[{"_id":"11432","publication":"Computer Graphics Forum","year":"2022","month":"05","publisher":"Wiley","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1111/cgf.14478","scopus_import":"1","date_published":"2022-05-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"external_id":{"isi":["000802723900027"]},"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria and MFX Team at INRIA for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","article_processing_charge":"No","volume":41,"citation":{"ieee":"C. Schreck and C. Wojtan, “Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method,” <i>Computer Graphics Forum</i>, vol. 41, no. 2. Wiley, pp. 343–353, 2022.","mla":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>, vol. 41, no. 2, Wiley, 2022, pp. 343–53, doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>.","chicago":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>.","ista":"Schreck C, Wojtan C. 2022. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. Computer Graphics Forum. 41(2), 343–353.","ama":"Schreck C, Wojtan C. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. 2022;41(2):343-353. doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>","apa":"Schreck, C., &#38; Wojtan, C. (2022). Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 41 (2022) 343–353."},"date_updated":"2024-10-22T09:58:19Z","ec_funded":1,"issue":"2","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"status":"public","publication_status":"published","day":"01","corr_author":"1","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03641349/","open_access":"1"}],"page":"343-353","intvolume":"        41","type":"journal_article","project":[{"call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"author":[{"last_name":"Schreck","full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546"}],"date_created":"2022-06-05T22:01:49Z","isi":1,"oa_version":"Submitted Version","doi":"10.1111/cgf.14478","article_type":"original","quality_controlled":"1","title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","department":[{"_id":"ChWo"}],"abstract":[{"text":"This paper proposes a method for simulating liquids in large bodies of water by coupling together a water surface wave simulator with a 3D Navier-Stokes simulator. The surface wave simulation uses the equivalent sources method (ESM) to efficiently animate large bodies of water with precisely controllable wave propagation behavior. The 3D liquid simulator animates complex non-linear fluid behaviors like splashes and breaking waves using off-the-shelf simulators using FLIP or the level set method with semi-Lagrangian advection.\r\nWe combine the two approaches by using the 3D solver to animate localized non-linear behaviors, and the 2D wave solver to animate larger regions with linear surface physics. We use the surface motion from the 3D solver as boundary conditions for 2D surface wave simulator, and we use the velocity and surface heights from the 2D surface wave simulator as boundary conditions for the 3D fluid simulation. We also introduce a novel technique for removing visual artifacts caused by numerical errors in 3D fluid solvers: we use experimental data to estimate the artificial dispersion caused by the 3D solver and we then carefully tune the wave speeds of the 2D solver to match it, effectively eliminating any differences in wave behavior across the boundary. To the best of our knowledge, this is the first time such a empirically driven error compensation approach has been used to remove coupling errors from a physics simulator.\r\nOur coupled simulation approach leverages the strengths of each simulation technique, animating large environments with seamless transitions between 2D and 3D physics.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}]},{"status":"public","publication_status":"published","issue":"2","publication_identifier":{"issn":["0895-4801"]},"date_updated":"2023-10-18T06:58:03Z","arxiv":1,"oa":1,"external_id":{"arxiv":["2103.04122"],"isi":["000793158200002"]},"acknowledgement":"G.I. acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and\r\nKKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI.","article_processing_charge":"No","citation":{"ieee":"G. Ivanov and M. Naszodi, “A quantitative Helly-type theorem: Containment in a homothet,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2. Society for Industrial and Applied Mathematics, pp. 951–957, 2022.","mla":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2, Society for Industrial and Applied Mathematics, 2022, pp. 951–57, doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>.","chicago":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>.","ama":"Ivanov G, Naszodi M. A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. 2022;36(2):951-957. doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>","ista":"Ivanov G, Naszodi M. 2022. A quantitative Helly-type theorem: Containment in a homothet. SIAM Journal on Discrete Mathematics. 36(2), 951–957.","apa":"Ivanov, G., &#38; Naszodi, M. (2022). A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>","short":"G. Ivanov, M. Naszodi, SIAM Journal on Discrete Mathematics 36 (2022) 951–957."},"volume":36,"fulldoi":"https://doi.org/10.1137/21M1403308","date_published":"2022-04-11T00:00:00Z","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","month":"04","publisher":"Society for Industrial and Applied Mathematics","_id":"11435","publication":"SIAM Journal on Discrete Mathematics","title":"A quantitative Helly-type theorem: Containment in a homothet","department":[{"_id":"UlWa"}],"abstract":[{"text":"We introduce a new variant of quantitative Helly-type theorems: the minimal homothetic distance of the intersection of a family of convex sets to the intersection of a subfamily of a fixed size. As an application, we establish the following quantitative Helly-type result for the diameter. If $K$ is the intersection of finitely many convex bodies in $\\mathbb{R}^d$, then one can select $2d$ of these bodies whose intersection is of diameter at most $(2d)^3{diam}(K)$. The best previously known estimate, due to Brazitikos [Bull. Hellenic Math. Soc., 62 (2018), pp. 19--25], is $c d^{11/2}$. Moreover, we confirm that the multiplicative factor $c d^{1/2}$ conjectured by Bárány, Katchalski, and Pach [Proc. Amer. Math. Soc., 86 (1982), pp. 109--114] cannot be improved. The bounds above follow from our key result that concerns sparse approximation of a convex polytope by the convex hull of a well-chosen subset of its vertices: Assume that $Q \\subset {\\mathbb R}^d$ is a polytope whose centroid is the origin. Then there exist at most 2d vertices of $Q$ whose convex hull $Q^{\\prime \\prime}$ satisfies $Q \\subset - 8d^3 Q^{\\prime \\prime}.$","lang":"eng"}],"quality_controlled":"1","doi":"10.1137/21M1403308","article_type":"original","oa_version":"Preprint","date_created":"2022-06-05T22:01:50Z","isi":1,"type":"journal_article","intvolume":"        36","author":[{"last_name":"Ivanov","full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory"},{"first_name":"Marton","full_name":"Naszodi, Marton","last_name":"Naszodi"}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2103.04122","open_access":"1"}],"page":"951-957","day":"11"},{"page":"1-26","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2102.11397","open_access":"1"}],"place":"Cham","day":"27","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"18667"}]},"date_created":"2022-06-07T08:21:11Z","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"}],"author":[{"last_name":"Bleile","full_name":"Bleile, Bea","first_name":"Bea"},{"last_name":"Garin","first_name":"Adélie","full_name":"Garin, Adélie"},{"full_name":"Heiss, Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa","orcid":"0000-0002-1780-2689","last_name":"Heiss"},{"first_name":"Kelly","full_name":"Maggs, Kelly","last_name":"Maggs"},{"full_name":"Robins, Vanessa","first_name":"Vanessa","last_name":"Robins"}],"type":"book_chapter","intvolume":"        30","doi":"10.1007/978-3-030-95519-9_1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"To compute the persistent homology of a grayscale digital image one needs to build a simplicial or cubical complex from it. For cubical complexes, the two commonly used constructions (corresponding to direct and indirect digital adjacencies) can give different results for the same image. The two constructions are almost dual to each other, and we use this relationship to extend and modify the cubical complexes to become dual filtered cell complexes. We derive a general relationship between the persistent homology of two dual filtered cell complexes, and also establish how various modifications to a filtered complex change the persistence diagram. Applying these results to images, we derive a method to transform the persistence diagram computed using one type of cubical complex into a persistence diagram for the other construction. This means software for computing persistent homology from images can now be easily adapted to produce results for either of the two cubical complex constructions without additional low-level code implementation."}],"department":[{"_id":"HeEd"}],"title":"The persistent homology of dual digital image constructions","quality_controlled":"1","alternative_title":["Association for Women in Mathematics Series"],"month":"01","publisher":"Springer Nature","year":"2022","editor":[{"first_name":"Ellen","full_name":"Gasparovic, Ellen","last_name":"Gasparovic"},{"full_name":"Robins, Vanessa","first_name":"Vanessa","last_name":"Robins"},{"first_name":"Katharine","full_name":"Turner, Katharine","last_name":"Turner"}],"publication":"Research in Computational Topology 2","_id":"11440","acknowledgement":"This project started during the Women in Computational Topology workshop held in Canberra in July of 2019. All authors are very grateful for its organisation and the financial support for the workshop from the Mathematical Sciences Institute at ANU, the US National Science Foundation through the award CCF-1841455, the Australian Mathematical Sciences Institute and the Association for Women in Mathematics. AG is supported by the Swiss National Science Foundation grant CRSII5_177237. TH is supported by the European Research Council (ERC) Horizon 2020 project “Alpha Shape Theory Extended” No. 788183. KM is supported by the ERC Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 859860. VR was supported by Australian Research Council Future Fellowship FT140100604 during the early stages of this project.","citation":{"ieee":"B. Bleile, A. Garin, T. Heiss, K. Maggs, and V. Robins, “The persistent homology of dual digital image constructions,” in <i>Research in Computational Topology 2</i>, 1st ed., vol. 30, E. Gasparovic, V. Robins, and K. Turner, Eds. Cham: Springer Nature, 2022, pp. 1–26.","mla":"Bleile, Bea, et al. “The Persistent Homology of Dual Digital Image Constructions.” <i>Research in Computational Topology 2</i>, edited by Ellen Gasparovic et al., 1st ed., vol. 30, Springer Nature, 2022, pp. 1–26, doi:<a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">10.1007/978-3-030-95519-9_1</a>.","chicago":"Bleile, Bea, Adélie Garin, Teresa Heiss, Kelly Maggs, and Vanessa Robins. “The Persistent Homology of Dual Digital Image Constructions.” In <i>Research in Computational Topology 2</i>, edited by Ellen Gasparovic, Vanessa Robins, and Katharine Turner, 1st ed., 30:1–26. AWMS. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">https://doi.org/10.1007/978-3-030-95519-9_1</a>.","ama":"Bleile B, Garin A, Heiss T, Maggs K, Robins V. The persistent homology of dual digital image constructions. In: Gasparovic E, Robins V, Turner K, eds. <i>Research in Computational Topology 2</i>. Vol 30. 1st ed. AWMS. Cham: Springer Nature; 2022:1-26. doi:<a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">10.1007/978-3-030-95519-9_1</a>","ista":"Bleile B, Garin A, Heiss T, Maggs K, Robins V. 2022.The persistent homology of dual digital image constructions. In: Research in Computational Topology 2. Association for Women in Mathematics Series, vol. 30, 1–26.","apa":"Bleile, B., Garin, A., Heiss, T., Maggs, K., &#38; Robins, V. (2022). The persistent homology of dual digital image constructions. In E. Gasparovic, V. Robins, &#38; K. Turner (Eds.), <i>Research in Computational Topology 2</i> (1st ed., Vol. 30, pp. 1–26). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">https://doi.org/10.1007/978-3-030-95519-9_1</a>","short":"B. Bleile, A. Garin, T. Heiss, K. Maggs, V. Robins, in:, E. Gasparovic, V. Robins, K. Turner (Eds.), Research in Computational Topology 2, 1st ed., Springer Nature, Cham, 2022, pp. 1–26."},"article_processing_charge":"No","volume":30,"arxiv":1,"oa":1,"external_id":{"arxiv":["2102.11397"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","fulldoi":"https://doi.org/10.1007/978-3-030-95519-9_1","language":[{"iso":"eng"}],"date_published":"2022-01-27T00:00:00Z","ec_funded":1,"series_title":"AWMS","date_updated":"2026-04-07T12:54:09Z","publication_status":"published","edition":"1","status":"public","publication_identifier":{"isbn":["9783030955182"],"eisbn":["9783030955199"]}},{"oa_version":"Submitted Version","PlanS_conform":"1","ddc":["000"],"doi":"10.1145/3528223.3530144","article_type":"original","quality_controlled":"1","OA_type":"hybrid","department":[{"_id":"BeBi"}],"title":"Closed-loop control of direct ink writing via reinforcement learning","abstract":[{"text":"Enabling additive manufacturing to employ a wide range of novel, functional materials can be a major boost to this technology. However, making such materials printable requires painstaking trial-and-error by an expert operator,\r\nas they typically tend to exhibit peculiar rheological or hysteresis properties. Even in the case of successfully finding the process parameters, there is no guarantee of print-to-print consistency due to material differences between batches. These challenges make closed-loop feedback an attractive option where the process parameters are adjusted on-the-fly. There are several challenges for designing an efficient controller: the deposition parameters are complex and highly coupled, artifacts occur after long time horizons, simulating the deposition is computationally costly, and learning on hardware is intractable. In this work, we demonstrate the feasibility of learning a closed-loop control policy for additive manufacturing using reinforcement learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient as long as it allows learning the behavioral patterns of deposition that translate to real-world experiences. In combination with reinforcement learning, our model can be used to discover control policies that outperform\r\nbaseline controllers. Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase this by applying our control policy in-vivo on a single-layer, direct ink writing printer. ","lang":"eng"}],"day":"01","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/","relation":"press_release"}]},"corr_author":"1","type":"journal_article","intvolume":"        41","project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","grant_number":"M03319","name":"Perception-Aware Appearance Fabrication"},{"call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"OA_place":"publisher","author":[{"first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael","last_name":"Piovarci","orcid":"0000-0002-5062-4474"},{"full_name":"Foshey, Michael","first_name":"Michael","last_name":"Foshey"},{"first_name":"Jie","full_name":"Xu, Jie","last_name":"Xu"},{"last_name":"Erps","full_name":"Erps, Timothy","first_name":"Timothy"},{"first_name":"Vahid","full_name":"Babaei, Vahid","last_name":"Babaei"},{"last_name":"Didyk","full_name":"Didyk, Piotr","first_name":"Piotr"},{"full_name":"Rusinkiewicz, Szymon","first_name":"Szymon","last_name":"Rusinkiewicz"},{"first_name":"Wojciech","full_name":"Matusik, Wojciech","last_name":"Matusik"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"}],"date_created":"2022-06-10T06:41:47Z","isi":1,"date_updated":"2025-09-10T09:36:45Z","ec_funded":1,"issue":"4","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"status":"public","publication_status":"published","article_number":"112","_id":"11442","publication":"ACM Transactions on Graphics","year":"2022","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"06","publisher":"Association for Computing Machinery","fulldoi":"https://doi.org/10.1145/3528223.3530144","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2022-06-01T00:00:00Z","file":[{"content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_name":"2022_ACM_acceptedversion_Piovarci.pdf","file_size":33994829,"file_id":"11467","date_updated":"2022-06-28T08:32:58Z","date_created":"2022-06-28T08:32:58Z","relation":"main_file","success":1,"checksum":"27f6fe41c6ff84d50445cc9b0176d45b"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"arxiv":1,"has_accepted_license":"1","external_id":{"arxiv":["2201.11819"],"isi":["000830989200091"]},"file_date_updated":"2022-06-28T08:32:58Z","acknowledgement":"This work is graciously supported by the following grant agencies: FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767), NSF (Grant IIS-181507).\r\n","volume":41,"citation":{"apa":"Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel, B. (2022). Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>","short":"M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz, W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022).","ista":"Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. 41(4), 112.","ama":"Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>","mla":"Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 112, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>.","chicago":"Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei, Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>.","ieee":"M. Piovarci <i>et al.</i>, “Closed-loop control of direct ink writing via reinforcement learning,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022."},"article_processing_charge":"No"},{"date_updated":"2024-10-09T21:02:31Z","publication_status":"published","status":"public","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"issue":"6","publisher":"American Mathematical Society","month":"06","year":"2022","publication":"Transactions of the American Mathematical Society","_id":"11443","article_processing_charge":"No","citation":{"ieee":"M. A. Kwan, L. Sauermann, and Y. Zhao, “Extension complexity of low-dimensional polytopes,” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6. American Mathematical Society, pp. 4209–4250, 2022.","mla":"Kwan, Matthew Alan, et al. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6, American Mathematical Society, 2022, pp. 4209–50, doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>.","chicago":"Kwan, Matthew Alan, Lisa Sauermann, and Yufei Zhao. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2022. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>.","ama":"Kwan MA, Sauermann L, Zhao Y. Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. 2022;375(6):4209-4250. doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>","ista":"Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional polytopes. Transactions of the American Mathematical Society. 375(6), 4209–4250.","apa":"Kwan, M. A., Sauermann, L., &#38; Zhao, Y. (2022). Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>","short":"M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical Society 375 (2022) 4209–4250."},"volume":375,"acknowledgement":"The research of the first author was supported by SNSF Project 178493 and NSF Award DMS-1953990. The research of the second author supported by NSF Award DMS-1953772.\r\nThe research of the third author was supported by NSF Award DMS-1764176, NSF CAREER Award DMS-2044606, a Sloan Research Fellowship, and the MIT Solomon Buchsbaum Fund. ","external_id":{"isi":["000798461500001"],"arxiv":["2006.08836"]},"oa":1,"arxiv":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-06-01T00:00:00Z","fulldoi":"https://doi.org/10.1090/tran/8614","language":[{"iso":"eng"}],"scopus_import":"1","article_type":"original","doi":"10.1090/tran/8614","oa_version":"Preprint","abstract":[{"text":"Sometimes, it is possible to represent a complicated polytope as a projection of a much simpler polytope. To quantify this phenomenon, the extension complexity of a polytope P is defined to be the minimum number of facets of a (possibly higher-dimensional) polytope from which P can be obtained as a (linear) projection. This notion is motivated by its relevance to combinatorial optimisation, and has been studied intensively for various specific polytopes associated with important optimisation problems. In this paper we study extension complexity as a parameter of general polytopes, more specifically considering various families of low-dimensional polytopes. First, we prove that for a fixed dimension d, the extension complexity of a random d-dimensional polytope (obtained as the convex hull of random points in a ball or on a sphere) is typically on the order of the square root of its number of vertices. Second, we prove that any cyclic n-vertex polygon (whose vertices lie on a circle) has extension complexity at most 24√n. This bound is tight up to the constant factor 24. Finally, we show that there exists an no(1)-dimensional polytope with at most n vertices and extension complexity n1−o(1). Our theorems are proved with a range of different techniques, which we hope will be of further interest.","lang":"eng"}],"title":"Extension complexity of low-dimensional polytopes","department":[{"_id":"MaKw"}],"quality_controlled":"1","page":"4209-4250","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2006.08836"}],"corr_author":"1","day":"01","isi":1,"date_created":"2022-06-12T22:01:45Z","author":[{"last_name":"Kwan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan"},{"full_name":"Sauermann, Lisa","first_name":"Lisa","last_name":"Sauermann"},{"first_name":"Yufei","full_name":"Zhao, Yufei","last_name":"Zhao"}],"intvolume":"       375","type":"journal_article"},{"issue":"1","publication_identifier":{"eissn":["1758-3497"],"issn":["1758-3489"]},"status":"public","publication_status":"published","date_updated":"2024-10-09T21:02:31Z","date_published":"2022-04-01T00:00:00Z","fulldoi":"https://doi.org/10.3366/lih.2022.0097","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"article_processing_charge":"No","volume":38,"citation":{"ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” <i>Library and Information History</i>, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>.","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>. Edinburgh University Press, 2022. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>.","ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. 2022;38(1):23-41. doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>","ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41.","apa":"Chlebak, C. A., &#38; Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. Edinburgh University Press. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41."},"_id":"11444","publication":"Library and Information History","year":"2022","publisher":"Edinburgh University Press","month":"04","quality_controlled":"1","department":[{"_id":"E-Lib"}],"title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","abstract":[{"text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride.","lang":"eng"}],"oa_version":"Submitted Version","doi":"10.3366/lih.2022.0097","article_type":"original","intvolume":"        38","type":"journal_article","author":[{"last_name":"Chlebak","orcid":"0000-0002-3385-3865","first_name":"Clara A","full_name":"Chlebak, Clara A","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"last_name":"Reid","full_name":"Reid, Peter H.","first_name":"Peter H."}],"date_created":"2022-06-12T22:01:45Z","day":"01","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://rgu-repository.worktribe.com/output/1635939"}],"page":"23-41"},{"date_created":"2022-06-17T16:16:15Z","isi":1,"project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"},{"grant_number":"I05127","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","name":"Evolutionary analysis of gene regulation"}],"author":[{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","orcid":"0000-0001-5103-038X","last_name":"Saona Urmeneta"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"first_name":"Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova","orcid":"0000-0002-6246-1465"}],"intvolume":"        84","type":"journal_article","corr_author":"1","day":"17","related_material":{"record":[{"id":"21918","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11538-022-01118-z"}]},"abstract":[{"lang":"eng","text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks."}],"title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"quality_controlled":"1","doi":"10.1007/s11538-022-01029-z","article_type":"original","ddc":["510","570"],"oa_version":"Published Version","acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","volume":84,"article_processing_charge":"Yes (via OA deal)","citation":{"short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022."},"has_accepted_license":"1","oa":1,"external_id":{"isi":["000812509800001"],"pmid":["35713756"]},"file_date_updated":"2022-06-20T07:51:32Z","file":[{"checksum":"05a1fe7d10914a00c2bca9b447993a65","success":1,"relation":"main_file","date_created":"2022-06-20T07:51:32Z","date_updated":"2022-06-20T07:51:32Z","file_id":"11455","file_name":"2022_BulletinMathBiology_Saona.pdf","file_size":463025,"creator":"dernst","access_level":"open_access","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-17T00:00:00Z","fulldoi":"https://doi.org/10.1007/s11538-022-01029-z","language":[{"iso":"eng"}],"scopus_import":"1","month":"06","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"year":"2022","publication":"Bulletin of Mathematical Biology","_id":"11447","publication_status":"published","article_number":"74","status":"public","publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"issue":"8","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"ec_funded":1,"pmid":1,"date_updated":"2026-06-12T12:43:34Z"},{"oa_version":"Published Version","ddc":["570"],"doi":"10.7554/elife.75842","article_type":"original","quality_controlled":"1","abstract":[{"text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17850"}],"link":[{"relation":"software","url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks"}]},"day":"05","author":[{"last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa"},{"last_name":"Fleiss","first_name":"Aubin","full_name":"Fleiss, Aubin"},{"last_name":"Mishin","first_name":"Alexander S","full_name":"Mishin, Alexander S"},{"full_name":"Bozhanova, Nina G","first_name":"Nina G","last_name":"Bozhanova"},{"full_name":"Igolkina, Anna A","first_name":"Anna A","last_name":"Igolkina"},{"last_name":"Meiler","first_name":"Jens","full_name":"Meiler, Jens"},{"last_name":"Alaball Pujol","full_name":"Alaball Pujol, Maria-Elisenda","first_name":"Maria-Elisenda"},{"first_name":"Ekaterina V","full_name":"Putintseva, Ekaterina V","last_name":"Putintseva"},{"last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S","first_name":"Karen S"},{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"project":[{"call_identifier":"H2020","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"intvolume":"        11","type":"journal_article","isi":1,"date_created":"2022-06-18T09:06:59Z","date_updated":"2026-04-07T13:25:01Z","ec_funded":1,"pmid":1,"publication_identifier":{"issn":["2050-084X"]},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"article_number":"75842","publication_status":"published","status":"public","publication":"eLife","_id":"11448","publisher":"eLife Sciences Publications","month":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","checksum":"7573c28f44028ab0cc81faef30039e44","success":1,"date_created":"2022-06-20T07:44:19Z","creator":"dernst","file_name":"2022_eLife_Somermeyer.pdf","file_size":5297213,"file_id":"11454","date_updated":"2022-06-20T07:44:19Z","content_type":"application/pdf","access_level":"open_access"}],"scopus_import":"1","fulldoi":"https://doi.org/10.7554/elife.75842","date_published":"2022-05-05T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"ieee":"L. Gonzalez Somermeyer <i>et al.</i>, “Heterogeneity of the GFP fitness landscape and data-driven protein design,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>, vol. 11, 75842, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>.","chicago":"Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>.","ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>","ista":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.","apa":"Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>","short":"L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022)."},"volume":11,"acknowledgement":"We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova for technical assistance and data interpretation. Core facility Biomolecular Interactions and Crystallization of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this paper. This research was supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF). MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility in the Vanderbilt University Center for Structural Biology. We are grateful to Joel M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4, the Imperial College Research Fellowship and the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\"). Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH). This work was supported by a Russian Science Foundation grant 19-74-10102.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385.","external_id":{"pmid":["35510622"],"isi":["000799197200001"]},"file_date_updated":"2022-06-20T07:44:19Z","has_accepted_license":"1","oa":1},{"project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002"}],"author":[{"first_name":"Donovan J.","full_name":"Anderson, Donovan J.","last_name":"Anderson"},{"orcid":"0000-0002-7462-0048","last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aaron","full_name":"Mckenna, Aaron","last_name":"Mckenna"},{"first_name":"Jay","full_name":"Shendure, Jay","last_name":"Shendure"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"last_name":"Horwitz","first_name":"Marshall S.","full_name":"Horwitz, Marshall S."}],"intvolume":"        13","type":"journal_article","date_created":"2022-06-19T22:01:57Z","isi":1,"day":"15","page":"438-453.e5","main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2022.03.006","open_access":"1"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Mutations are acquired frequently, such that each cell's genome inscribes its history of cell divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH accumulates throughout the genome, offering large encoding capacity for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq) of mouse brain cells, we found that LOH events spanning multiple genes are revealed as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide variants (SNVs). We simultaneously inferred cell lineage and marked developmental time points based on X chromosome inactivation and the total number of LOH events while identifying cell types from gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and, compared with experimental approaches for determining lineage in model organisms, is applicable where genetic engineering is prohibited, such as humans."}],"department":[{"_id":"SiHi"}],"title":"Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development","oa_version":"Published Version","ddc":["570"],"doi":"10.1016/j.cels.2022.03.006","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.cels.2022.03.006","date_published":"2022-06-15T00:00:00Z","scopus_import":"1","acknowledgement":"D.J.A. thanks Wayne K. Potts, Alan R. Rogers, Kristen Hawkes, Ryk Ward, and Jon Seger for inspiring a young undergraduate to apply evolutionary theory to intraorganism development. Supported by the Paul G. Allen Frontiers Group (University of Washington); NIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program 725780 LinPro to S.H.","article_processing_charge":"No","volume":13,"citation":{"ieee":"D. J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development,” <i>Cell Systems</i>, vol. 13, no. 6. Elsevier, p. 438–453.e5, 2022.","mla":"Anderson, Donovan J., et al. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>, vol. 13, no. 6, Elsevier, 2022, p. 438–453.e5, doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>.","chicago":"Anderson, Donovan J., Florian Pauler, Aaron Mckenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>.","ama":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. 2022;13(6):438-453.e5. doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>","ista":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Systems. 13(6), 438–453.e5.","apa":"Anderson, D. J., Pauler, F., Mckenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (2022). Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>","short":"D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, Cell Systems 13 (2022) 438–453.e5."},"oa":1,"external_id":{"pmid":["35452605"],"isi":["000814124400002"]},"publication":"Cell Systems","_id":"11449","month":"06","publisher":"Elsevier","year":"2022","publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"issue":"6","publication_status":"published","status":"public","date_updated":"2026-06-18T17:15:22Z","pmid":1,"ec_funded":1},{"publication_identifier":{"eisbn":["9781071623213"],"eissn":["1940-6045"],"issn":["0893-2336"],"isbn":["9781071623206"]},"status":"public","publication_status":"published","date_updated":"2025-04-14T07:43:58Z","ec_funded":1,"series_title":"NM","fulldoi":"https://doi.org/10.1007/978-1-0716-2321-3_15","language":[{"iso":"eng"}],"date_published":"2022-06-04T00:00:00Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank de Bono lab members for the helpful comments on the manuscript. The biotin-auxotrophic E. coli strain MG1655bioB:kan was a generous gift from J. Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3’UTR entry vector were kindly sent by Dr. Dominique Glauser (University of Fribourg). This work was supported by an Advanced ERC Grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).","citation":{"ama":"Artan M, de Bono M. Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Yamamoto D, ed. <i>Behavioral Neurogenetics</i>. Vol 181. NM. New York: Springer Nature; 2022:277-294. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>","ista":"Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.","short":"M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer Nature, New York, 2022, pp. 277–294.","apa":"Artan, M., &#38; de Bono, M. (2022). Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In D. Yamamoto (Ed.), <i>Behavioral Neurogenetics</i> (Vol. 181, pp. 277–294). New York: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>","ieee":"M. Artan and M. de Bono, “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling,” in <i>Behavioral Neurogenetics</i>, vol. 181, D. Yamamoto, Ed. New York: Springer Nature, 2022, pp. 277–294.","chicago":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” In <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>.","mla":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>."},"article_processing_charge":"No","volume":181,"_id":"11456","editor":[{"last_name":"Yamamoto","first_name":"Daisuke","full_name":"Yamamoto, Daisuke"}],"publication":"Behavioral Neurogenetics","year":"2022","month":"06","publisher":"Springer Nature","alternative_title":["Neuromethods"],"quality_controlled":"1","department":[{"_id":"MaDe"}],"title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","abstract":[{"lang":"eng","text":"The proteomes of specialized structures, and the interactomes of proteins of interest, provide entry points to elucidate the functions of molecular machines. Here, we review a proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes. Although the focus is on C. elegans neurons, the method is applicable regardless of cell type. We describe detailed extraction procedures that solubilize the bulk of C. elegans proteins and highlight the importance of tagging endogenous genes, to ensure physiological expression levels. We review issues associated with non-specific background noise and the importance of appropriate controls. As proof of principle, we review our analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our aim is to provide a detailed protocol for TurboID-based proximity labeling in C. elegans and to highlight its potential and its limitations to characterize protein complexes and subcellular compartments in this animal."}],"oa_version":"None","doi":"10.1007/978-1-0716-2321-3_15","type":"book_chapter","intvolume":"       181","project":[{"name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"author":[{"orcid":"0000-0001-8945-6992","last_name":"Artan","full_name":"Artan, Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat"},{"first_name":"Mario","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","last_name":"de Bono"}],"date_created":"2022-06-20T08:10:34Z","day":"04","place":"New York","corr_author":"1","page":"277-294"},{"oa_version":"Published Version","ddc":["000"],"doi":"10.1145/3519939.3523435","quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"title":"Differential cost analysis with simultaneous potentials and anti-potentials","abstract":[{"text":"We present a novel approach to differential cost analysis that, given a program revision, attempts to statically bound the difference in resource usage, or cost, between the two program versions. Differential cost analysis is particularly interesting because of the many compelling applications for it, such as detecting resource-use regressions at code-review time or proving the absence of certain side-channel vulnerabilities. One prior approach to differential cost analysis is to apply relational reasoning that conceptually constructs a product program on which one can over-approximate the difference in costs between the two program versions. However, a significant challenge in any relational approach is effectively aligning the program versions to get precise results. In this paper, our key insight is that we can avoid the need for and the limitations of program alignment if, instead, we bound the difference of two cost-bound summaries rather than directly bounding the concrete cost difference. In particular, our method computes a threshold value for the maximal difference in cost between two program versions simultaneously using two kinds of cost-bound summaries---a potential function that evaluates to an upper bound for the cost incurred in the first program and an anti-potential function that evaluates to a lower bound for the cost incurred in the second. Our method has a number of desirable properties: it can be fully automated, it allows optimizing the threshold value on relative cost, it is suitable for programs that are not syntactically similar, and it supports non-determinism. We have evaluated an implementation of our approach on a number of program pairs collected from the literature, and we find that our method computes tight threshold values on relative cost in most examples.","lang":"eng"}],"day":"09","corr_author":"1","page":"442-457","type":"conference","author":[{"last_name":"Zikelic","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","first_name":"Dorde"},{"last_name":"Chang","first_name":"Bor-Yuh Evan","full_name":"Chang, Bor-Yuh Evan"},{"last_name":"Bolignano","first_name":"Pauline","full_name":"Bolignano, Pauline"},{"last_name":"Raimondi","first_name":"Franco","full_name":"Raimondi, Franco"}],"project":[{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"isi":1,"date_created":"2022-06-21T09:26:15Z","date_updated":"2025-04-14T07:52:47Z","ec_funded":1,"publication_identifier":{"isbn":["9781450392655"]},"status":"public","publication_status":"published","_id":"11459","publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"year":"2022","publisher":"Association for Computing Machinery","month":"06","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1145/3519939.3523435","date_published":"2022-06-09T00:00:00Z","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","relation":"main_file","date_created":"2022-06-27T07:38:21Z","date_updated":"2022-06-27T07:38:21Z","file_id":"11466","creator":"dernst","file_name":"2022_PLDI_Zikelic.pdf","file_size":318697,"access_level":"open_access","content_type":"application/pdf"}],"external_id":{"arxiv":["2204.00870"],"isi":["000850435600030"]},"file_date_updated":"2022-06-27T07:38:21Z","conference":{"name":"PLDI: Programming Language Design and Implementation","end_date":"2022-06-17","location":"San Diego, CA, United States","start_date":"2022-06-13"},"has_accepted_license":"1","arxiv":1,"oa":1,"article_processing_charge":"No","citation":{"chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 442–57. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>.","mla":"Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2022, pp. 442–57, doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>.","ieee":"D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost analysis with simultaneous potentials and anti-potentials,” in <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, San Diego, CA, United States, 2022, pp. 442–457.","short":"D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2022, pp. 442–457.","apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., &#38; Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>","ista":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 442–457.","ama":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis with simultaneous potentials and anti-potentials. In: <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2022:442-457. doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>"},"acknowledgement":"We thank Shaun Willows, Thomas Lugnet, and the Living Room Application Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe, and the Prime Video Automated Reasoning team for their support and helpful suggestions throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier version of this paper. And finally, we thank the anonymous reviewers for their useful feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt)."},{"abstract":[{"lang":"eng","text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life."}],"title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","department":[{"_id":"SiHi"}],"quality_controlled":"1","article_type":"original","doi":"10.1186/s13229-022-00508-3","ddc":["570"],"oa_version":"Published Version","date_created":"2022-06-23T14:28:55Z","isi":1,"author":[{"full_name":"Schaaf, Zachary A.","first_name":"Zachary A.","last_name":"Schaaf"},{"first_name":"Lyvin","full_name":"Tat, Lyvin","last_name":"Tat"},{"last_name":"Cannizzaro","first_name":"Noemi","full_name":"Cannizzaro, Noemi"},{"first_name":"Ralph","full_name":"Green, Ralph","last_name":"Green"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Konstantinos S.","full_name":"Zarbalis, Konstantinos S.","last_name":"Zarbalis"}],"type":"journal_article","intvolume":"        13","day":"22","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13229-023-00539-4"}]},"publication_status":"published","article_number":"27","status":"public","publication_identifier":{"issn":["2040-2392"]},"keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"pmid":1,"date_updated":"2025-06-11T13:34:57Z","acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","citation":{"ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27.","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>","ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022.","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>.","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>."},"volume":13,"article_processing_charge":"No","oa":1,"has_accepted_license":"1","file_date_updated":"2022-06-24T08:22:59Z","external_id":{"pmid":["35733184"],"isi":["000814641400001"]},"file":[{"date_updated":"2022-06-24T08:22:59Z","file_id":"11461","creator":"dernst","file_name":"2022_MolecularAutism_Schaaf.pdf","file_size":7552298,"access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"525d2618e855139089bbfc3e3d49d1b2","relation":"main_file","date_created":"2022-06-24T08:22:59Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1186/s13229-022-00508-3","date_published":"2022-06-22T00:00:00Z","scopus_import":"1","month":"06","publisher":"Springer Nature","year":"2022","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"Molecular Autism","_id":"11460"},{"author":[{"last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri","first_name":"Dmitri"},{"last_name":"Shapira","first_name":"Michail","full_name":"Shapira, Michail"},{"last_name":"Karputs","first_name":"Alena","full_name":"Karputs, Alena"},{"last_name":"Kavaleuski","orcid":"0000-0003-2091-526X","id":"62304f89-eb97-11eb-a6c2-8903dd183976","full_name":"Kavaleuski, Anton","first_name":"Anton"},{"last_name":"Kuzminski","first_name":"Ivan","full_name":"Kuzminski, Ivan"},{"first_name":"Elena","full_name":"Stepanova, Elena","last_name":"Stepanova"},{"full_name":"Gilep, Andrei","first_name":"Andrei","last_name":"Gilep"}],"intvolume":"       106","type":"journal_article","date_created":"2022-06-26T22:01:34Z","isi":1,"day":"01","page":"5093-5103","quality_controlled":"1","abstract":[{"lang":"eng","text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens."}],"title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"oa_version":"None","article_type":"original","doi":"10.1007/s00253-022-12022-w","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1007/s00253-022-12022-w","scopus_import":"1","date_published":"2022-08-01T00:00:00Z","acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","volume":106,"article_processing_charge":"No","citation":{"chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>.","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>.","ieee":"D. Dormeshkin <i>et al.</i>, “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” <i>Applied Microbiology and Biotechnology</i>, vol. 106. Springer Nature, pp. 5093–5103, 2022.","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., &#38; Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>","ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103.","ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. 2022;106:5093-5103. doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>"},"external_id":{"isi":["000813677500001"],"pmid":["35723693"]},"publication":"Applied Microbiology and Biotechnology","_id":"11462","month":"08","publisher":"Springer Nature","year":"2022","publication_identifier":{"issn":["0175-7598"],"eissn":["1432-0614"]},"publication_status":"published","status":"public","date_updated":"2023-10-10T07:15:02Z","pmid":1},{"related_material":{"record":[{"id":"12732","status":"public","relation":"dissertation_contains"}]},"day":"27","corr_author":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2111.08603"}],"type":"journal_article","intvolume":"       105","author":[{"first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","full_name":"Brighi, Pietro","last_name":"Brighi","orcid":"0000-0002-7969-2729"},{"full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis"},{"last_name":"Kirova","first_name":"Kristina","full_name":"Kirova, Kristina","id":"4aeda2ae-f847-11ec-98e0-c4a66fe174d4"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"isi":1,"date_created":"2022-06-29T20:19:51Z","oa_version":"Preprint","doi":"10.1103/physrevb.105.224208","article_type":"original","quality_controlled":"1","department":[{"_id":"MaSe"}],"title":"Localization of a mobile impurity interacting with an Anderson insulator","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Thermalizing and localized many-body quantum systems present two distinct dynamical phases of matter. Recently the fate of a localized system coupled to a thermalizing system viewed as a quantum bath received significant theoretical and experimental attention. In this work, we study a mobile impurity, representing a small quantum bath, that interacts locally with an Anderson insulator with a finite density of localized particles. Using static Hartree approximation to obtain an effective disorder strength, we formulate an analytic criterion for the perturbative stability of the localization. Next, we use an approximate dynamical Hartree method and the quasi-exact time-evolved block decimation (TEBD) algorithm to study the dynamics of the system. We find that the dynamical Hartree approach which completely ignores entanglement between the impurity and localized particles predicts the delocalization of the system. In contrast, the full numerical simulation of the unitary dynamics with TEBD suggests the stability of localization on numerically accessible timescales. Finally, using an extension of the density matrix renormalization group algorithm to excited states (DMRG-X), we approximate the highly excited eigenstates of the system. We find that the impurity remains localized in the eigenstates and entanglement is enhanced in a finite region around the position of the impurity, confirming the dynamical predictions. Dynamics and the DMRG-X results provide compelling evidence for the stability of localization.","lang":"eng"}],"_id":"11469","publication":"Physical Review B","year":"2022","publisher":"American Physical Society","month":"06","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1103/physrevb.105.224208","scopus_import":"1","date_published":"2022-06-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2111.08603"],"isi":["000823050000001"]},"arxiv":1,"oa":1,"article_processing_charge":"No","citation":{"apa":"Brighi, P., Michailidis, A., Kirova, K., Abanin, D. A., &#38; Serbyn, M. (2022). Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>","short":"P. Brighi, A. Michailidis, K. Kirova, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022).","ista":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. 2022. Localization of a mobile impurity interacting with an Anderson insulator. Physical Review B. 105(22), 224208.","ama":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>","mla":"Brighi, Pietro, et al. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, 224208, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>.","chicago":"Brighi, Pietro, Alexios Michailidis, Kristina Kirova, Dmitry A. Abanin, and Maksym Serbyn. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>.","ieee":"P. Brighi, A. Michailidis, K. Kirova, D. A. Abanin, and M. Serbyn, “Localization of a mobile impurity interacting with an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022."},"volume":105,"acknowledgement":"We thank M. Ljubotina for insightful discussions. P. B., A. M. and M. S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D. A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","date_updated":"2026-04-07T13:26:31Z","ec_funded":1,"issue":"22","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"status":"public","publication_status":"published","article_number":"224208"},{"isi":1,"date_created":"2022-06-29T20:20:47Z","author":[{"full_name":"Brighi, Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro","last_name":"Brighi","orcid":"0000-0002-7969-2729"},{"full_name":"Michailidis, Alexios A.","first_name":"Alexios A.","last_name":"Michailidis"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"intvolume":"       105","type":"journal_article","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.07332"}],"corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"12732","status":"public"}]},"day":"27","abstract":[{"text":"Many-body localization (MBL) is an example of a dynamical phase of matter that avoids thermalization. While the MBL phase is robust to weak local perturbations, the fate of an MBL system coupled to a thermalizing quantum system that represents a “heat bath” is an open question that is actively investigated theoretically and experimentally. In this work, we consider the stability of an Anderson insulator with a finite density of particles interacting with a single mobile impurity—a small quantum bath. We give perturbative arguments that support the stability of localization in the strong interaction regime. Large-scale tensor network simulations of dynamics are employed to corroborate the presence of the localized phase and give quantitative predictions in the thermodynamic limit. We develop a phenomenological description of the dynamics in the strong interaction regime, and we demonstrate that the impurity effectively turns the Anderson insulator into an MBL phase, giving rise to nontrivial entanglement dynamics well captured by our phenomenology.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Propagation of many-body localization in an Anderson insulator","department":[{"_id":"MaSe"}],"quality_controlled":"1","doi":"10.1103/physrevb.105.l220203","article_type":"original","oa_version":"Preprint","volume":105,"citation":{"chicago":"Brighi, Pietro, Alexios A. Michailidis, Dmitry A. Abanin, and Maksym Serbyn. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>.","mla":"Brighi, Pietro, et al. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, L220203, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>.","ieee":"P. Brighi, A. A. Michailidis, D. A. Abanin, and M. Serbyn, “Propagation of many-body localization in an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","short":"P. Brighi, A.A. Michailidis, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022).","apa":"Brighi, P., Michailidis, A. A., Abanin, D. A., &#38; Serbyn, M. (2022). Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>","ama":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>","ista":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. 2022. Propagation of many-body localization in an Anderson insulator. Physical Review B. 105(22), L220203."},"article_processing_charge":"No","acknowledgement":"We acknowledge useful discussions with M. Ljubotina. P. B., A. M., and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","external_id":{"arxiv":["2109.07332"],"isi":["000823050000012"]},"arxiv":1,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","fulldoi":"https://doi.org/10.1103/physrevb.105.l220203","language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2022-06-27T00:00:00Z","publisher":"American Physical Society","month":"06","year":"2022","publication":"Physical Review B","_id":"11470","publication_status":"published","article_number":"L220203","status":"public","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"issue":"22","ec_funded":1,"date_updated":"2026-04-07T13:26:31Z"},{"date_created":"2022-06-30T12:15:03Z","type":"dissertation","author":[{"full_name":"Mysliwy, Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof","last_name":"Mysliwy"}],"OA_place":"publisher","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"page":"138","related_material":{"record":[{"relation":"part_of_dissertation","id":"10564","status":"public"},{"id":"8705","status":"public","relation":"part_of_dissertation"}]},"day":"01","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n"}],"acknowledged_ssus":[{"_id":"SSU"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"doi":"10.15479/at:ista:11473","ddc":["515","539"],"oa_version":"Published Version","file_date_updated":"2022-07-05T08:17:12Z","has_accepted_license":"1","oa":1,"citation":{"short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","apa":"Mysliwy, K. (2022). <i>Polarons in Bose gases and polar crystals: Some rigorous energy estimates</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>.","mla":"Mysliwy, Krzysztof. <i>Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>.","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022."},"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/at:ista:11473","language":[{"iso":"eng"}],"date_published":"2022-07-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"success":1,"checksum":"7970714a20a6052f75fb27a6c3e9976e","relation":"main_file","date_created":"2022-07-05T08:12:56Z","date_updated":"2022-07-05T08:12:56Z","file_id":"11486","file_size":1830973,"file_name":"thes1_no_isbn_2_1b.pdf","creator":"kmysliwy","access_level":"open_access","content_type":"application/pdf"},{"checksum":"647a2011fdf56277096c9350fefe1097","relation":"source_file","date_created":"2022-07-05T08:15:52Z","date_updated":"2022-07-05T08:17:12Z","file_id":"11487","creator":"kmysliwy","file_name":"thes_source.zip","file_size":5831060,"access_level":"closed","content_type":"application/zip"}],"year":"2022","publisher":"Institute of Science and Technology Austria","month":"07","_id":"11473","status":"public","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"date_updated":"2026-04-07T14:14:52Z"},{"date_updated":"2025-04-15T08:12:07Z","pmid":1,"publication_identifier":{"issn":["1422-0067"]},"issue":"11","publication_status":"published","status":"public","publication":"International Journal of Molecular Sciences","_id":"11489","month":"06","publisher":"MDPI","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"year":"2022","file":[{"relation":"main_file","success":1,"checksum":"e997a57a928ec9d51fad8ce824a05935","date_created":"2022-07-06T07:36:59Z","file_size":2324542,"file_name":"2022_IntJMolSci_Bilanovicova.pdf","creator":"cchlebak","date_updated":"2022-07-06T07:36:59Z","file_id":"11492","content_type":"application/pdf","access_level":"open_access"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","fulldoi":"https://doi.org/10.3390/ijms23116352","language":[{"iso":"eng"}],"date_published":"2022-06-06T00:00:00Z","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","citation":{"ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022.","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>.","mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>","ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352.","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>"},"volume":23,"article_processing_charge":"Yes","oa":1,"has_accepted_license":"1","file_date_updated":"2022-07-06T07:36:59Z","external_id":{"pmid":["35683031"],"isi":["000808733300001"]},"ddc":["570"],"oa_version":"Published Version","article_type":"original","doi":"10.3390/ijms23116352","quality_controlled":"1","abstract":[{"lang":"eng","text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors."}],"title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","department":[{"_id":"JiFr"}],"corr_author":"1","day":"06","page":"6352","project":[{"call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development"}],"author":[{"full_name":"Bilanovičová, V","first_name":"V","last_name":"Bilanovičová"},{"last_name":"Rýdza","full_name":"Rýdza, N","first_name":"N"},{"first_name":"L","full_name":"Koczka, L","last_name":"Koczka"},{"last_name":"Hess","first_name":"M","full_name":"Hess, M"},{"full_name":"Feraru, E","first_name":"E","last_name":"Feraru"},{"first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Nodzyński, T","first_name":"T","last_name":"Nodzyński"}],"type":"journal_article","intvolume":"        23","date_created":"2022-07-05T15:14:34Z","isi":1},{"date_updated":"2025-04-15T07:27:21Z","oa_version":"None","doi":"10.15479/AT:ISTA:11542","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)","status":"public","_id":"11542","related_material":{"record":[{"status":"public","id":"11995","relation":"used_in_publication"}],"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1","relation":"contains"}]},"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"year":"2022","publisher":"Institute of Science and Technology Austria","fulldoi":"https://doi.org/10.15479/AT:ISTA:11542","date_published":"2022-01-01T00:00:00Z","type":"research_data","file":[{"date_created":"2022-07-08T10:56:52Z","success":1,"checksum":"71e8186583f3adbb6c69a88ac9e6e49b","relation":"main_file","access_level":"open_access","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"11543","date_updated":"2022-07-08T10:56:52Z","file_size":135784571,"file_name":"Source Data.xlsx","creator":"rschulz"}],"author":[{"last_name":"Schulz","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","full_name":"Schulz, Rouven","first_name":"Rouven"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-07-08T11:03:02Z","oa":1,"has_accepted_license":"1","contributor":[{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","last_name":"Siegert","contributor_type":"contact_person"}],"file_date_updated":"2022-07-08T10:56:52Z","article_processing_charge":"No","citation":{"mla":"Schulz, Rouven. <i>Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses)</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>.","ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022.","apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>","short":"R. Schulz, (2022).","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>","ista":"Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>."}},{"file":[{"file_name":"2022_JournalAlgebra_Brown.pdf","file_size":582962,"creator":"dernst","file_id":"12473","date_updated":"2023-02-02T07:32:48Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"82abaee3d7837f703e499a9ecbb25b7c","success":1,"date_created":"2023-02-02T07:32:48Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","fulldoi":"https://doi.org/10.1016/j.jalgebra.2022.06.017","date_published":"2022-11-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","acknowledgement":"We thank Catharina Stroppel and Jens Niklas Eberhardt for interesting discussions. The first author acknowledges the support of the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. The second author is supported by the National Science Foundation Award No. 1803059 and the Australian Research Council grant DP170101579.","volume":609,"article_processing_charge":"Yes (via OA deal)","citation":{"mla":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>, vol. 609, no. 11, Elsevier, 2022, pp. 145–79, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>.","chicago":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>.","ieee":"A. Brown and A. Romanov, “Contravariant pairings between standard Whittaker modules and Verma modules,” <i>Journal of Algebra</i>, vol. 609, no. 11. Elsevier, pp. 145–179, 2022.","apa":"Brown, A., &#38; Romanov, A. (2022). Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>","short":"A. Brown, A. Romanov, Journal of Algebra 609 (2022) 145–179.","ama":"Brown A, Romanov A. Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. 2022;609(11):145-179. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>","ista":"Brown A, Romanov A. 2022. Contravariant pairings between standard Whittaker modules and Verma modules. Journal of Algebra. 609(11), 145–179."},"has_accepted_license":"1","oa":1,"external_id":{"isi":["000861841100004"]},"file_date_updated":"2023-02-02T07:32:48Z","publication":"Journal of Algebra","_id":"11545","month":"11","publisher":"Elsevier","year":"2022","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["0021-8693"]},"issue":"11","keyword":["Algebra and Number Theory"],"publication_status":"published","status":"public","date_updated":"2025-04-14T07:43:58Z","ec_funded":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Brown","full_name":"Brown, Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam"},{"last_name":"Romanov","full_name":"Romanov, Anna","first_name":"Anna"}],"intvolume":"       609","type":"journal_article","date_created":"2022-07-08T11:40:07Z","isi":1,"corr_author":"1","day":"01","page":"145-179","quality_controlled":"1","abstract":[{"text":"We classify contravariant pairings between standard Whittaker modules and Verma modules over a complex semisimple Lie algebra. These contravariant pairings are useful in extending several classical techniques for category O to the Miličić–Soergel category N . We introduce a class of costandard modules which generalize dual Verma modules, and describe canonical maps from standard to costandard modules in terms of contravariant pairings.\r\nWe show that costandard modules have unique irreducible submodules and share the same composition factors as the corresponding standard Whittaker modules. We show that costandard modules give an algebraic characterization of the global sections of costandard twisted Harish-Chandra sheaves on the associated flag variety, which are defined using holonomic duality of D-modules. We prove that with these costandard modules, blocks of category\r\nN have the structure of highest weight categories and we establish a BGG reciprocity theorem for N .","lang":"eng"}],"department":[{"_id":"HeEd"}],"title":"Contravariant pairings between standard Whittaker modules and Verma modules","oa_version":"Published Version","ddc":["510"],"doi":"10.1016/j.jalgebra.2022.06.017","article_type":"original"},{"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"issue":"1856","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"publication_status":"published","article_number":"20210203","status":"public","date_updated":"2025-06-12T06:10:18Z","pmid":1,"file":[{"content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","file_size":920304,"date_updated":"2023-02-02T08:20:29Z","file_id":"12479","date_created":"2023-02-02T08:20:29Z","relation":"main_file","success":1,"checksum":"49f69428f3dcf5ce3ff281f7d199e9df"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1098/rstb.2021.0203","date_published":"2022-08-01T00:00:00Z","scopus_import":"1","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","citation":{"ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>"},"article_processing_charge":"Yes (via OA deal)","volume":377,"oa":1,"has_accepted_license":"1","external_id":{"pmid":["35694747"],"isi":["000812317300005"]},"file_date_updated":"2023-02-02T08:20:29Z","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","_id":"11546","month":"08","publisher":"Royal Society of London","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"year":"2022","quality_controlled":"1","abstract":[{"text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.","lang":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Inversions and parallel evolution","ddc":["570"],"oa_version":"Published Version","article_type":"original","doi":"10.1098/rstb.2021.0203","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"Snapdragon Speciation"}],"author":[{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"intvolume":"       377","type":"journal_article","date_created":"2022-07-08T11:41:56Z","isi":1,"corr_author":"1","day":"01"}]