[{"_id":"8574","date_published":"2020-09-20T00:00:00Z","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","file":[{"file_name":"thesis_EnikoSzep_final.pdf","file_id":"8575","date_updated":"2020-09-28T07:25:35Z","checksum":"20e71f015fbbd78fea708893ad634ed0","success":1,"file_size":6354833,"date_created":"2020-09-28T07:25:35Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"},{"relation":"source_file","creator":"dernst","access_level":"closed","content_type":"application/x-zip-compressed","date_created":"2020-09-28T07:25:37Z","file_size":23020401,"checksum":"a8de2c14a1bb4e53c857787efbb289e1","date_updated":"2020-09-28T07:25:37Z","file_name":"thesisFiles_EnikoSzep.zip","file_id":"8576"}],"doi":"10.15479/AT:ISTA:8574","publication_identifier":{"eissn":["2663-337X"]},"article_processing_charge":"No","department":[{"_id":"NiBa"}],"day":"20","oa":1,"title":"Local adaptation in metapopulations","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","mla":"Szep, Eniko. <i>Local Adaptation in Metapopulations</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>","apa":"Szep, E. (2020). <i>Local adaptation in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes,  such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. ","lang":"eng"}],"has_accepted_license":"1","status":"public","oa_version":"Published Version","date_created":"2020-09-28T07:33:38Z","corr_author":"1","type":"dissertation","date_updated":"2026-04-08T07:21:44Z","ddc":["570"],"OA_place":"publisher","page":"158","author":[{"full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","first_name":"Eniko"}],"alternative_title":["ISTA Thesis"],"month":"09","publication_status":"published","file_date_updated":"2020-09-28T07:25:37Z","year":"2020"},{"ddc":["570"],"date_updated":"2026-04-02T14:29:28Z","intvolume":"        10","language":[{"iso":"eng"}],"citation":{"chicago":"Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis in Bacteria: The Ins and Outs.” <i>Membranes</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/membranes10090242\">https://doi.org/10.3390/membranes10090242</a>.","mla":"Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” <i>Membranes</i>, vol. 10, no. 9, 242, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/membranes10090242\">10.3390/membranes10090242</a>.","short":"A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).","apa":"Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. <i>Membranes</i>. MDPI. <a href=\"https://doi.org/10.3390/membranes10090242\">https://doi.org/10.3390/membranes10090242</a>","ieee":"A. Andrei <i>et al.</i>, “Cu homeostasis in bacteria: The ins and outs,” <i>Membranes</i>, vol. 10, no. 9. MDPI, 2020.","ista":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes. 10(9), 242.","ama":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria: The ins and outs. <i>Membranes</i>. 2020;10(9). doi:<a href=\"https://doi.org/10.3390/membranes10090242\">10.3390/membranes10090242</a>"},"article_type":"original","has_accepted_license":"1","status":"public","external_id":{"isi":["000581446000001"]},"abstract":[{"lang":"eng","text":"Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells."}],"type":"journal_article","date_created":"2020-09-28T08:59:26Z","scopus_import":"1","publication":"Membranes","oa_version":"Published Version","month":"09","volume":10,"issue":"9","publication_status":"published","file_date_updated":"2020-09-28T11:36:50Z","year":"2020","author":[{"last_name":"Andrei","first_name":"Andreea","full_name":"Andrei, Andreea"},{"last_name":"Öztürk","first_name":"Yavuz","full_name":"Öztürk, Yavuz"},{"full_name":"Khalfaoui-Hassani, Bahia","last_name":"Khalfaoui-Hassani","first_name":"Bahia"},{"full_name":"Rauch, Juna","first_name":"Juna","last_name":"Rauch"},{"first_name":"Dorian","last_name":"Marckmann","full_name":"Marckmann, Dorian"},{"full_name":"Trasnea, Petru Iulian","id":"D560034C-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Petru Iulian","last_name":"Trasnea"},{"first_name":"Fevzi","last_name":"Daldal","full_name":"Daldal, Fevzi"},{"first_name":"Hans-Georg","last_name":"Koch","full_name":"Koch, Hans-Georg"}],"publisher":"MDPI","doi":"10.3390/membranes10090242","isi":1,"file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2020-09-28T11:36:50Z","file_size":4612258,"success":1,"checksum":"ceb43d7554e712dea6f36f9287271737","date_updated":"2020-09-28T11:36:50Z","file_name":"2020_Membranes_Andrei.pdf","file_id":"8583"}],"article_number":"242","_id":"8579","quality_controlled":"1","date_published":"2020-09-01T00:00:00Z","department":[{"_id":"LeSa"}],"day":"01","title":"Cu homeostasis in bacteria: The ins and outs","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2077-0375"]},"article_processing_charge":"No"},{"month":"08","department":[{"_id":"HeEd"}],"day":"01","title":"The application of persistent homology in the analysis of heart rate variability","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2020","publication_identifier":{"isbn":["9781728157511"]},"article_processing_charge":"No","author":[{"last_name":"Graff","first_name":"Grzegorz","full_name":"Graff, Grzegorz"},{"full_name":"Graff, Beata","last_name":"Graff","first_name":"Beata"},{"first_name":"Grzegorz","orcid":"0000-0002-3536-9866","last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz"},{"full_name":"Narkiewicz, Krzysztof","last_name":"Narkiewicz","first_name":"Krzysztof"}],"publisher":"IEEE","doi":"10.1109/ESGCO49734.2020.9158054","isi":1,"date_updated":"2023-08-22T09:33:34Z","conference":{"name":"ESGCO: European Study Group on Cardiovascular Oscillations","end_date":"2020-07-15","location":"Pisa, Italy","start_date":"2020-07-15"},"language":[{"iso":"eng"}],"article_number":"9158054","citation":{"chicago":"Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” In <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/ESGCO49734.2020.9158054\">https://doi.org/10.1109/ESGCO49734.2020.9158054</a>.","mla":"Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>, 9158054, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/ESGCO49734.2020.9158054\">10.1109/ESGCO49734.2020.9158054</a>.","short":"G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , IEEE, 2020.","apa":"Graff, G., Graff, B., Jablonski, G., &#38; Narkiewicz, K. (2020). The application of persistent homology in the analysis of heart rate variability. In <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>. Pisa, Italy: IEEE. <a href=\"https://doi.org/10.1109/ESGCO49734.2020.9158054\">https://doi.org/10.1109/ESGCO49734.2020.9158054</a>","ieee":"G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of persistent homology in the analysis of heart rate variability,” in <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>, Pisa, Italy, 2020.","ista":"Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent homology in the analysis of heart rate variability. 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular Oscillations, 9158054.","ama":"Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent homology in the analysis of heart rate variability. In: <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/ESGCO49734.2020.9158054\">10.1109/ESGCO49734.2020.9158054</a>"},"date_published":"2020-08-01T00:00:00Z","_id":"8580","quality_controlled":"1","external_id":{"isi":["000621172600045"]},"status":"public","abstract":[{"lang":"eng","text":"We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients."}],"type":"conference","publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","date_created":"2020-09-28T08:59:27Z","scopus_import":"1","oa_version":"None"},{"page":"1077-1085","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"author":[{"full_name":"Pinke, Gergely","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Pinke"},{"full_name":"Zhou, Long","id":"3E751364-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1864-8951","first_name":"Long","last_name":"Zhou"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A"}],"month":"11","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/structure-of-atpase-solved/"}]},"issue":"11","volume":27,"publication_status":"published","year":"2020","article_type":"original","citation":{"ieee":"G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian F-type ATP synthase,” <i>Nature Structural and Molecular Biology</i>, vol. 27, no. 11. Springer Nature, pp. 1077–1085, 2020.","ama":"Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type ATP synthase. <i>Nature Structural and Molecular Biology</i>. 2020;27(11):1077-1085. doi:<a href=\"https://doi.org/10.1038/s41594-020-0503-8\">10.1038/s41594-020-0503-8</a>","ista":"Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085.","apa":"Pinke, G., Zhou, L., &#38; Sazanov, L. A. (2020). Cryo-EM structure of the entire mammalian F-type ATP synthase. <i>Nature Structural and Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-020-0503-8\">https://doi.org/10.1038/s41594-020-0503-8</a>","short":"G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085.","mla":"Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” <i>Nature Structural and Molecular Biology</i>, vol. 27, no. 11, Springer Nature, 2020, pp. 1077–85, doi:<a href=\"https://doi.org/10.1038/s41594-020-0503-8\">10.1038/s41594-020-0503-8</a>.","chicago":"Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” <i>Nature Structural and Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41594-020-0503-8\">https://doi.org/10.1038/s41594-020-0503-8</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.","lang":"eng"}],"status":"public","external_id":{"isi":["000569299400004"],"pmid":["32929284"]},"date_created":"2020-09-28T08:59:27Z","publication":"Nature Structural and Molecular Biology","oa_version":"None","scopus_import":"1","type":"journal_article","date_updated":"2025-07-10T11:57:09Z","intvolume":"        27","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"article_processing_charge":"No","department":[{"_id":"LeSa"}],"day":"01","title":"Cryo-EM structure of the entire mammalian F-type ATP synthase","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-11-01T00:00:00Z","_id":"8581","quality_controlled":"1","publisher":"Springer Nature","isi":1,"doi":"10.1038/s41594-020-0503-8","acknowledgement":"We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC. We thank the IST Austria EM facility for access and assistance with collecting the FEI Glacios dataset. Data processing was performed at the IST high-performance computing cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by the Horizon 2020 Programme of the European Commission."},{"pmid":1,"author":[{"first_name":"Xiang","last_name":"Li","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Xiang"},{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","first_name":"Enderalp","last_name":"Yakaboylu"},{"last_name":"Bighin","orcid":"0000-0001-8823-9777","first_name":"Giacomo","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas","orcid":"0000-0003-3146-6746"}],"month":"04","volume":152,"related_material":{"record":[{"id":"8958","status":"public","relation":"dissertation_contains"}]},"issue":"16","publication_status":"published","year":"2020","language":[{"iso":"eng"}],"citation":{"chicago":"Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/1.5144759\">https://doi.org/10.1063/1.5144759</a>.","mla":"Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” <i>The Journal of Chemical Physics</i>, vol. 152, no. 16, 164302, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/1.5144759\">10.1063/1.5144759</a>.","short":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020).","apa":"Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., &#38; Deuchert, A. (2020). Intermolecular forces and correlations mediated by a phonon bath. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5144759\">https://doi.org/10.1063/1.5144759</a>","ista":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 152(16), 164302.","ieee":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert, “Intermolecular forces and correlations mediated by a phonon bath,” <i>The Journal of Chemical Physics</i>, vol. 152, no. 16. AIP Publishing, 2020.","ama":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular forces and correlations mediated by a phonon bath. <i>The Journal of Chemical Physics</i>. 2020;152(16). doi:<a href=\"https://doi.org/10.1063/1.5144759\">10.1063/1.5144759</a>"},"article_type":"original","ec_funded":1,"external_id":{"pmid":["32357791"],"isi":["000530448300001"],"arxiv":["1912.02658"]},"status":"public","abstract":[{"text":"Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1912.02658","open_access":"1"}],"type":"journal_article","corr_author":"1","oa_version":"Preprint","publication":"The Journal of Chemical Physics","date_created":"2020-09-30T10:33:17Z","project":[{"grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"},{"grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"name":"A path-integral approach to composite impurities","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"},{"grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"date_updated":"2026-04-08T07:26:09Z","intvolume":"       152","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"article_processing_charge":"No","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"day":"27","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"title":"Intermolecular forces and correlations mediated by a phonon bath","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"164302","_id":"8587","quality_controlled":"1","date_published":"2020-04-27T00:00:00Z","publisher":"AIP Publishing","isi":1,"doi":"10.1063/1.5144759","acknowledgement":"We are grateful to Areg Ghazaryan for valuable discussions. M.L. acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27 and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No. M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the European Research Council (ERC) Grant Agreement No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2111 – 390814868."},{"publisher":"American Physical Society","doi":"10.1103/physrevb.102.045307","isi":1,"acknowledgement":"We thank W. Kaganer for discussions and for comment on the manuscript. We acknowledge the financial support from the German-Israeli Foundation (GIF), grant agreement I-1277-303.10/2014. M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.G. acknowledges support by the European Unions Horizon 2020 research and innovation\r\nprogram under the Marie Skodowska-Curie grant agreement No 754411. P.V.S acknowledges financial support\r\nfrom the Deutsche Forschungsgemeinschaft (DFG) under\r\nProject No. SA 598/12-1.","article_number":"045307","_id":"8588","quality_controlled":"1","date_published":"2020-07-21T00:00:00Z","department":[{"_id":"MiLe"}],"day":"21","title":"Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"article_processing_charge":"No","project":[{"grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"arxiv":1,"date_updated":"2025-04-14T07:43:49Z","intvolume":"       102","language":[{"iso":"eng"}],"article_type":"original","ec_funded":1,"citation":{"short":"C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, P.V. Santos, Physical Review B 102 (2020).","mla":"Hubert, C., et al. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” <i>Physical Review B</i>, vol. 102, no. 4, 045307, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.045307\">10.1103/physrevb.102.045307</a>.","ama":"Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. <i>Physical Review B</i>. 2020;102(4). doi:<a href=\"https://doi.org/10.1103/physrevb.102.045307\">10.1103/physrevb.102.045307</a>","ista":"Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. 2020. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. 102(4), 045307.","ieee":"C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, and P. V. Santos, “Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids,” <i>Physical Review B</i>, vol. 102, no. 4. American Physical Society, 2020.","apa":"Hubert, C., Cohen, K., Ghazaryan, A., Lemeshko, M., Rapaport, R., &#38; Santos, P. V. (2020). Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.045307\">https://doi.org/10.1103/physrevb.102.045307</a>","chicago":"Hubert, C., K. Cohen, Areg Ghazaryan, Mikhail Lemeshko, R. Rapaport, and P. V. Santos. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.045307\">https://doi.org/10.1103/physrevb.102.045307</a>."},"status":"public","external_id":{"isi":["000550579100004"],"arxiv":["1910.06015"]},"abstract":[{"text":"Dipolar (or spatially indirect) excitons (IXs) in semiconductor double quantum well (DQW) subjected to an electric field are neutral species with a dipole moment oriented perpendicular to the DQW plane. Here, we theoretically study interactions between IXs in stacked DQW bilayers, where the dipolar coupling can be either attractive or repulsive depending on the relative positions of the particles. By using microscopic band structure calculations to determine the electronic states forming the excitons, we show that the attractive dipolar interaction between stacked IXs deforms their electronic wave function, thereby increasing the inter-DQW interaction energy and making the IX even more electrically polarizable. Many-particle interaction effects are addressed by considering the coupling between a single IX in one of the DQWs to a cloud of IXs in the other DQW, which is modeled either as a closed-packed lattice or as a continuum IX fluid. We find that the lattice model yields IX interlayer binding energies decreasing with increasing lattice density. This behavior is due to the dominating role of the intra-DQW dipolar repulsion, which prevents more than one exciton from entering the attractive region of the inter-DQW coupling. Finally, both models shows that the single IX distorts the distribution of IXs in the adjacent DQW, thus inducing the formation of an IX dipolar polaron (dipolaron). While the interlayer binding energy reduces with IX density for lattice dipolarons, the continuous polaron model predicts a nonmonotonous dependence on density in semiquantitative agreement with a recent experimental study [cf. Hubert et al., Phys. Rev. X 9, 021026 (2019)].","lang":"eng"}],"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1910.06015","open_access":"1"}],"scopus_import":"1","publication":"Physical Review B","oa_version":"Preprint","date_created":"2020-09-30T10:33:43Z","month":"07","volume":102,"issue":"4","publication_status":"published","year":"2020","author":[{"first_name":"C.","last_name":"Hubert","full_name":"Hubert, C."},{"full_name":"Cohen, K.","first_name":"K.","last_name":"Cohen"},{"last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"full_name":"Rapaport, R.","first_name":"R.","last_name":"Rapaport"},{"full_name":"Santos, P. V.","last_name":"Santos","first_name":"P. V."}]},{"article_number":"2001724","date_published":"2020-11-04T00:00:00Z","_id":"8592","quality_controlled":"1","publisher":"Wiley","doi":"10.1002/advs.202001724","acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","isi":1,"file":[{"content_type":"application/pdf","date_created":"2020-12-10T14:07:24Z","relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"92818c23ecc70e35acfa671f3cfb9909","success":1,"date_updated":"2020-12-10T14:07:24Z","file_name":"2020_AdvScience_Tian.pdf","file_id":"8938","file_size":7835833}],"publication_identifier":{"issn":["2198-3844"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","department":[{"_id":"SiHi"}],"keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"day":"04","oa":1,"title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"citation":{"mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” <i>Advanced Science</i>, vol. 7, no. 21, 2001724, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/advs.202001724\">10.1002/advs.202001724</a>.","short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020).","apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. <i>Advanced Science</i>. Wiley. <a href=\"https://doi.org/10.1002/advs.202001724\">https://doi.org/10.1002/advs.202001724</a>","ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. <i>Advanced Science</i>. 2020;7(21). doi:<a href=\"https://doi.org/10.1002/advs.202001724\">10.1002/advs.202001724</a>","ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.","ieee":"A. Tian <i>et al.</i>, “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” <i>Advanced Science</i>, vol. 7, no. 21. Wiley, 2020.","chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” <i>Advanced Science</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/advs.202001724\">https://doi.org/10.1002/advs.202001724</a>."},"article_type":"original","language":[{"iso":"eng"}],"abstract":[{"text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.","lang":"eng"}],"external_id":{"isi":["000573860700001"],"pmid":["33173731"]},"has_accepted_license":"1","status":"public","date_created":"2020-10-01T09:44:13Z","oa_version":"Published Version","publication":"Advanced Science","scopus_import":"1","type":"journal_article","project":[{"grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-06-12T06:59:38Z","ddc":["570"],"intvolume":"         7","pmid":1,"author":[{"full_name":"Tian, Anhao","last_name":"Tian","first_name":"Anhao"},{"first_name":"Bo","last_name":"Kang","full_name":"Kang, Bo"},{"last_name":"Li","first_name":"Baizhou","full_name":"Li, Baizhou"},{"last_name":"Qiu","first_name":"Biying","full_name":"Qiu, Biying"},{"first_name":"Wenhong","last_name":"Jiang","full_name":"Jiang, Wenhong"},{"full_name":"Shao, Fangjie","first_name":"Fangjie","last_name":"Shao"},{"last_name":"Gao","first_name":"Qingqing","full_name":"Gao, Qingqing"},{"first_name":"Rui","last_name":"Liu","full_name":"Liu, Rui"},{"full_name":"Cai, Chengwei","last_name":"Cai","first_name":"Chengwei"},{"full_name":"Jing, Rui","last_name":"Jing","first_name":"Rui"},{"last_name":"Wang","first_name":"Wei","full_name":"Wang, Wei"},{"full_name":"Chen, Pengxiang","first_name":"Pengxiang","last_name":"Chen"},{"first_name":"Qinghui","last_name":"Liang","full_name":"Liang, Qinghui"},{"first_name":"Lili","last_name":"Bao","full_name":"Bao, Lili"},{"first_name":"Jianghong","last_name":"Man","full_name":"Man, Jianghong"},{"full_name":"Wang, Yan","first_name":"Yan","last_name":"Wang"},{"full_name":"Shi, Yu","first_name":"Yu","last_name":"Shi"},{"full_name":"Li, Jin","last_name":"Li","first_name":"Jin"},{"full_name":"Yang, Minmin","first_name":"Minmin","last_name":"Yang"},{"first_name":"Lisha","last_name":"Wang","full_name":"Wang, Lisha"},{"last_name":"Zhang","first_name":"Jianmin","full_name":"Zhang, Jianmin"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhu, Junming","last_name":"Zhu","first_name":"Junming"},{"last_name":"Bian","first_name":"Xiuwu","full_name":"Bian, Xiuwu"},{"full_name":"Wang, Ying‐Jie","last_name":"Wang","first_name":"Ying‐Jie"},{"last_name":"Liu","first_name":"Chong","full_name":"Liu, Chong"}],"month":"11","issue":"21","volume":7,"file_date_updated":"2020-12-10T14:07:24Z","publication_status":"published","year":"2020"},{"article_number":"2","quality_controlled":"1","_id":"8599","date_published":"2020-08-06T00:00:00Z","conference":{"location":"Virtual","start_date":"2020-09-01","end_date":"2020-09-04","name":"CONCUR: Conference on Concurrency Theory"},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"We would like to thank all our collaborators Milad Aghajohari, Ventsislav Chonev, Rasmus Ibsen-Jensen, Ismäel Jecker, Petr Novotný, Josef Tkadlec, and Ðorđe Žikelić; we hope the collaboration was as fun and meaningful for you as it was for us.","file":[{"date_created":"2020-10-05T14:13:19Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2020-10-05T14:13:19Z","file_id":"8611","file_name":"2020_LIPIcsCONCUR_Avni.pdf","success":1,"checksum":"8f33b098e73724e0ac817f764d8e1a2d","file_size":868510}],"doi":"10.4230/LIPIcs.CONCUR.2020.2","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)"},"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771603"]},"article_processing_charge":"No","title":"A survey of bidding games on graphs","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by/3.0/","department":[{"_id":"ToHe"}],"day":"06","has_accepted_license":"1","status":"public","abstract":[{"text":"A graph game is a two-player zero-sum game in which the players move a token throughout a graph to produce an infinite path, which determines the winner or payoff of the game. In bidding games, both players have budgets, and in each turn, we hold an \"auction\" (bidding) to determine which player moves the token. In this survey, we consider several bidding mechanisms and study their effect on the properties of the game. Specifically, bidding games, and in particular bidding games of infinite duration, have an intriguing equivalence with random-turn games in which in each turn, the player who moves is chosen randomly. We show how minor changes in the bidding mechanism lead to unexpected differences in the equivalence with random-turn games.","lang":"eng"}],"type":"conference","corr_author":"1","publication":"31st International Conference on Concurrency Theory","scopus_import":"1","date_created":"2020-10-04T22:01:36Z","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"chicago":"Avni, Guy, and Thomas A Henzinger. “A Survey of Bidding Games on Graphs.” In <i>31st International Conference on Concurrency Theory</i>, Vol. 171. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2020.2\">https://doi.org/10.4230/LIPIcs.CONCUR.2020.2</a>.","short":"G. Avni, T.A. Henzinger, in:, 31st International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","mla":"Avni, Guy, and Thomas A. Henzinger. “A Survey of Bidding Games on Graphs.” <i>31st International Conference on Concurrency Theory</i>, vol. 171, 2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2020.2\">10.4230/LIPIcs.CONCUR.2020.2</a>.","ama":"Avni G, Henzinger TA. A survey of bidding games on graphs. In: <i>31st International Conference on Concurrency Theory</i>. Vol 171. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2020.2\">10.4230/LIPIcs.CONCUR.2020.2</a>","ista":"Avni G, Henzinger TA. 2020. A survey of bidding games on graphs. 31st International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 171, 2.","ieee":"G. Avni and T. A. Henzinger, “A survey of bidding games on graphs,” in <i>31st International Conference on Concurrency Theory</i>, Virtual, 2020, vol. 171.","apa":"Avni, G., &#38; Henzinger, T. A. (2020). A survey of bidding games on graphs. In <i>31st International Conference on Concurrency Theory</i> (Vol. 171). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2020.2\">https://doi.org/10.4230/LIPIcs.CONCUR.2020.2</a>"},"ddc":["000"],"date_updated":"2025-07-10T11:57:09Z","intvolume":"       171","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"}],"alternative_title":["LIPIcs"],"file_date_updated":"2020-10-05T14:13:19Z","publication_status":"published","year":"2020","month":"08","volume":171},{"file":[{"file_size":601231,"date_updated":"2020-10-05T14:04:25Z","file_name":"2020_LIPIcsCONCUR_Chatterjee.pdf","file_id":"8610","checksum":"5039752f644c4b72b9361d21a5e31baf","success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_created":"2020-10-05T14:04:25Z"}],"doi":"10.4230/LIPIcs.CONCUR.2020.23","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"start_date":"2020-09-01","location":"Virtual","end_date":"2020-09-04","name":"CONCUR: Conference on Concurrency Theory"},"_id":"8600","quality_controlled":"1","date_published":"2020-08-06T00:00:00Z","article_number":"23","day":"06","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Multi-dimensional long-run average problems for vector addition systems with states","article_processing_charge":"No","publication_identifier":{"isbn":["9783959771603"],"issn":["1868-8969"]},"tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)"},"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"intvolume":"       171","date_updated":"2025-07-10T11:57:10Z","ddc":["000"],"arxiv":1,"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Multi-Dimensional Long-Run Average Problems for Vector Addition Systems with States.” In <i>31st International Conference on Concurrency Theory</i>, Vol. 171. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2020.23\">https://doi.org/10.4230/LIPIcs.CONCUR.2020.23</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2020). Multi-dimensional long-run average problems for vector addition systems with states. In <i>31st International Conference on Concurrency Theory</i> (Vol. 171). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2020.23\">https://doi.org/10.4230/LIPIcs.CONCUR.2020.23</a>","ama":"Chatterjee K, Henzinger TA, Otop J. Multi-dimensional long-run average problems for vector addition systems with states. In: <i>31st International Conference on Concurrency Theory</i>. Vol 171. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2020.23\">10.4230/LIPIcs.CONCUR.2020.23</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Multi-dimensional long-run average problems for vector addition systems with states,” in <i>31st International Conference on Concurrency Theory</i>, Virtual, 2020, vol. 171.","ista":"Chatterjee K, Henzinger TA, Otop J. 2020. Multi-dimensional long-run average problems for vector addition systems with states. 31st International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 171, 23.","mla":"Chatterjee, Krishnendu, et al. “Multi-Dimensional Long-Run Average Problems for Vector Addition Systems with States.” <i>31st International Conference on Concurrency Theory</i>, vol. 171, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2020.23\">10.4230/LIPIcs.CONCUR.2020.23</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, 31st International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020."},"language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2020-10-04T22:01:36Z","publication":"31st International Conference on Concurrency Theory","oa_version":"Published Version","type":"conference","corr_author":"1","abstract":[{"lang":"eng","text":"A vector addition system with states (VASS) consists of a finite set of states and counters. A transition changes the current state to the next state, and every counter is either incremented, or decremented, or left unchanged. A state and value for each counter is a configuration; and a computation is an infinite sequence of configurations with transitions between successive configurations. A probabilistic VASS consists of a VASS along with a probability distribution over the transitions for each state. Qualitative properties such as state and configuration reachability have been widely studied for VASS. In this work we consider multi-dimensional long-run average objectives for VASS and probabilistic VASS. For a counter, the cost of a configuration is the value of the counter; and the long-run average value of a computation for the counter is the long-run average of the costs of the configurations in the computation. The multi-dimensional long-run average problem given a VASS and a threshold value for each counter, asks whether there is a computation such that for each counter the long-run average value for the counter does not exceed the respective threshold. For probabilistic VASS, instead of the existence of a computation, we consider whether the expected long-run average value for each counter does not exceed the respective threshold. Our main results are as follows: we show that the multi-dimensional long-run average problem (a) is NP-complete for integer-valued VASS; (b) is undecidable for natural-valued VASS (i.e., nonnegative counters); and (c) can be solved in polynomial time for probabilistic integer-valued VASS, and probabilistic natural-valued VASS when all computations are non-terminating."}],"has_accepted_license":"1","external_id":{"arxiv":["2007.08917"]},"status":"public","volume":171,"month":"08","year":"2020","publication_status":"published","file_date_updated":"2020-10-05T14:04:25Z","alternative_title":["LIPIcs"],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"last_name":"Otop","first_name":"Jan","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}]},{"publisher":"American Society of Plant Biologists","doi":"10.1105/tpc.20.00384","isi":1,"_id":"8607","quality_controlled":"1","date_published":"2020-11-01T00:00:00Z","department":[{"_id":"JiFr"}],"day":"01","oa":1,"title":"Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"article_processing_charge":"No","project":[{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"date_updated":"2026-06-18T19:35:07Z","ddc":["580"],"intvolume":"        32","ec_funded":1,"article_type":"original","citation":{"apa":"Liu, D., Kumar, R., LAN, C., Johnson, A. J., Siao, W., Vanhoutte, I., … Russinova, E. (2020). Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.20.00384\">https://doi.org/10.1105/tpc.20.00384</a>","ama":"Liu D, Kumar R, LAN C, et al. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. <i>Plant Cell</i>. 2020;32(11):3598-3612. doi:<a href=\"https://doi.org/10.1105/tpc.20.00384\">10.1105/tpc.20.00384</a>","ieee":"D. Liu <i>et al.</i>, “Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif,” <i>Plant Cell</i>, vol. 32, no. 11. American Society of Plant Biologists, pp. 3598–3612, 2020.","ista":"Liu D, Kumar R, LAN C, Johnson AJ, Siao W, Vanhoutte I, Wang P, Bender K, Yperman K, Martins S, Zhao X, Vert G, Van Damme D, Friml J, Russinova E. 2020. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. 32(11), 3598–3612.","mla":"Liu, D., et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” <i>Plant Cell</i>, vol. 32, no. 11, American Society of Plant Biologists, 2020, pp. 3598–612, doi:<a href=\"https://doi.org/10.1105/tpc.20.00384\">10.1105/tpc.20.00384</a>.","short":"D. Liu, R. Kumar, C. LAN, A.J. Johnson, W. Siao, I. Vanhoutte, P. Wang, K. Bender, K. Yperman, S. Martins, X. Zhao, G. Vert, D. Van Damme, J. Friml, E. Russinova, Plant Cell 32 (2020) 3598–3612.","chicago":"Liu, D, R Kumar, Claus LAN, Alexander J Johnson, W Siao, I Vanhoutte, P Wang, et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” <i>Plant Cell</i>. American Society of Plant Biologists, 2020. <a href=\"https://doi.org/10.1105/tpc.20.00384\">https://doi.org/10.1105/tpc.20.00384</a>."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles through the recognition of motifs based on tyrosine or di-leucine in their cytoplasmic tails. However, in plants, very little is known on how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis thaliana, the brassinosteroid (BR) receptor, BR INSENSITIVE1 (BRI1), undergoes endocytosis that depends on clathrin and AP-2. Here we demonstrate that BRI1 binds directly to the medium AP-2 subunit, AP2M. The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed tyrosine-based endocytic motifs. The tyrosine-to-phenylalanine substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2-dependent internalization of PM proteins via the recognition of functional tyrosine motifs also operates in plants."}],"status":"public","external_id":{"isi":["000600226800021"],"pmid":["32958564"]},"date_created":"2020-10-05T12:45:16Z","scopus_import":"1","publication":"Plant Cell","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://europepmc.org/article/MED/32958564"}],"type":"journal_article","month":"11","issue":"11","volume":32,"publication_status":"published","year":"2020","page":"3598-3612","pmid":1,"author":[{"full_name":"Liu, D","first_name":"D","last_name":"Liu"},{"full_name":"Kumar, R","first_name":"R","last_name":"Kumar"},{"full_name":"LAN, Claus","last_name":"LAN","first_name":"Claus"},{"last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"W","last_name":"Siao","full_name":"Siao, W"},{"full_name":"Vanhoutte, I","last_name":"Vanhoutte","first_name":"I"},{"first_name":"P","last_name":"Wang","full_name":"Wang, P"},{"full_name":"Bender, KW","first_name":"KW","last_name":"Bender"},{"full_name":"Yperman, K","first_name":"K","last_name":"Yperman"},{"full_name":"Martins, S","first_name":"S","last_name":"Martins"},{"full_name":"Zhao, X","last_name":"Zhao","first_name":"X"},{"full_name":"Vert, G","last_name":"Vert","first_name":"G"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Russinova","first_name":"E","full_name":"Russinova, E"}]},{"month":"10","volume":12399,"file_date_updated":"2020-10-15T14:28:06Z","publication_status":"published","year":"2020","page":"3-18","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","last_name":"Sarac","first_name":"Naci E"}],"alternative_title":["LNCS"],"project":[{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"date_updated":"2026-04-16T10:22:01Z","ddc":["000"],"intvolume":"     12399","citation":{"short":"T.A. Henzinger, N.E. Sarac, in:, Runtime Verification, Springer Nature, 2020, pp. 3–18.","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Monitorability under Assumptions.” <i>Runtime Verification</i>, vol. 12399, Springer Nature, 2020, pp. 3–18, doi:<a href=\"https://doi.org/10.1007/978-3-030-60508-7_1\">10.1007/978-3-030-60508-7_1</a>.","ista":"Henzinger TA, Sarac NE. 2020. Monitorability under assumptions. Runtime Verification. RV: Runtime Verification, LNCS, vol. 12399, 3–18.","ieee":"T. A. Henzinger and N. E. Sarac, “Monitorability under assumptions,” in <i>Runtime Verification</i>, Los Angeles, CA, United States, 2020, vol. 12399, pp. 3–18.","ama":"Henzinger TA, Sarac NE. Monitorability under assumptions. In: <i>Runtime Verification</i>. Vol 12399. Springer Nature; 2020:3-18. doi:<a href=\"https://doi.org/10.1007/978-3-030-60508-7_1\">10.1007/978-3-030-60508-7_1</a>","apa":"Henzinger, T. A., &#38; Sarac, N. E. (2020). Monitorability under assumptions. In <i>Runtime Verification</i> (Vol. 12399, pp. 3–18). Los Angeles, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-60508-7_1\">https://doi.org/10.1007/978-3-030-60508-7_1</a>","chicago":"Henzinger, Thomas A, and Naci E Sarac. “Monitorability under Assumptions.” In <i>Runtime Verification</i>, 12399:3–18. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-60508-7_1\">https://doi.org/10.1007/978-3-030-60508-7_1</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"We introduce the monitoring of trace properties under assumptions. An assumption limits the space of possible traces that the monitor may encounter. An assumption may result from knowledge about the system that is being monitored, about the environment, or about another, connected monitor. We define monitorability under assumptions and study its theoretical properties. In particular, we show that for every assumption A, the boolean combinations of properties that are safe or co-safe relative to A are monitorable under A. We give several examples and constructions on how an assumption can make a non-monitorable property monitorable, and how an assumption can make a monitorable property monitorable with fewer resources, such as integer registers.","lang":"eng"}],"has_accepted_license":"1","status":"public","external_id":{"isi":["000728160600001"]},"oa_version":"Submitted Version","date_created":"2020-10-07T15:05:37Z","publication":"Runtime Verification","scopus_import":"1","type":"conference","department":[{"_id":"ToHe"}],"day":"02","oa":1,"title":"Monitorability under assumptions","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783030605087"],"eissn":["1611-3349"],"isbn":["9783030605070"]},"article_processing_charge":"No","publisher":"Springer Nature","file":[{"date_created":"2020-10-15T14:28:06Z","content_type":"application/pdf","relation":"main_file","creator":"esarac","access_level":"open_access","checksum":"00661f9b7034f52e18bf24fa552b8194","success":1,"date_updated":"2020-10-15T14:28:06Z","file_id":"8665","file_name":"monitorability.pdf","file_size":478148}],"isi":1,"doi":"10.1007/978-3-030-60508-7_1","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","conference":{"end_date":"2020-10-09","location":"Los Angeles, CA, United States","start_date":"2020-10-06","name":"RV: Runtime Verification"},"quality_controlled":"1","_id":"8623","date_published":"2020-10-02T00:00:00Z"},{"acknowledgement":"M. F. S. and R. O. G. acknowledge funding from the National Science Foundation (CMMI-1234436, DMS1125302, CMMI-1725587) and Defense Advanced Research Projects Agency (HR0011-16-2-0033). B. S.has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007–2013/ under REA Grant Agreement No. 291734.","isi":1,"doi":"10.1103/physrevlett.125.064501","publisher":"American Physical Society","date_published":"2020-08-05T00:00:00Z","_id":"8634","quality_controlled":"1","article_number":"064501","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"title":"Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits","day":"05","keyword":["General Physics and Astronomy"],"department":[{"_id":"BjHo"}],"article_processing_charge":"No","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"intvolume":"       125","date_updated":"2025-04-15T06:50:02Z","arxiv":1,"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication":"Physical Review Letters","date_created":"2020-10-08T17:27:32Z","scopus_import":"1","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2008.02367","open_access":"1"}],"type":"journal_article","abstract":[{"text":"In laboratory studies and numerical simulations, we observe clear signatures of unstable time-periodic solutions in a moderately turbulent quasi-two-dimensional flow. We validate the dynamical relevance of such solutions by demonstrating that turbulent flows in both experiment and numerics transiently display time-periodic dynamics when they shadow unstable periodic orbits (UPOs). We show that UPOs we computed are also statistically significant, with turbulent flows spending a sizable fraction of the total time near these solutions. As a result, the average rates of energy input and dissipation for the turbulent flow and frequently visited UPOs differ only by a few percent.","lang":"eng"}],"status":"public","external_id":{"isi":["000555785600005"],"arxiv":["2008.02367"]},"ec_funded":1,"citation":{"short":"B. Suri, L. Kageorge, R.O. Grigoriev, M.F. Schatz, Physical Review Letters 125 (2020).","mla":"Suri, Balachandra, et al. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” <i>Physical Review Letters</i>, vol. 125, no. 6, 064501, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevlett.125.064501\">10.1103/physrevlett.125.064501</a>.","ama":"Suri B, Kageorge L, Grigoriev RO, Schatz MF. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. <i>Physical Review Letters</i>. 2020;125(6). doi:<a href=\"https://doi.org/10.1103/physrevlett.125.064501\">10.1103/physrevlett.125.064501</a>","ista":"Suri B, Kageorge L, Grigoriev RO, Schatz MF. 2020. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. 125(6), 064501.","ieee":"B. Suri, L. Kageorge, R. O. Grigoriev, and M. F. Schatz, “Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits,” <i>Physical Review Letters</i>, vol. 125, no. 6. American Physical Society, 2020.","apa":"Suri, B., Kageorge, L., Grigoriev, R. O., &#38; Schatz, M. F. (2020). Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.125.064501\">https://doi.org/10.1103/physrevlett.125.064501</a>","chicago":"Suri, Balachandra, Logan Kageorge, Roman O. Grigoriev, and Michael F. Schatz. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevlett.125.064501\">https://doi.org/10.1103/physrevlett.125.064501</a>."},"article_type":"original","language":[{"iso":"eng"}],"year":"2020","publication_status":"published","issue":"6","volume":125,"month":"08","author":[{"last_name":"Suri","first_name":"Balachandra","full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Logan","last_name":"Kageorge","full_name":"Kageorge, Logan"},{"first_name":"Roman O.","last_name":"Grigoriev","full_name":"Grigoriev, Roman O."},{"first_name":"Michael F.","last_name":"Schatz","full_name":"Schatz, Michael F."}]},{"intvolume":"        10","ddc":["570"],"date_updated":"2026-04-03T09:26:41Z","type":"journal_article","oa_version":"Published Version","date_created":"2020-10-11T22:01:14Z","scopus_import":"1","publication":"Scientific Reports","external_id":{"isi":["000577142600032"],"pmid":["33004866"]},"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors."}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"ieee":"A. Deichler <i>et al.</i>, “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” <i>Scientific Reports</i>, vol. 10. Springer Nature, 2020.","ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220.","ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. <i>Scientific Reports</i>. 2020;10. doi:<a href=\"https://doi.org/10.1038/s41598-020-72848-0\">10.1038/s41598-020-72848-0</a>","apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., &#38; Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-72848-0\">https://doi.org/10.1038/s41598-020-72848-0</a>","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” <i>Scientific Reports</i>, vol. 10, 16220, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-72848-0\">10.1038/s41598-020-72848-0</a>.","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-72848-0\">https://doi.org/10.1038/s41598-020-72848-0</a>."},"year":"2020","file_date_updated":"2020-10-12T12:39:10Z","publication_status":"published","volume":10,"month":"10","author":[{"full_name":"Deichler, Alfonso","last_name":"Deichler","first_name":"Alfonso"},{"last_name":"Carrasco","first_name":"Denisse","full_name":"Carrasco, Denisse"},{"last_name":"Lopez-Jury","first_name":"Luciana","full_name":"Lopez-Jury, Luciana"},{"first_name":"Tomas A","last_name":"Vega Zuniga","full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Natalia","last_name":"Marquez","full_name":"Marquez, Natalia"},{"full_name":"Mpodozis, Jorge","last_name":"Mpodozis","first_name":"Jorge"},{"last_name":"Marin","first_name":"Gonzalo","full_name":"Marin, Gonzalo"}],"pmid":1,"doi":"10.1038/s41598-020-72848-0","file":[{"date_created":"2020-10-12T12:39:10Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2020-10-12T12:39:10Z","file_id":"8651","file_name":"2020_ScientificReport_Deichler.pdf","checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","success":1,"file_size":3906744}],"isi":1,"acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).","publisher":"Springer Nature","date_published":"2020-10-01T00:00:00Z","_id":"8643","quality_controlled":"1","article_number":"16220","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","oa":1,"day":"01","department":[{"_id":"MaJö"}],"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2045-2322"]}},{"publisher":"IOP Publishing","doi":"10.1088/1367-2630/abae44","acknowledgement":"We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various stages of this work. WR has received funding from the EU Horizon 2020 program under the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster).","file":[{"date_updated":"2020-10-12T12:18:47Z","file_id":"8650","file_name":"2020_NewJournalPhysics_Rzdkowski.pdf","checksum":"c9238fff422e7a957c3a0d559f756b3a","success":1,"file_size":2725143,"content_type":"application/pdf","date_created":"2020-10-12T12:18:47Z","access_level":"open_access","relation":"main_file","creator":"dernst"}],"isi":1,"article_number":"093026","_id":"8644","quality_controlled":"1","date_published":"2020-09-01T00:00:00Z","oa":1,"title":"Detecting composite orders in layered models via machine learning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiLe"}],"day":"01","publication_identifier":{"issn":["1367-2630"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","date_updated":"2026-04-07T14:20:12Z","ddc":["530"],"intvolume":"        22","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"_id":"05A235A0-7A3F-11EA-A408-12923DDC885E","name":"Analytic and machine learning approaches to composite quantum impurities","grant_number":"25681"},{"grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425","name":"A path-integral approach to composite impurities","call_identifier":"FWF"}],"abstract":[{"lang":"eng","text":"Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures."}],"has_accepted_license":"1","status":"public","external_id":{"isi":["000573298000001"]},"oa_version":"Published Version","publication":"New Journal of Physics","date_created":"2020-10-11T22:01:14Z","scopus_import":"1","type":"journal_article","corr_author":"1","article_type":"original","ec_funded":1,"citation":{"apa":"Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., &#38; Bighin, G. (2020). Detecting composite orders in layered models via machine learning. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/abae44\">https://doi.org/10.1088/1367-2630/abae44</a>","ista":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting composite orders in layered models via machine learning. New Journal of Physics. 22(9), 093026.","ieee":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting composite orders in layered models via machine learning,” <i>New Journal of Physics</i>, vol. 22, no. 9. IOP Publishing, 2020.","ama":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite orders in layered models via machine learning. <i>New Journal of Physics</i>. 2020;22(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/abae44\">10.1088/1367-2630/abae44</a>","mla":"Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models via Machine Learning.” <i>New Journal of Physics</i>, vol. 22, no. 9, 093026, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.1088/1367-2630/abae44\">10.1088/1367-2630/abae44</a>.","short":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020).","chicago":"Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” <i>New Journal of Physics</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1367-2630/abae44\">https://doi.org/10.1088/1367-2630/abae44</a>."},"language":[{"iso":"eng"}],"file_date_updated":"2020-10-12T12:18:47Z","publication_status":"published","year":"2020","month":"09","issue":"9","related_material":{"record":[{"status":"public","id":"10759","relation":"dissertation_contains"}]},"volume":22,"author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","orcid":"0000-0002-1106-4419","last_name":"Rzadkowski"},{"first_name":"N","last_name":"Defenu","full_name":"Defenu, N"},{"first_name":"S","last_name":"Chiacchiera","full_name":"Chiacchiera, S"},{"first_name":"A","last_name":"Trombettoni","full_name":"Trombettoni, A"},{"full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","last_name":"Bighin"}]},{"author":[{"first_name":"Laura A","last_name":"Esteban","full_name":"Esteban, Laura A"},{"full_name":"Lonishin, Lyubov R","first_name":"Lyubov R","last_name":"Lonishin"},{"full_name":"Bobrovskiy, Daniil M","first_name":"Daniil M","last_name":"Bobrovskiy"},{"full_name":"Leleytner, Gregory","last_name":"Leleytner","first_name":"Gregory"},{"full_name":"Bogatyreva, Natalya S","last_name":"Bogatyreva","first_name":"Natalya S"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"last_name":"Ivankov","first_name":"Dmitry N ","full_name":"Ivankov, Dmitry N "}],"pmid":1,"page":"1960-1962","year":"2020","publication_status":"published","file_date_updated":"2020-10-12T12:02:09Z","issue":"6","volume":36,"month":"03","publication":"Bioinformatics","scopus_import":"1","oa_version":"Published Version","date_created":"2020-10-11T22:01:14Z","type":"journal_article","abstract":[{"lang":"eng","text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data."}],"status":"public","external_id":{"isi":["000538696800054"],"pmid":["31742320"]},"has_accepted_license":"1","citation":{"apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., &#38; Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btz841\">https://doi.org/10.1093/bioinformatics/btz841</a>","ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.","ieee":"L. A. Esteban <i>et al.</i>, “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” <i>Bioinformatics</i>, vol. 36, no. 6. Oxford University Press, pp. 1960–1962, 2020.","ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. <i>Bioinformatics</i>. 2020;36(6):1960-1962. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btz841\">10.1093/bioinformatics/btz841</a>","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” <i>Bioinformatics</i>, vol. 36, no. 6, Oxford University Press, 2020, pp. 1960–62, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btz841\">10.1093/bioinformatics/btz841</a>.","short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N  Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” <i>Bioinformatics</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/bioinformatics/btz841\">https://doi.org/10.1093/bioinformatics/btz841</a>."},"article_type":"original","ec_funded":1,"language":[{"iso":"eng"}],"intvolume":"        36","date_updated":"2025-05-14T11:04:01Z","ddc":["000","570"],"project":[{"grant_number":"335980","call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","name":"Systematic investigation of epistasis in molecular evolution"}],"article_processing_charge":"No","publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","day":"15","department":[{"_id":"FyKo"}],"date_published":"2020-03-15T00:00:00Z","_id":"8645","quality_controlled":"1","isi":1,"doi":"10.1093/bioinformatics/btz841","acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","file":[{"file_size":308341,"success":1,"checksum":"21d6f71839deb3b83e4a356193f72767","file_name":"2020_Bioinformatics_Esteban.pdf","file_id":"8649","date_updated":"2020-10-12T12:02:09Z","creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2020-10-12T12:02:09Z","content_type":"application/pdf"}],"publisher":"Oxford University Press"},{"year":"2020","publication_status":"published","file_date_updated":"2020-10-14T15:16:28Z","volume":3,"month":"10","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","first_name":"Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"}],"intvolume":"         3","date_updated":"2025-04-14T07:43:50Z","ddc":["530"],"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"oa_version":"Published Version","scopus_import":"1","publication":"Communications Physics","date_created":"2020-10-13T09:48:59Z","type":"journal_article","corr_author":"1","abstract":[{"text":"Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules.","lang":"eng"}],"external_id":{"isi":["000581681000001"]},"has_accepted_license":"1","status":"public","citation":{"chicago":"Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins by Scattering from a Lattice of Point Magnets.” <i>Communications Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s42005-020-00445-8\">https://doi.org/10.1038/s42005-020-00445-8</a>.","apa":"Ghazaryan, A., Lemeshko, M., &#38; Volosniev, A. (2020). Filtering spins by scattering from a lattice of point magnets. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-020-00445-8\">https://doi.org/10.1038/s42005-020-00445-8</a>","ista":"Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178.","ama":"Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a lattice of point magnets. <i>Communications Physics</i>. 2020;3. doi:<a href=\"https://doi.org/10.1038/s42005-020-00445-8\">10.1038/s42005-020-00445-8</a>","ieee":"A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering from a lattice of point magnets,” <i>Communications Physics</i>, vol. 3. Springer Nature, 2020.","mla":"Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point Magnets.” <i>Communications Physics</i>, vol. 3, 178, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s42005-020-00445-8\">10.1038/s42005-020-00445-8</a>.","short":"A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020)."},"article_type":"original","ec_funded":1,"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"title":"Filtering spins by scattering from a lattice of point magnets","day":"09","department":[{"_id":"MiLe"}],"article_processing_charge":"Yes","publication_identifier":{"issn":["2399-3650"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1038/s42005-020-00445-8","file":[{"content_type":"application/pdf","date_created":"2020-10-14T15:16:28Z","relation":"main_file","creator":"dernst","access_level":"open_access","checksum":"60cd35b99f0780acffc7b6060e49ec8b","success":1,"date_updated":"2020-10-14T15:16:28Z","file_id":"8662","file_name":"2020_CommPhysics_Ghazaryan.pdf","file_size":1462934}],"isi":1,"acknowledgement":"This work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting\r\nGrant No. 801770 (ANGULON).","publisher":"Springer Nature","_id":"8652","quality_controlled":"1","date_published":"2020-10-09T00:00:00Z","article_number":"178"},{"quality_controlled":"1","_id":"8669","date_published":"2020-10-07T00:00:00Z","article_number":"5037","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2020-10-19T11:27:46Z","content_type":"application/pdf","file_size":5540540,"checksum":"0ecc0eab72d2d50694852579611a6624","success":1,"date_updated":"2020-10-19T11:27:46Z","file_name":"2020_NatureComm_Sznurkowska.pdf","file_id":"8677"}],"doi":"10.1038/s41467-020-18837-3","isi":1,"publisher":"Springer Nature","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2041-1723"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Tracing the cellular basis of islet specification in mouse pancreas","oa":1,"day":"07","department":[{"_id":"EdHa"}],"type":"journal_article","date_created":"2020-10-18T22:01:35Z","oa_version":"Published Version","scopus_import":"1","publication":"Nature Communications","status":"public","has_accepted_license":"1","external_id":{"pmid":["33028844"],"isi":["000577244600003"]},"abstract":[{"text":"Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","mla":"Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” <i>Nature Communications</i>, vol. 11, 5037, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18837-3\">10.1038/s41467-020-18837-3</a>.","ieee":"M. K. Sznurkowska <i>et al.</i>, “Tracing the cellular basis of islet specification in mouse pancreas,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037.","ama":"Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18837-3\">10.1038/s41467-020-18837-3</a>","apa":"Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18837-3\">https://doi.org/10.1038/s41467-020-18837-3</a>","chicago":"Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18837-3\">https://doi.org/10.1038/s41467-020-18837-3</a>."},"article_type":"original","intvolume":"        11","ddc":["570"],"date_updated":"2026-04-02T14:29:58Z","author":[{"last_name":"Sznurkowska","first_name":"Magdalena K.","full_name":"Sznurkowska, Magdalena K."},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"first_name":"Roberta","last_name":"Azzarelli","full_name":"Azzarelli, Roberta"},{"first_name":"Lemonia","last_name":"Chatzeli","full_name":"Chatzeli, Lemonia"},{"full_name":"Ikeda, Tatsuro","last_name":"Ikeda","first_name":"Tatsuro"},{"full_name":"Yoshida, Shosei","last_name":"Yoshida","first_name":"Shosei"},{"full_name":"Philpott, Anna","last_name":"Philpott","first_name":"Anna"},{"first_name":"Benjamin D","last_name":"Simons","full_name":"Simons, Benjamin D"}],"pmid":1,"year":"2020","file_date_updated":"2020-10-19T11:27:46Z","publication_status":"published","volume":11,"month":"10"},{"main_file_link":[{"url":"https://arxiv.org/abs/2007.06644","open_access":"1"}],"type":"journal_article","corr_author":"1","scopus_import":"1","oa_version":"Preprint","publication":"Journal of Mathematical Physics","date_created":"2020-10-18T22:01:36Z","status":"public","external_id":{"isi":["000578529200001"],"arxiv":["2007.06644"]},"abstract":[{"lang":"eng","text":"The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)]."}],"language":[{"iso":"eng"}],"citation":{"mla":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” <i>Journal of Mathematical Physics</i>, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/5.0022787\">10.1063/5.0022787</a>.","short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","apa":"Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0022787\">https://doi.org/10.1063/5.0022787</a>","ieee":"H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” <i>Journal of Mathematical Physics</i>, vol. 61, no. 10. AIP Publishing, 2020.","ama":"Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. <i>Journal of Mathematical Physics</i>. 2020;61(10). doi:<a href=\"https://doi.org/10.1063/5.0022787\">10.1063/5.0022787</a>","ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201.","chicago":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/5.0022787\">https://doi.org/10.1063/5.0022787</a>."},"ec_funded":1,"article_type":"original","intvolume":"        61","arxiv":1,"date_updated":"2025-07-10T11:57:14Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"author":[{"last_name":"Zhang","first_name":"Haonan","full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"year":"2020","publication_status":"published","volume":61,"issue":"10","month":"10","_id":"8670","date_published":"2020-10-01T00:00:00Z","quality_controlled":"1","article_number":"102201","isi":1,"doi":"10.1063/5.0022787","acknowledgement":"This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments.","publisher":"AIP Publishing","article_processing_charge":"No","publication_identifier":{"issn":["0022-2488"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Equality conditions of data processing inequality for α-z Rényi relative entropies","oa":1,"day":"01","department":[{"_id":"JaMa"}]},{"article_processing_charge":"No","publication_identifier":{"issn":["1735-4463"],"eissn":["2008-9473"]},"day":"01","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"A note on belief structures and s-approximation spaces","_id":"8671","quality_controlled":"1","date_published":"2020-10-01T00:00:00Z","file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2020-10-19T11:14:20Z","content_type":"application/pdf","file_size":261688,"file_name":"2020_ijmsi_Shakiba_accepted.pdf","file_id":"8676","date_updated":"2020-10-19T11:14:20Z","checksum":"f299661a6d51cda6d255a76be696f48d","success":1}],"acknowledgement":"We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences.","doi":"10.29252/ijmsi.15.2.117","publisher":"Iranian Academic Center for Education, Culture and Research","page":"117-128","author":[{"last_name":"Shakiba","first_name":"A.","full_name":"Shakiba, A."},{"last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Hooshmandasl, M.R.","first_name":"M.R.","last_name":"Hooshmandasl"},{"last_name":"Alambardar Meybodi","first_name":"M.","full_name":"Alambardar Meybodi, M."}],"issue":"2","volume":15,"month":"10","year":"2020","publication_status":"published","file_date_updated":"2020-10-19T11:14:20Z","citation":{"apa":"Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., &#38; Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. <i>Iranian Journal of Mathematical Sciences and Informatics</i>. Iranian Academic Center for Education, Culture and Research. <a href=\"https://doi.org/10.29252/ijmsi.15.2.117\">https://doi.org/10.29252/ijmsi.15.2.117</a>","ama":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. <i>Iranian Journal of Mathematical Sciences and Informatics</i>. 2020;15(2):117-128. doi:<a href=\"https://doi.org/10.29252/ijmsi.15.2.117\">10.29252/ijmsi.15.2.117</a>","ieee":"A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” <i>Iranian Journal of Mathematical Sciences and Informatics</i>, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020.","ista":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128.","mla":"Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” <i>Iranian Journal of Mathematical Sciences and Informatics</i>, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:<a href=\"https://doi.org/10.29252/ijmsi.15.2.117\">10.29252/ijmsi.15.2.117</a>.","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.","chicago":"Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” <i>Iranian Journal of Mathematical Sciences and Informatics</i>. Iranian Academic Center for Education, Culture and Research, 2020. <a href=\"https://doi.org/10.29252/ijmsi.15.2.117\">https://doi.org/10.29252/ijmsi.15.2.117</a>."},"article_type":"original","language":[{"iso":"eng"}],"date_created":"2020-10-18T22:01:36Z","scopus_import":"1","publication":"Iranian Journal of Mathematical Sciences and Informatics","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. ","lang":"eng"}],"external_id":{"arxiv":["1805.10672"]},"has_accepted_license":"1","status":"public","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"}],"intvolume":"        15","date_updated":"2025-04-15T07:55:04Z","ddc":["000"],"arxiv":1},{"department":[{"_id":"EdHa"}],"day":"26","title":"Abscission couples cell division to embryonic stem cell fate","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"article_processing_charge":"No","publisher":"Elsevier","isi":1,"acknowledgement":"This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015).","file":[{"date_created":"2021-02-04T10:20:02Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2021-02-04T10:20:02Z","file_id":"9086","file_name":"2020_DevelopmCell_Chaigne.pdf","checksum":"88e1a031a61689165d19a19c2f16d795","success":1,"file_size":6929686}],"doi":"10.1016/j.devcel.2020.09.001","date_published":"2020-10-26T00:00:00Z","_id":"8672","quality_controlled":"1","month":"10","volume":55,"issue":"2","publication_status":"published","file_date_updated":"2021-02-04T10:20:02Z","year":"2020","page":"195-208","pmid":1,"author":[{"last_name":"Chaigne","first_name":"Agathe","full_name":"Chaigne, Agathe"},{"last_name":"Labouesse","first_name":"Céline","full_name":"Labouesse, Céline"},{"last_name":"White","first_name":"Ian J.","full_name":"White, Ian J."},{"full_name":"Agnew, Meghan","first_name":"Meghan","last_name":"Agnew"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"first_name":"Kevin J.","last_name":"Chalut","full_name":"Chalut, Kevin J."},{"last_name":"Paluch","first_name":"Ewa K.","full_name":"Paluch, Ewa K."}],"ddc":["570"],"date_updated":"2025-07-10T11:57:15Z","intvolume":"        55","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” <i>Developmental Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.devcel.2020.09.001\">https://doi.org/10.1016/j.devcel.2020.09.001</a>.","apa":"Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., &#38; Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.09.001\">https://doi.org/10.1016/j.devcel.2020.09.001</a>","ista":"Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208.","ama":"Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. <i>Developmental Cell</i>. 2020;55(2):195-208. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.09.001\">10.1016/j.devcel.2020.09.001</a>","ieee":"A. Chaigne <i>et al.</i>, “Abscission couples cell division to embryonic stem cell fate,” <i>Developmental Cell</i>, vol. 55, no. 2. Elsevier, pp. 195–208, 2020.","mla":"Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” <i>Developmental Cell</i>, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.09.001\">10.1016/j.devcel.2020.09.001</a>.","short":"A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208."},"status":"public","external_id":{"pmid":["32979313"],"isi":["000582501100012"]},"has_accepted_license":"1","abstract":[{"text":"Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","scopus_import":"1","date_created":"2020-10-18T22:01:37Z","publication":"Developmental Cell"}]