last_name":"Sakimura","first_name":"Kenji","full_name":"Sakimura, Kenji"},{"last_name":"Watanabe","full_name":"Watanabe, Masahiko","first_name":"Masahiko"}],"article_type":"original","date_updated":"2023-08-17T14:06:50Z","publication_status":"published","department":[{"_id":"RySh"}],"type":"journal_article","has_accepted_license":"1","date_published":"2020-04-01T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2019-12-04T16:09:29Z","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","intvolume":"       528","citation":{"chicago":"Nakamoto, Chihiro, Kohtarou Konno, Taisuke Miyazaki, Ena Nakatsukasa, Rie Natsume, Manabu Abe, Meiko Kawamura, et al. “Expression Mapping, Quantification, and Complex Formation of GluD1 and GluD2 Glutamate Receptors in Adult Mouse Brain.” <i>Journal of Comparative Neurology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/cne.24792\">https://doi.org/10.1002/cne.24792</a>.","ieee":"C. Nakamoto <i>et al.</i>, “Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain,” <i>Journal of Comparative Neurology</i>, vol. 528, no. 6. Wiley, pp. 1003–1027, 2020.","short":"C. Nakamoto, K. Konno, T. Miyazaki, E. Nakatsukasa, R. Natsume, M. Abe, M. Kawamura, Y. Fukazawa, R. Shigemoto, M. Yamasaki, K. Sakimura, M. Watanabe, Journal of Comparative Neurology 528 (2020) 1003–1027.","ista":"Nakamoto C, Konno K, Miyazaki T, Nakatsukasa E, Natsume R, Abe M, Kawamura M, Fukazawa Y, Shigemoto R, Yamasaki M, Sakimura K, Watanabe M. 2020. Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain. Journal of Comparative Neurology. 528(6), 1003–1027.","ama":"Nakamoto C, Konno K, Miyazaki T, et al. Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain. <i>Journal of Comparative Neurology</i>. 2020;528(6):1003-1027. doi:<a href=\"https://doi.org/10.1002/cne.24792\">10.1002/cne.24792</a>","apa":"Nakamoto, C., Konno, K., Miyazaki, T., Nakatsukasa, E., Natsume, R., Abe, M., … Watanabe, M. (2020). Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain. <i>Journal of Comparative Neurology</i>. Wiley. <a href=\"https://doi.org/10.1002/cne.24792\">https://doi.org/10.1002/cne.24792</a>","mla":"Nakamoto, Chihiro, et al. “Expression Mapping, Quantification, and Complex Formation of GluD1 and GluD2 Glutamate Receptors in Adult Mouse Brain.” <i>Journal of Comparative Neurology</i>, vol. 528, no. 6, Wiley, 2020, pp. 1003–27, doi:<a href=\"https://doi.org/10.1002/cne.24792\">10.1002/cne.24792</a>."},"page":"1003-1027","external_id":{"isi":["000496410200001"],"pmid":["31625608"]},"issue":"6","volume":528,"acknowledgement":"This study was supported by Grants-in-Aid for Scientific Research to K.K. (18K06813), Y.M. (17K08503, 17H0631319), and K.S. (16H04650) and a grant for Scientific Research on Innovative Areas to K.S (16H06276) from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT). We thank K. Akashi, I. Watanabe-Iida, Y. Suzuki, and H. Azechi for technical assistance and advice, and H. Uchida for valuable discussions. We thank E. Kushiya,I. Yabe, C. Ohori, Y. Mochizuki, Y. Ishikawa, and N. Ishimoto for technical assistance in generating GluD1-KO mice."},{"date_updated":"2023-08-17T14:06:20Z","publication_status":"published","department":[{"_id":"GaNo"}],"article_type":"review","date_created":"2019-12-04T16:10:59Z","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        97","type":"journal_article","date_published":"2020-01-01T00:00:00Z","issue":"1","external_id":{"pmid":["31721174"],"isi":["000562561800001"]},"page":"3-11","citation":{"ista":"Avagliano L, Parenti I, Grazioli P, Di Fede E, Parodi C, Mariani M, Kaiser FJ, Selicorni A, Gervasini C, Massa V. 2020. Chromatinopathies: A focus on Cornelia de Lange syndrome. Clinical Genetics. 97(1), 3–11.","ama":"Avagliano L, Parenti I, Grazioli P, et al. Chromatinopathies: A focus on Cornelia de Lange syndrome. <i>Clinical Genetics</i>. 2020;97(1):3-11. doi:<a href=\"https://doi.org/10.1111/cge.13674\">10.1111/cge.13674</a>","mla":"Avagliano, Laura, et al. “Chromatinopathies: A Focus on Cornelia de Lange Syndrome.” <i>Clinical Genetics</i>, vol. 97, no. 1, Wiley, 2020, pp. 3–11, doi:<a href=\"https://doi.org/10.1111/cge.13674\">10.1111/cge.13674</a>.","apa":"Avagliano, L., Parenti, I., Grazioli, P., Di Fede, E., Parodi, C., Mariani, M., … Massa, V. (2020). Chromatinopathies: A focus on Cornelia de Lange syndrome. <i>Clinical Genetics</i>. Wiley. <a href=\"https://doi.org/10.1111/cge.13674\">https://doi.org/10.1111/cge.13674</a>","ieee":"L. Avagliano <i>et al.</i>, “Chromatinopathies: A focus on Cornelia de Lange syndrome,” <i>Clinical Genetics</i>, vol. 97, no. 1. Wiley, pp. 3–11, 2020.","short":"L. Avagliano, I. Parenti, P. Grazioli, E. Di Fede, C. Parodi, M. Mariani, F.J. Kaiser, A. Selicorni, C. Gervasini, V. Massa, Clinical Genetics 97 (2020) 3–11.","chicago":"Avagliano, Laura, Ilaria Parenti, Paolo Grazioli, Elisabetta Di Fede, Chiara Parodi, Milena Mariani, Frank J. Kaiser, Angelo Selicorni, Cristina Gervasini, and Valentina Massa. “Chromatinopathies: A Focus on Cornelia de Lange Syndrome.” <i>Clinical Genetics</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/cge.13674\">https://doi.org/10.1111/cge.13674</a>."},"volume":97,"acknowledgement":" Dipartimento DiSS, Università degli Studi di Milano, Grant/Award Number: Linea 2; Fondazione Cariplo, Grant/Award Number: 2015-0783; German Federal Ministry of Education and Research (BMBF), Grant/Award Number: CHROMATIN-Net; Medical Faculty of the University of Lübeck, Grant/Award Number: J09-2017; Nickel & Co S.p.A.; Università degli Studi di Milano, Grant/Award Numbers: Molecular & Translational Medicine PhD Scholarship, Translational Medicine PhD Scholarship","publication_identifier":{"eissn":["1399-0004"],"issn":["0009-9163"]},"day":"01","fulldoi":"https://doi.org/10.1111/cge.13674","publisher":"Wiley","doi":"10.1111/cge.13674","article_processing_charge":"No","title":"Chromatinopathies: A focus on Cornelia de Lange syndrome","scopus_import":"1","publication":"Clinical Genetics","year":"2020","_id":"7149","status":"public","month":"01","isi":1,"pmid":1,"author":[{"first_name":"Laura","full_name":"Avagliano, Laura","last_name":"Avagliano"},{"full_name":"Parenti, Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","first_name":"Ilaria","last_name":"Parenti"},{"last_name":"Grazioli","full_name":"Grazioli, Paolo","first_name":"Paolo"},{"first_name":"Elisabetta","full_name":"Di Fede, Elisabetta","last_name":"Di Fede"},{"last_name":"Parodi","full_name":"Parodi, Chiara","first_name":"Chiara"},{"first_name":"Milena","full_name":"Mariani, Milena","last_name":"Mariani"},{"last_name":"Kaiser","first_name":"Frank J.","full_name":"Kaiser, Frank J."},{"first_name":"Angelo","full_name":"Selicorni, Angelo","last_name":"Selicorni"},{"first_name":"Cristina","full_name":"Gervasini, Cristina","last_name":"Gervasini"},{"last_name":"Massa","full_name":"Massa, Valentina","first_name":"Valentina"}],"abstract":[{"lang":"eng","text":"In recent years, many genes have been associated with chromatinopathies classified as “Cornelia de Lange Syndrome‐like.” It is known that the phenotype of these patients becomes less recognizable, overlapping to features characteristic of other syndromes caused by genetic variants affecting different regulators of chromatin structure and function. Therefore, Cornelia de Lange syndrome diagnosis might be arduous due to the seldom discordance between unexpected molecular diagnosis and clinical evaluation. Here, we review the molecular features of Cornelia de Lange syndrome, supporting the hypothesis that “CdLS‐like syndromes” are part of a larger “rare disease family” sharing multiple clinical features and common disrupted molecular pathways."}]},{"isi":1,"author":[{"last_name":"Salazar","full_name":"Salazar, Juan Esteban","first_name":"Juan Esteban"},{"first_name":"Daniel","full_name":"Severin, Daniel","last_name":"Severin"},{"last_name":"Vega Zuniga","first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fernández-Aburto, Pedro","first_name":"Pedro","last_name":"Fernández-Aburto"},{"first_name":"Alfonso","full_name":"Deichler, Alfonso","last_name":"Deichler"},{"last_name":"Sallaberry A.","first_name":"Michel","full_name":"Sallaberry A., Michel"},{"full_name":"Mpodozis, Jorge","first_name":"Jorge","last_name":"Mpodozis"}],"pmid":1,"abstract":[{"lang":"eng","text":"Nocturnal animals that rely on their visual system for foraging, mating, and navigation usually exhibit specific traits associated with living in scotopic conditions. Most nocturnal birds have several visual specializations, such as enlarged eyes and an increased orbital convergence. However, the actual role of binocular vision in nocturnal foraging is still debated. Nightjars (Aves: Caprimulgidae) are predators that actively pursue and capture flying insects in crepuscular and nocturnal environments, mainly using a conspicuous “sit-and-wait” tactic on which pursuit begins with an insect flying over the bird that sits on the ground. In this study, we describe the visual system of the band-winged nightjar (Systellura longirostris), with emphasis on anatomical features previously described as relevant for nocturnal birds. Orbit convergence, determined by 3D scanning of the skull, was 73.28°. The visual field, determined by ophthalmoscopic reflex, exhibits an area of maximum binocular overlap of 42°, and it is dorsally oriented. The eyes showed a nocturnal-like normalized corneal aperture/axial length index. Retinal ganglion cells (RGCs) were relatively scant, and distributed in an unusual oblique-band pattern, with higher concentrations in the ventrotemporal quadrant. Together, these results indicate that the band-winged nightjar exhibits a retinal specialization associated with the binocular area of their dorsal visual field, a relevant area for pursuit triggering and prey attacks. The RGC distribution observed is unusual among birds, but similar to that of some visually dependent insectivorous bats, suggesting that those features might be convergent in relation to feeding strategies."}],"day":"01","publication_identifier":{"issn":["0006-8977"],"eissn":["1421-9743"]},"doi":"10.1159/000504162","publisher":"Karger Publishers","fulldoi":"https://doi.org/10.1159/000504162","scopus_import":"1","title":"Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes)","article_processing_charge":"No","_id":"7160","status":"public","month":"01","year":"2020","publication":"Brain, Behavior and Evolution","issue":"1-4","citation":{"chicago":"Salazar, Juan Esteban, Daniel Severin, Tomas A Vega Zuniga, Pedro Fernández-Aburto, Alfonso Deichler, Michel Sallaberry A., and Jorge Mpodozis. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” <i>Brain, Behavior and Evolution</i>. Karger Publishers, 2020. <a href=\"https://doi.org/10.1159/000504162\">https://doi.org/10.1159/000504162</a>.","ieee":"J. E. Salazar <i>et al.</i>, “Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes),” <i>Brain, Behavior and Evolution</i>, vol. 94, no. 1–4. Karger Publishers, pp. 27–36, 2020.","short":"J.E. Salazar, D. Severin, T.A. Vega Zuniga, P. Fernández-Aburto, A. Deichler, M. Sallaberry A., J. Mpodozis, Brain, Behavior and Evolution 94 (2020) 27–36.","ista":"Salazar JE, Severin D, Vega Zuniga TA, Fernández-Aburto P, Deichler A, Sallaberry A. M, Mpodozis J. 2020. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 94(1–4), 27–36.","ama":"Salazar JE, Severin D, Vega Zuniga TA, et al. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). <i>Brain, Behavior and Evolution</i>. 2020;94(1-4):27-36. doi:<a href=\"https://doi.org/10.1159/000504162\">10.1159/000504162</a>","mla":"Salazar, Juan Esteban, et al. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” <i>Brain, Behavior and Evolution</i>, vol. 94, no. 1–4, Karger Publishers, 2020, pp. 27–36, doi:<a href=\"https://doi.org/10.1159/000504162\">10.1159/000504162</a>.","apa":"Salazar, J. E., Severin, D., Vega Zuniga, T. A., Fernández-Aburto, P., Deichler, A., Sallaberry A., M., &#38; Mpodozis, J. (2020). Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). <i>Brain, Behavior and Evolution</i>. Karger Publishers. <a href=\"https://doi.org/10.1159/000504162\">https://doi.org/10.1159/000504162</a>"},"page":"27-36","external_id":{"pmid":["31751995"],"isi":["000522856600004"]},"volume":94,"department":[{"_id":"MaJö"}],"publication_status":"published","date_updated":"2024-02-22T15:18:34Z","article_type":"original","quality_controlled":"1","intvolume":"        94","language":[{"iso":"eng"}],"oa_version":"None","date_created":"2019-12-09T09:04:13Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2020-01-01T00:00:00Z","type":"journal_article"},{"author":[{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec"}],"degree_awarded":"PhD","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"5751"},{"status":"public","relation":"dissertation_contains","id":"7210"},{"status":"public","relation":"dissertation_contains","id":"7212"}]},"abstract":[{"text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.","lang":"eng"}],"corr_author":"1","title":"A role of graphs in evolutionary processes","article_processing_charge":"No","oa":1,"_id":"7196","status":"public","month":"01","year":"2020","alternative_title":["ISTA Thesis"],"day":"12","publication_identifier":{"eissn":["2663-337X"]},"OA_place":"publisher","file_date_updated":"2020-07-14T12:47:52Z","doi":"10.15479/AT:ISTA:7196","publisher":"Institute of Science and Technology Austria","ddc":["519"],"fulldoi":"https://doi.org/10.15479/AT:ISTA:7196","supervisor":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"page":"144","citation":{"apa":"Tkadlec, J. (2020). <i>A role of graphs in evolutionary processes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7196\">https://doi.org/10.15479/AT:ISTA:7196</a>","mla":"Tkadlec, Josef. <i>A Role of Graphs in Evolutionary Processes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7196\">10.15479/AT:ISTA:7196</a>.","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7196\">10.15479/AT:ISTA:7196</a>","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7196\">https://doi.org/10.15479/AT:ISTA:7196</a>."},"language":[{"iso":"eng"}],"date_created":"2019-12-20T12:26:36Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","date_published":"2020-01-12T00:00:00Z","type":"dissertation","has_accepted_license":"1","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_updated":"2026-04-16T08:32:37Z","file":[{"file_size":21100497,"creator":"jtkadlec","date_created":"2020-01-12T11:49:49Z","access_level":"closed","file_id":"7255","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","relation":"source_file","date_updated":"2020-07-14T12:47:52Z","content_type":"application/zip","file_name":"thesis.zip"},{"content_type":"application/pdf","file_name":"2020_Tkadlec_Thesis.pdf","file_id":"7367","relation":"main_file","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","date_updated":"2020-07-14T12:47:52Z","access_level":"open_access","file_size":11670983,"creator":"dernst","date_created":"2020-01-28T07:32:42Z"}]},{"volume":7,"citation":{"mla":"Li, Yang, et al. “Root Growth Adaptation Is Mediated by PYLs ABA Receptor-PP2A Protein Phosphatase Complex.” <i>Advanced Science</i>, vol. 7, no. 3, 1901455, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/advs.201901455\">10.1002/advs.201901455</a>.","apa":"Li, Y., Wang, Y., Tan, S., Li, Z., Yuan, Z., Glanc, M., … Zhang, J. (2020). Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex. <i>Advanced Science</i>. Wiley. <a href=\"https://doi.org/10.1002/advs.201901455\">https://doi.org/10.1002/advs.201901455</a>","ama":"Li Y, Wang Y, Tan S, et al. Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex. <i>Advanced Science</i>. 2020;7(3). doi:<a href=\"https://doi.org/10.1002/advs.201901455\">10.1002/advs.201901455</a>","ista":"Li Y, Wang Y, Tan S, Li Z, Yuan Z, Glanc M, Domjan D, Wang K, Xuan W, Guo Y, Gong Z, Friml J, Zhang J. 2020. Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex. Advanced Science. 7(3), 1901455.","short":"Y. Li, Y. Wang, S. Tan, Z. Li, Z. Yuan, M. Glanc, D. Domjan, K. Wang, W. Xuan, Y. Guo, Z. Gong, J. Friml, J. Zhang, Advanced Science 7 (2020).","ieee":"Y. Li <i>et al.</i>, “Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex,” <i>Advanced Science</i>, vol. 7, no. 3. Wiley, 2020.","chicago":"Li, Yang, Yaping Wang, Shutang Tan, Zhen Li, Zhi Yuan, Matous Glanc, David Domjan, et al. “Root Growth Adaptation Is Mediated by PYLs ABA Receptor-PP2A Protein Phosphatase Complex.” <i>Advanced Science</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/advs.201901455\">https://doi.org/10.1002/advs.201901455</a>."},"external_id":{"pmid":["32042554"],"isi":["000501912800001"]},"issue":"3","type":"journal_article","has_accepted_license":"1","date_published":"2020-02-05T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-12-22T23:00:43Z","intvolume":"         7","quality_controlled":"1","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)"},"file":[{"creator":"dernst","file_size":3586924,"date_created":"2020-02-24T14:29:54Z","access_level":"open_access","checksum":"016eeab5860860af038e2da95ffe75c3","relation":"main_file","file_id":"7519","date_updated":"2020-07-14T12:47:53Z","file_name":"2020_AdvScience_Li.pdf","content_type":"application/pdf"}],"article_type":"original","date_updated":"2023-08-17T14:13:17Z","publication_status":"published","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"Plant root architecture dynamically adapts to various environmental conditions, such as salt‐containing soil. The phytohormone abscisic acid (ABA) is involved among others also in these developmental adaptations, but the underlying molecular mechanism remains elusive. Here, a novel branch of the ABA signaling pathway in Arabidopsis involving PYR/PYL/RCAR (abbreviated as PYLs) receptor‐protein phosphatase 2A (PP2A) complex that acts in parallel to the canonical PYLs‐protein phosphatase 2C (PP2C) mechanism is identified. The PYLs‐PP2A signaling modulates root gravitropism and lateral root formation through regulating phytohormone auxin transport. In optimal conditions, PYLs ABA receptor interacts with the catalytic subunits of PP2A, increasing their phosphatase activity and thus counteracting PINOID (PID) kinase‐mediated phosphorylation of PIN‐FORMED (PIN) auxin transporters. By contrast, in salt and osmotic stress conditions, ABA binds to PYLs, inhibiting the PP2A activity, which leads to increased PIN phosphorylation and consequently modulated directional auxin transport leading to adapted root architecture. This work reveals an adaptive mechanism that may flexibly adjust plant root growth to withstand saline and osmotic stresses. It occurs via the cross‐talk between the stress hormone ABA and the versatile developmental regulator auxin."}],"pmid":1,"author":[{"full_name":"Li, Yang","first_name":"Yang","last_name":"Li"},{"first_name":"Yaping","full_name":"Wang, Yaping","last_name":"Wang"},{"last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"first_name":"Zhen","full_name":"Li, Zhen","last_name":"Li"},{"last_name":"Yuan","full_name":"Yuan, Zhi","first_name":"Zhi"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"first_name":"David","orcid":"0000-0003-2267-106X","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","full_name":"Domjan, David","last_name":"Domjan"},{"last_name":"Wang","first_name":"Kai","full_name":"Wang, Kai"},{"first_name":"Wei","full_name":"Xuan, Wei","last_name":"Xuan"},{"last_name":"Guo","full_name":"Guo, Yan","first_name":"Yan"},{"full_name":"Gong, Zhizhong","first_name":"Zhizhong","last_name":"Gong"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Zhang, Jing","first_name":"Jing","last_name":"Zhang"}],"isi":1,"article_number":"1901455","publication":"Advanced Science","status":"public","_id":"7204","month":"02","year":"2020","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex","fulldoi":"https://doi.org/10.1002/advs.201901455","ddc":["580"],"file_date_updated":"2020-07-14T12:47:53Z","doi":"10.1002/advs.201901455","publisher":"Wiley","publication_identifier":{"eissn":["2198-3844"]},"day":"05"},{"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)"},"file":[{"access_level":"open_access","creator":"dernst","file_size":885611,"date_created":"2020-09-22T09:42:18Z","success":1,"file_name":"2020_EvolBiology_Johannesson.pdf","content_type":"application/pdf","checksum":"7534ff0839709c0c5265c12d29432f03","relation":"main_file","file_id":"8553","date_updated":"2020-09-22T09:42:18Z"}],"article_type":"original","date_updated":"2025-07-10T11:54:22Z","department":[{"_id":"NiBa"}],"publication_status":"published","type":"journal_article","has_accepted_license":"1","date_published":"2020-03-01T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2019-12-22T23:00:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        33","quality_controlled":"1","citation":{"apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., &#38; Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13570\">https://doi.org/10.1111/jeb.13570</a>","mla":"Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” <i>Journal of Evolutionary Biology</i>, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:<a href=\"https://doi.org/10.1111/jeb.13570\">10.1111/jeb.13570</a>.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? <i>Journal of Evolutionary Biology</i>. 2020;33(3):342-351. doi:<a href=\"https://doi.org/10.1111/jeb.13570\">10.1111/jeb.13570</a>","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351.","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” <i>Journal of Evolutionary Biology</i>, vol. 33, no. 3. Wiley, pp. 342–351, 2020.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” <i>Journal of Evolutionary Biology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/jeb.13570\">https://doi.org/10.1111/jeb.13570</a>."},"page":"342-351","external_id":{"pmid":["31724256"],"isi":["000500954800001"]},"issue":"3","volume":33,"ddc":["570"],"fulldoi":"https://doi.org/10.1111/jeb.13570","file_date_updated":"2020-09-22T09:42:18Z","doi":"10.1111/jeb.13570","publisher":"Wiley","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"day":"01","publication":"Journal of Evolutionary Biology","status":"public","_id":"7205","month":"03","year":"2020","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?","isi":1,"abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13067"}]},"pmid":1,"author":[{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Zagrodzka, Zuzanna","first_name":"Zuzanna","last_name":"Zagrodzka"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}]},{"isi":1,"abstract":[{"text":"The hippocampus plays key roles in learning and memory and is a main target of Alzheimer's disease (AD), which causes progressive memory impairments. Despite numerous investigations about the processes required for the normal hippocampal functions, the neurotransmitter receptors involved in the synaptic deficits by which AD disables the hippocampus are not yet characterized. By combining histoblots, western blots, immunohistochemistry and high‐resolution immunoelectron microscopic methods for GABAB receptors, this study provides a quantitative description of the expression and the subcellular localization of GABAB1 in the hippocampus in a mouse model of AD at 1, 6 and 12 months of age. Western blots and histoblots showed that the total amount of protein and the laminar expression pattern of GABAB1 were similar in APP/PS1 mice and in age‐matched wild‐type mice. In contrast, immunoelectron microscopic techniques showed that the subcellular localization of GABAB1 subunit did not change significantly in APP/PS1 mice at 1 month of age, was significantly reduced in the stratum lacunosum‐moleculare of CA1 pyramidal cells at 6 months of age and significantly reduced at the membrane surface of CA1 pyramidal cells at 12 months of age. This reduction of plasma membrane GABAB1 was paralleled by a significant increase of the subunit at the intracellular sites. We further observed a decrease of membrane‐targeted GABAB receptors in axon terminals contacting CA1 pyramidal cells. Our data demonstrate compartment‐ and age‐dependent reduction of plasma membrane‐targeted GABAB receptors in the CA1 region of the hippocampus, suggesting that this decrease might be enough to alter the GABAB‐mediated synaptic transmission taking place in AD.","lang":"eng"}],"pmid":1,"author":[{"first_name":"Alejandro","full_name":"Martín-Belmonte, Alejandro","last_name":"Martín-Belmonte"},{"full_name":"Aguado, Carolina","first_name":"Carolina","last_name":"Aguado"},{"last_name":"Alfaro-Ruíz","first_name":"Rocío","full_name":"Alfaro-Ruíz, Rocío"},{"last_name":"Moreno-Martínez","full_name":"Moreno-Martínez, Ana Esther","first_name":"Ana Esther"},{"full_name":"De La Ossa, Luis","first_name":"Luis","last_name":"De La Ossa"},{"full_name":"Martínez-Hernández, José","first_name":"José","last_name":"Martínez-Hernández"},{"last_name":"Buisson","first_name":"Alain","full_name":"Buisson, Alain"},{"last_name":"Früh","full_name":"Früh, Simon","first_name":"Simon"},{"full_name":"Bettler, Bernhard","first_name":"Bernhard","last_name":"Bettler"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"last_name":"Luján","full_name":"Luján, Rafael","first_name":"Rafael"}],"ddc":["570"],"fulldoi":"https://doi.org/10.1111/bpa.12802","publisher":"Wiley","file_date_updated":"2020-09-22T09:47:19Z","doi":"10.1111/bpa.12802","publication_identifier":{"eissn":["1750-3639"],"issn":["1015-6305"]},"day":"01","publication":"Brain Pathology","year":"2020","status":"public","_id":"7207","month":"05","oa":1,"article_processing_charge":"No","title":"Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer's disease","scopus_import":"1","external_id":{"pmid":["31729777"],"isi":["000502270900001"]},"citation":{"chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA&#62;B&#60; Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” <i>Brain Pathology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/bpa.12802\">https://doi.org/10.1111/bpa.12802</a>.","ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Reduction in the neuronal surface of post and presynaptic GABA&#62;B&#60; receptors in the hippocampus in a mouse model of Alzheimer’s disease. <i>Brain Pathology</i>. 2020;30(3):554-575. doi:<a href=\"https://doi.org/10.1111/bpa.12802\">10.1111/bpa.12802</a>","ista":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Früh S, Bettler B, Shigemoto R, Fukazawa Y, Luján R. 2020. Reduction in the neuronal surface of post and presynaptic GABA&#62;B&#60; receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 30(3), 554–575.","mla":"Martín-Belmonte, Alejandro, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA&#62;B&#60; Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” <i>Brain Pathology</i>, vol. 30, no. 3, Wiley, 2020, pp. 554–75, doi:<a href=\"https://doi.org/10.1111/bpa.12802\">10.1111/bpa.12802</a>.","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Reduction in the neuronal surface of post and presynaptic GABA&#62;B&#60; receptors in the hippocampus in a mouse model of Alzheimer’s disease. <i>Brain Pathology</i>. Wiley. <a href=\"https://doi.org/10.1111/bpa.12802\">https://doi.org/10.1111/bpa.12802</a>","ieee":"A. Martín-Belmonte <i>et al.</i>, “Reduction in the neuronal surface of post and presynaptic GABA&#62;B&#60; receptors in the hippocampus in a mouse model of Alzheimer’s disease,” <i>Brain Pathology</i>, vol. 30, no. 3. Wiley, pp. 554–575, 2020.","short":"A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, S. Früh, B. Bettler, R. Shigemoto, Y. Fukazawa, R. Luján, Brain Pathology 30 (2020) 554–575."},"page":"554-575","issue":"3","ec_funded":1,"volume":30,"project":[{"call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425"},{"_id":"26436750-B435-11E9-9278-68D0E5697425","grant_number":"785907","name":"Human Brain Project Specific Grant Agreement 2","call_identifier":"H2020"}],"file":[{"date_updated":"2020-09-22T09:47:19Z","file_id":"8554","checksum":"549cc1b18f638a21d17a939ba5563fa9","relation":"main_file","content_type":"application/pdf","file_name":"2020_BrainPathology_MartinBelmonte.pdf","success":1,"date_created":"2020-09-22T09:47:19Z","file_size":4220935,"creator":"dernst","access_level":"open_access"}],"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)"},"article_type":"original","date_updated":"2025-07-10T11:54:22Z","department":[{"_id":"RySh"}],"publication_status":"published","has_accepted_license":"1","type":"journal_article","date_published":"2020-05-01T00:00:00Z","oa_version":"Published Version","date_created":"2019-12-22T23:00:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"intvolume":"        30","quality_controlled":"1"},{"ec_funded":1,"external_id":{"arxiv":["1906.02785"],"isi":["000510916500025"]},"citation":{"chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” <i>PLoS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007494\">https://doi.org/10.1371/journal.pcbi.1007494</a>.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007494\">https://doi.org/10.1371/journal.pcbi.1007494</a>","mla":"Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” <i>PLoS Computational Biology</i>, vol. 16, e1007494, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007494\">10.1371/journal.pcbi.1007494</a>.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. <i>PLoS computational biology</i>. 2020;16. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007494\">10.1371/journal.pcbi.1007494</a>","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020).","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” <i>PLoS computational biology</i>, vol. 16. Public Library of Science, 2020."},"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"volume":16,"department":[{"_id":"KrCh"}],"publication_status":"published","date_updated":"2026-04-16T08:32:38Z","article_type":"original","file":[{"file_name":"2020_PlosCompBio_Tkadlec.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:53Z","relation":"main_file","checksum":"ce32ee2d2f53aed832f78bbd47e882df","file_id":"7441","access_level":"open_access","date_created":"2020-02-03T07:32:42Z","creator":"dernst","file_size":1817531}],"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)"},"intvolume":"        16","quality_controlled":"1","arxiv":1,"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2019-12-23T13:45:11Z","language":[{"iso":"eng"}],"date_published":"2020-01-17T00:00:00Z","has_accepted_license":"1","type":"journal_article","article_number":"e1007494","isi":1,"author":[{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"related_material":{"record":[{"status":"public","id":"7196","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process."}],"day":"17","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1007494","file_date_updated":"2020-07-14T12:47:53Z","fulldoi":"https://doi.org/10.1371/journal.pcbi.1007494","ddc":["000"],"title":"Limits on amplifiers of natural selection under death-Birth updating","scopus_import":"1","oa":1,"article_processing_charge":"No","year":"2020","_id":"7212","status":"public","month":"01","publication":"PLoS computational biology"},{"fulldoi":"https://doi.org/10.1007/978-3-030-36687-2_3","ddc":["004"],"publisher":"Springer Nature","doi":"10.1007/978-3-030-36687-2_3","file_date_updated":"2020-10-08T08:16:48Z","publication_identifier":{"eissn":["1860-9503"],"issn":["1860-949X"],"isbn":["9783030366865"]},"day":"01","conference":{"start_date":"2019-12-10","end_date":"2019-12-12","name":"COMPLEX: International Conference on Complex Networks and their Applications","location":"Lisbon, Portugal"},"publication":"Complex Networks and their applications VIII","alternative_title":["SCI"],"year":"2020","status":"public","_id":"7213","month":"01","oa":1,"article_processing_charge":"No","title":"A persistent homology perspective to the link prediction problem","scopus_import":"1","isi":1,"abstract":[{"lang":"eng","text":"Persistent homology is a powerful tool in Topological Data Analysis (TDA) to capture the topological properties of data succinctly at different spatial resolutions. For graphical data, the shape, and structure of the neighborhood of individual data items (nodes) are an essential means of characterizing their properties. We propose the use of persistent homology methods to capture structural and topological properties of graphs and use it to address the problem of link prediction. We achieve encouraging results on nine different real-world datasets that attest to the potential of persistent homology-based methods for network analysis."}],"author":[{"full_name":"Bhatia, Sumit","first_name":"Sumit","last_name":"Bhatia"},{"last_name":"Chatterjee","orcid":"0000-0002-2742-4028","first_name":"Bapi","full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nathani","first_name":"Deepak","full_name":"Nathani, Deepak"},{"first_name":"Manohar","full_name":"Kaul, Manohar","last_name":"Kaul"}],"file":[{"access_level":"open_access","date_created":"2020-10-08T08:16:48Z","creator":"bchatter","file_size":310598,"file_name":"main.pdf","content_type":"application/pdf","success":1,"date_updated":"2020-10-08T08:16:48Z","relation":"main_file","checksum":"8951f094c8c7dae9ff8db885199bc296","file_id":"8625"}],"date_updated":"2025-07-10T11:54:23Z","department":[{"_id":"DaAl"}],"publication_status":"published","has_accepted_license":"1","type":"conference","date_published":"2020-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-12-29T23:00:45Z","oa_version":"Submitted Version","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       881","external_id":{"isi":["000843927300003"]},"citation":{"chicago":"Bhatia, Sumit, Bapi Chatterjee, Deepak Nathani, and Manohar Kaul. “A Persistent Homology Perspective to the Link Prediction Problem.” In <i>Complex Networks and Their Applications VIII</i>, 881:27–39. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-36687-2_3\">https://doi.org/10.1007/978-3-030-36687-2_3</a>.","short":"S. Bhatia, B. Chatterjee, D. Nathani, M. Kaul, in:, Complex Networks and Their Applications VIII, Springer Nature, 2020, pp. 27–39.","ieee":"S. Bhatia, B. Chatterjee, D. Nathani, and M. Kaul, “A persistent homology perspective to the link prediction problem,” in <i>Complex Networks and their applications VIII</i>, Lisbon, Portugal, 2020, vol. 881, pp. 27–39.","mla":"Bhatia, Sumit, et al. “A Persistent Homology Perspective to the Link Prediction Problem.” <i>Complex Networks and Their Applications VIII</i>, vol. 881, Springer Nature, 2020, pp. 27–39, doi:<a href=\"https://doi.org/10.1007/978-3-030-36687-2_3\">10.1007/978-3-030-36687-2_3</a>.","apa":"Bhatia, S., Chatterjee, B., Nathani, D., &#38; Kaul, M. (2020). A persistent homology perspective to the link prediction problem. In <i>Complex Networks and their applications VIII</i> (Vol. 881, pp. 27–39). Lisbon, Portugal: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-36687-2_3\">https://doi.org/10.1007/978-3-030-36687-2_3</a>","ista":"Bhatia S, Chatterjee B, Nathani D, Kaul M. 2020. A persistent homology perspective to the link prediction problem. Complex Networks and their applications VIII. COMPLEX: International Conference on Complex Networks and their Applications, SCI, vol. 881, 27–39.","ama":"Bhatia S, Chatterjee B, Nathani D, Kaul M. A persistent homology perspective to the link prediction problem. In: <i>Complex Networks and Their Applications VIII</i>. Vol 881. Springer Nature; 2020:27-39. doi:<a href=\"https://doi.org/10.1007/978-3-030-36687-2_3\">10.1007/978-3-030-36687-2_3</a>"},"page":"27-39","ec_funded":1,"volume":881,"project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}]}]