[{"article_processing_charge":"No","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"department":[{"_id":"ToHe"}],"citation":{"short":"L. Geretti, J. Alexandre Dit Sandretto, M. Althoff, L. Benet, A. Chapoutot, X. Chen, P. Collins, M. Forets, D. Freire, F. Immler, N. Kochdumper, D. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair, 2020, pp. 49–75.","mla":"Geretti, Luca, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” <i>EPiC Series in Computing</i>, vol. 74, EasyChair, 2020, pp. 49–75, doi:<a href=\"https://doi.org/10.29007/zkf6\">10.29007/zkf6</a>.","ista":"Geretti L, Alexandre Dit Sandretto J, Althoff M, Benet L, Chapoutot A, Chen X, Collins P, Forets M, Freire D, Immler F, Kochdumper N, Sanders D, Schilling C. 2020. ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 74, 49–75.","ama":"Geretti L, Alexandre Dit Sandretto J, Althoff M, et al. ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: <i>EPiC Series in Computing</i>. Vol 74. EasyChair; 2020:49-75. doi:<a href=\"https://doi.org/10.29007/zkf6\">10.29007/zkf6</a>","chicago":"Geretti, Luca, Julien Alexandre Dit Sandretto, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Pieter Collins, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In <i>EPiC Series in Computing</i>, 74:49–75. EasyChair, 2020. <a href=\"https://doi.org/10.29007/zkf6\">https://doi.org/10.29007/zkf6</a>.","ieee":"L. Geretti <i>et al.</i>, “ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in <i>EPiC Series in Computing</i>, 2020, vol. 74, pp. 49–75.","apa":"Geretti, L., Alexandre Dit Sandretto, J., Althoff, M., Benet, L., Chapoutot, A., Chen, X., … Schilling, C. (2020). ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics. In <i>EPiC Series in Computing</i> (Vol. 74, pp. 49–75). EasyChair. <a href=\"https://doi.org/10.29007/zkf6\">https://doi.org/10.29007/zkf6</a>"},"month":"09","main_file_link":[{"url":"https://easychair.org/publications/download/nrdD","open_access":"1"}],"abstract":[{"lang":"eng","text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These tools are applied to solve reachability analysis problems on six benchmark problems, two of them featuring hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools."}],"acknowledgement":"Christian Schilling acknowledges support in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411.","conference":{"name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","end_date":"2020-07-12","start_date":"2020-07-12"},"page":"49-75","date_created":"2020-09-26T14:41:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Geretti, Luca","last_name":"Geretti","first_name":"Luca"},{"full_name":"Alexandre Dit Sandretto, Julien","last_name":"Alexandre Dit Sandretto","first_name":"Julien"},{"first_name":"Matthias","last_name":"Althoff","full_name":"Althoff, Matthias"},{"full_name":"Benet, Luis","last_name":"Benet","first_name":"Luis"},{"last_name":"Chapoutot","full_name":"Chapoutot, Alexandre","first_name":"Alexandre"},{"first_name":"Xin","full_name":"Chen, Xin","last_name":"Chen"},{"last_name":"Collins","full_name":"Collins, Pieter","first_name":"Pieter"},{"full_name":"Forets, Marcelo","last_name":"Forets","first_name":"Marcelo"},{"last_name":"Freire","full_name":"Freire, Daniel","first_name":"Daniel"},{"last_name":"Immler","full_name":"Immler, Fabian","first_name":"Fabian"},{"last_name":"Kochdumper","full_name":"Kochdumper, Niklas","first_name":"Niklas"},{"first_name":"David","last_name":"Sanders","full_name":"Sanders, David"},{"orcid":"0000-0003-3658-1065","first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian"}],"publication_status":"published","date_published":"2020-09-25T00:00:00Z","year":"2020","status":"public","intvolume":"        74","_id":"8571","date_updated":"2021-01-12T08:20:06Z","ec_funded":1,"oa_version":"Published Version","volume":74,"language":[{"iso":"eng"}],"day":"25","oa":1,"type":"conference","quality_controlled":"1","title":"ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics","publisher":"EasyChair","doi":"10.29007/zkf6","publication":"EPiC Series in Computing"},{"abstract":[{"lang":"eng","text":"We present the results of the ARCH 2020 friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. In its fourth edition, eight tools have been applied to solve eight different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, C2E2, HyDRA, Hylaa, Hylaa-Continuous, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date."}],"main_file_link":[{"url":"https://easychair.org/publications/download/DRpS","open_access":"1"}],"acknowledgement":"The authors gratefully acknowledge financial support by the European Commission project\r\njustITSELF under grant number 817629, by the Austrian Science Fund (FWF) under grant\r\nZ211-N23 (Wittgenstein Award), by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411, and by the\r\nScience and Engineering Research Board (SERB) project with file number IMP/2018/000523.\r\nThis material is based upon work supported by the Air Force Office of Scientific Research under\r\naward number FA9550-19-1-0288. Any opinions, finding, and conclusions or recommendations\r\nexpressed in this material are those of the author(s) and do not necessarily reflect the views of\r\nthe United States Air Force.","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","citation":{"ieee":"M. Althoff <i>et al.</i>, “ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics,” in <i>EPiC Series in Computing</i>, 2020, vol. 74, pp. 16–48.","apa":"Althoff, M., Bak, S., Bao, Z., Forets, M., Frehse, G., Freire, D., … Wetzlinger, M. (2020). ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics. In <i>EPiC Series in Computing</i> (Vol. 74, pp. 16–48). EasyChair. <a href=\"https://doi.org/10.29007/7dt2\">https://doi.org/10.29007/7dt2</a>","chicago":"Althoff, Matthias, Stanley Bak, Zongnan Bao, Marcelo Forets, Goran Frehse, Daniel Freire, Niklas Kochdumper, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Linear Dynamics.” In <i>EPiC Series in Computing</i>, 74:16–48. EasyChair, 2020. <a href=\"https://doi.org/10.29007/7dt2\">https://doi.org/10.29007/7dt2</a>.","short":"M. Althoff, S. Bak, Z. Bao, M. Forets, G. Frehse, D. Freire, N. Kochdumper, Y. Li, S. Mitra, R. Ray, C. Schilling, S. Schupp, M. Wetzlinger, in:, EPiC Series in Computing, EasyChair, 2020, pp. 16–48.","mla":"Althoff, Matthias, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Linear Dynamics.” <i>EPiC Series in Computing</i>, vol. 74, EasyChair, 2020, pp. 16–48, doi:<a href=\"https://doi.org/10.29007/7dt2\">10.29007/7dt2</a>.","ista":"Althoff M, Bak S, Bao Z, Forets M, Frehse G, Freire D, Kochdumper N, Li Y, Mitra S, Ray R, Schilling C, Schupp S, Wetzlinger M. 2020. ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 74, 16–48.","ama":"Althoff M, Bak S, Bao Z, et al. ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics. In: <i>EPiC Series in Computing</i>. Vol 74. EasyChair; 2020:16-48. doi:<a href=\"https://doi.org/10.29007/7dt2\">10.29007/7dt2</a>"},"month":"09","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"first_name":"Matthias","full_name":"Althoff, Matthias","last_name":"Althoff"},{"last_name":"Bak","full_name":"Bak, Stanley","first_name":"Stanley"},{"full_name":"Bao, Zongnan","last_name":"Bao","first_name":"Zongnan"},{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"first_name":"Daniel","full_name":"Freire, Daniel","last_name":"Freire"},{"full_name":"Kochdumper, Niklas","last_name":"Kochdumper","first_name":"Niklas"},{"first_name":"Yangge","full_name":"Li, Yangge","last_name":"Li"},{"first_name":"Sayan","last_name":"Mitra","full_name":"Mitra, Sayan"},{"full_name":"Ray, Rajarshi","last_name":"Ray","first_name":"Rajarshi"},{"last_name":"Schilling","full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0003-3658-1065"},{"last_name":"Schupp","full_name":"Schupp, Stefan","first_name":"Stefan"},{"first_name":"Mark","full_name":"Wetzlinger, Mark","last_name":"Wetzlinger"}],"page":"16-48","conference":{"start_date":"2020-07-12","end_date":"2020-07-12","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-26T14:49:43Z","oa_version":"Published Version","volume":74,"ec_funded":1,"date_updated":"2021-01-12T08:20:06Z","year":"2020","date_published":"2020-09-25T00:00:00Z","intvolume":"        74","_id":"8572","status":"public","title":"ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics","publication":"EPiC Series in Computing","publisher":"EasyChair","doi":"10.29007/7dt2","oa":1,"type":"conference","day":"25","language":[{"iso":"eng"}],"quality_controlled":"1"},{"article_processing_charge":"No","department":[{"_id":"NiBa"}],"alternative_title":["ISTA Thesis"],"citation":{"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>","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>.","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>.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","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>"},"month":"09","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"}],"file":[{"file_id":"8575","success":1,"relation":"main_file","date_created":"2020-09-28T07:25:35Z","file_name":"thesis_EnikoSzep_final.pdf","date_updated":"2020-09-28T07:25:35Z","creator":"dernst","file_size":6354833,"checksum":"20e71f015fbbd78fea708893ad634ed0","access_level":"open_access","content_type":"application/pdf"},{"content_type":"application/x-zip-compressed","access_level":"closed","creator":"dernst","file_size":23020401,"date_updated":"2020-09-28T07:25:37Z","checksum":"a8de2c14a1bb4e53c857787efbb289e1","date_created":"2020-09-28T07:25:37Z","relation":"source_file","file_id":"8576","file_name":"thesisFiles_EnikoSzep.zip"}],"has_accepted_license":"1","page":"158","degree_awarded":"PhD","date_created":"2020-09-28T07:33:38Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["2663-337X"]},"supervisor":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publication_status":"published","author":[{"first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"}],"year":"2020","file_date_updated":"2020-09-28T07:25:37Z","date_published":"2020-09-20T00:00:00Z","_id":"8574","ddc":["570"],"status":"public","oa_version":"Published Version","date_updated":"2023-09-07T13:11:39Z","day":"20","type":"dissertation","oa":1,"language":[{"iso":"eng"}],"title":"Local adaptation in metapopulations","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:8574"},{"month":"09","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>.","ieee":"A. Andrei <i>et al.</i>, “Cu homeostasis in bacteria: The ins and outs,” <i>Membranes</i>, vol. 10, no. 9. MDPI, 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>","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.","short":"A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).","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>.","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>"},"department":[{"_id":"LeSa"}],"article_number":"242","article_processing_charge":"No","has_accepted_license":"1","file":[{"success":1,"relation":"main_file","date_created":"2020-09-28T11:36:50Z","file_id":"8583","file_name":"2020_Membranes_Andrei.pdf","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_size":4612258,"date_updated":"2020-09-28T11:36:50Z","checksum":"ceb43d7554e712dea6f36f9287271737"}],"scopus_import":"1","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."}],"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-09-28T08:59:26Z","issue":"9","external_id":{"isi":["000581446000001"]},"publication_status":"published","author":[{"first_name":"Andreea","full_name":"Andrei, Andreea","last_name":"Andrei"},{"last_name":"Öztürk","full_name":"Öztürk, Yavuz","first_name":"Yavuz"},{"first_name":"Bahia","full_name":"Khalfaoui-Hassani, Bahia","last_name":"Khalfaoui-Hassani"},{"first_name":"Juna","last_name":"Rauch","full_name":"Rauch, Juna"},{"last_name":"Marckmann","full_name":"Marckmann, Dorian","first_name":"Dorian"},{"id":"D560034C-10C4-11EA-ABF4-A4B43DDC885E","full_name":"Trasnea, Petru Iulian","last_name":"Trasnea","first_name":"Petru Iulian"},{"first_name":"Fevzi","full_name":"Daldal, Fevzi","last_name":"Daldal"},{"first_name":"Hans-Georg","last_name":"Koch","full_name":"Koch, Hans-Georg"}],"publication_identifier":{"eissn":["20770375"]},"article_type":"original","_id":"8579","intvolume":"        10","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"file_date_updated":"2020-09-28T11:36:50Z","year":"2020","date_published":"2020-09-01T00:00:00Z","oa_version":"Published Version","volume":10,"date_updated":"2023-08-22T09:34:06Z","quality_controlled":"1","oa":1,"type":"journal_article","day":"01","language":[{"iso":"eng"}],"publication":"Membranes","publisher":"MDPI","doi":"10.3390/membranes10090242","isi":1,"title":"Cu homeostasis in bacteria: The ins and outs"},{"scopus_import":"1","oa_version":"None","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."}],"date_updated":"2023-08-22T09:33:34Z","_id":"8580","month":"08","citation":{"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>.","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>","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.","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.","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>."},"status":"public","department":[{"_id":"HeEd"}],"article_number":"9158054","year":"2020","date_published":"2020-08-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","author":[{"first_name":"Grzegorz","full_name":"Graff, Grzegorz","last_name":"Graff"},{"last_name":"Graff","full_name":"Graff, Beata","first_name":"Beata"},{"last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz","first_name":"Grzegorz","orcid":"0000-0002-3536-9866"},{"first_name":"Krzysztof","last_name":"Narkiewicz","full_name":"Narkiewicz, Krzysztof"}],"publisher":"IEEE","doi":"10.1109/ESGCO49734.2020.9158054","isi":1,"publication_identifier":{"isbn":["9781728157511"]},"title":"The application of persistent homology in the analysis of heart rate variability","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-09-28T08:59:27Z","type":"conference","day":"01","external_id":{"isi":["000621172600045"]},"conference":{"location":"Pisa, Italy","start_date":"2020-07-15","name":"ESGCO: European Study Group on Cardiovascular Oscillations","end_date":"2020-07-15"},"language":[{"iso":"eng"}]},{"page":"1077-1085","external_id":{"isi":["000569299400004"],"pmid":["32929284"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"11","date_created":"2020-09-28T08:59:27Z","publication_identifier":{"eissn":["15459985"],"issn":["15459993"]},"article_type":"original","publication_status":"published","author":[{"id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","full_name":"Pinke, Gergely","last_name":"Pinke","first_name":"Gergely"},{"orcid":"0000-0002-1864-8951","full_name":"Zhou, Long","id":"3E751364-F248-11E8-B48F-1D18A9856A87","last_name":"Zhou","first_name":"Long"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"}],"article_processing_charge":"No","citation":{"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>.","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.","short":"G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085.","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>.","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.","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>"},"month":"11","department":[{"_id":"LeSa"}],"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"}],"scopus_import":"1","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.","type":"journal_article","day":"01","language":[{"iso":"eng"}],"quality_controlled":"1","pmid":1,"title":"Cryo-EM structure of the entire mammalian F-type ATP synthase","publication":"Nature Structural and Molecular Biology","doi":"10.1038/s41594-020-0503-8","publisher":"Springer Nature","isi":1,"year":"2020","date_published":"2020-11-01T00:00:00Z","intvolume":"        27","_id":"8581","status":"public","oa_version":"None","volume":27,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"date_updated":"2023-08-22T09:33:09Z","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-atpase-solved/","description":"News on IST Homepage"}]}},{"volume":212,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"date_updated":"2024-03-25T23:30:04Z","related_material":{"record":[{"relation":"used_in_publication","id":"14592","status":"public"},{"id":"12491","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2020-12-10T14:01:10Z","year":"2020","date_published":"2020-12-01T00:00:00Z","_id":"8586","intvolume":"       212","status":"public","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","publication":"Journal of Structural Biology","publisher":"Elsevier","doi":"10.1016/j.jsb.2020.107633","isi":1,"type":"journal_article","oa":1,"day":"01","language":[{"iso":"eng"}],"quality_controlled":"1","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"has_accepted_license":"1","acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","file":[{"date_updated":"2020-12-10T14:01:10Z","creator":"dernst","file_size":7076870,"checksum":"c48cbf594e84fc2f91966ffaafc0918c","content_type":"application/pdf","access_level":"open_access","file_id":"8937","relation":"main_file","success":1,"date_created":"2020-12-10T14:01:10Z","file_name":"2020_JourStrucBiology_Faessler.pdf"}],"scopus_import":"1","article_number":"107633","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"article_processing_charge":"Yes (via OA deal)","citation":{"ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. 2020;212(3). doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>, vol. 212, no. 3, 107633, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>.","chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>.","ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” <i>Journal of Structural Biology</i>, vol. 212, no. 3. Elsevier, 2020.","apa":"Fäßler, F., Zens, B., Hauschild, R., &#38; Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>"},"month":"12","department":[{"_id":"FlSc"}],"publication_identifier":{"issn":["1047-8477"]},"article_type":"original","publication_status":"published","author":[{"full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X"},{"last_name":"Zens","full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"external_id":{"isi":["000600997800008"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","date_created":"2020-09-29T13:24:06Z"},{"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":[{"open_access":"1","url":"https://arxiv.org/abs/1912.02658"}],"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.","article_number":"164302","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"name":"A path-integral approach to composite impurities","call_identifier":"FWF","grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","citation":{"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.","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>","short":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020).","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>.","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>.","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>","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."},"month":"04","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"article_type":"original","publication_status":"published","author":[{"first_name":"Xiang","full_name":"Li, Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","first_name":"Enderalp"},{"orcid":"0000-0001-8823-9777","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo","last_name":"Bighin"},{"last_name":"Schmidt","full_name":"Schmidt, Richard","first_name":"Richard"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"},{"orcid":"0000-0003-3146-6746","first_name":"Andreas","last_name":"Deuchert","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","full_name":"Deuchert, Andreas"}],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"external_id":{"arxiv":["1912.02658"],"isi":["000530448300001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"16","date_created":"2020-09-30T10:33:17Z","volume":152,"oa_version":"Preprint","date_updated":"2024-08-07T07:16:53Z","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"8958","status":"public"}]},"year":"2020","date_published":"2020-04-27T00:00:00Z","_id":"8587","intvolume":"       152","status":"public","title":"Intermolecular forces and correlations mediated by a phonon bath","arxiv":1,"publication":"The Journal of Chemical Physics","publisher":"AIP Publishing","doi":"10.1063/1.5144759","isi":1,"type":"journal_article","oa":1,"day":"27","language":[{"iso":"eng"}],"quality_controlled":"1"},{"department":[{"_id":"MiLe"}],"citation":{"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>.","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>","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>.","short":"C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, P.V. Santos, Physical Review B 102 (2020).","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."},"month":"07","article_processing_charge":"No","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","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"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"045307","scopus_import":"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.","main_file_link":[{"url":"https://arxiv.org/abs/1910.06015","open_access":"1"}],"abstract":[{"lang":"eng","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)]."}],"date_created":"2020-09-30T10:33:43Z","issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000550579100004"],"arxiv":["1910.06015"]},"author":[{"last_name":"Hubert","full_name":"Hubert, C.","first_name":"C."},{"last_name":"Cohen","full_name":"Cohen, K.","first_name":"K."},{"first_name":"Areg","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802"},{"first_name":"R.","full_name":"Rapaport, R.","last_name":"Rapaport"},{"first_name":"P. V.","full_name":"Santos, P. V.","last_name":"Santos"}],"publication_status":"published","article_type":"original","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"status":"public","intvolume":"       102","_id":"8588","date_published":"2020-07-21T00:00:00Z","year":"2020","ec_funded":1,"date_updated":"2023-09-05T12:12:10Z","volume":102,"oa_version":"Preprint","quality_controlled":"1","language":[{"iso":"eng"}],"day":"21","oa":1,"type":"journal_article","isi":1,"doi":"10.1103/physrevb.102.045307","publisher":"American Physical Society","publication":"Physical Review B","title":"Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids","arxiv":1},{"language":[{"iso":"eng"}],"day":"30","oa":1,"type":"dissertation","doi":"10.15479/AT:ISTA:8589","publisher":"Institute of Science and Technology Austria","title":"Novel insights into PIN polarity regulation during Arabidopsis development","ddc":["580"],"status":"public","_id":"8589","date_published":"2020-09-30T00:00:00Z","year":"2020","file_date_updated":"2021-10-01T13:33:02Z","related_material":{"record":[{"status":"public","id":"7643","relation":"part_of_dissertation"}]},"date_updated":"2023-09-07T13:13:05Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","date_created":"2020-09-30T14:50:51Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","degree_awarded":"PhD","page":"164","author":[{"id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin"}],"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"department":[{"_id":"JiFr"}],"month":"09","citation":{"ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8589\">10.15479/AT:ISTA:8589</a>","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","mla":"Han, Huibin. <i>Novel Insights into PIN Polarity Regulation during Arabidopsis Development</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8589\">10.15479/AT:ISTA:8589</a>.","chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8589\">https://doi.org/10.15479/AT:ISTA:8589</a>.","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","apa":"Han, H. (2020). <i>Novel insights into PIN polarity regulation during Arabidopsis development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8589\">https://doi.org/10.15479/AT:ISTA:8589</a>"},"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","file":[{"date_updated":"2020-09-30T14:50:20Z","file_size":49198118,"creator":"dernst","checksum":"c4bda1947d4c09c428ac9ce667b02327","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"8590","date_created":"2020-09-30T14:50:20Z","relation":"source_file","file_name":"2020_Han_Thesis.docx"},{"file_name":"2020_Han_Thesis.pdf","date_created":"2020-09-30T14:49:59Z","relation":"main_file","file_id":"8591","checksum":"3f4f5d1718c2230adf30639ecaf8a00b","creator":"dernst","file_size":15513963,"date_updated":"2021-10-01T13:33:02Z","access_level":"open_access","content_type":"application/pdf"}],"acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development."}]},{"language":[{"iso":"eng"}],"type":"journal_article","oa":1,"day":"04","quality_controlled":"1","title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","publisher":"Wiley","doi":"10.1002/advs.202001724","isi":1,"publication":"Advanced Science","date_published":"2020-11-04T00:00:00Z","file_date_updated":"2020-12-10T14:07:24Z","year":"2020","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"intvolume":"         7","_id":"8592","date_updated":"2023-08-22T09:53:01Z","ec_funded":1,"volume":7,"oa_version":"Published Version","keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"external_id":{"isi":["000573860700001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-10-01T09:44:13Z","issue":"21","article_type":"original","publication_identifier":{"issn":["2198-3844"]},"author":[{"first_name":"Anhao","last_name":"Tian","full_name":"Tian, Anhao"},{"first_name":"Bo","last_name":"Kang","full_name":"Kang, Bo"},{"first_name":"Baizhou","full_name":"Li, Baizhou","last_name":"Li"},{"last_name":"Qiu","full_name":"Qiu, Biying","first_name":"Biying"},{"first_name":"Wenhong","last_name":"Jiang","full_name":"Jiang, Wenhong"},{"last_name":"Shao","full_name":"Shao, Fangjie","first_name":"Fangjie"},{"first_name":"Qingqing","last_name":"Gao","full_name":"Gao, Qingqing"},{"full_name":"Liu, Rui","last_name":"Liu","first_name":"Rui"},{"first_name":"Chengwei","last_name":"Cai","full_name":"Cai, Chengwei"},{"first_name":"Rui","full_name":"Jing, Rui","last_name":"Jing"},{"full_name":"Wang, Wei","last_name":"Wang","first_name":"Wei"},{"last_name":"Chen","full_name":"Chen, Pengxiang","first_name":"Pengxiang"},{"full_name":"Liang, Qinghui","last_name":"Liang","first_name":"Qinghui"},{"last_name":"Bao","full_name":"Bao, Lili","first_name":"Lili"},{"last_name":"Man","full_name":"Man, Jianghong","first_name":"Jianghong"},{"full_name":"Wang, Yan","last_name":"Wang","first_name":"Yan"},{"full_name":"Shi, Yu","last_name":"Shi","first_name":"Yu"},{"last_name":"Li","full_name":"Li, Jin","first_name":"Jin"},{"last_name":"Yang","full_name":"Yang, Minmin","first_name":"Minmin"},{"full_name":"Wang, Lisha","last_name":"Wang","first_name":"Lisha"},{"first_name":"Jianmin","last_name":"Zhang","full_name":"Zhang, Jianmin"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"},{"full_name":"Zhu, Junming","last_name":"Zhu","first_name":"Junming"},{"first_name":"Xiuwu","last_name":"Bian","full_name":"Bian, Xiuwu"},{"first_name":"Ying‐Jie","last_name":"Wang","full_name":"Wang, Ying‐Jie"},{"first_name":"Chong","last_name":"Liu","full_name":"Liu, Chong"}],"publication_status":"published","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"article_processing_charge":"No","article_number":"2001724","month":"11","citation":{"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>","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>.","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>.","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.","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)."},"department":[{"_id":"SiHi"}],"abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","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.","file":[{"file_name":"2020_AdvScience_Tian.pdf","file_id":"8938","success":1,"date_created":"2020-12-10T14:07:24Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"92818c23ecc70e35acfa671f3cfb9909","date_updated":"2020-12-10T14:07:24Z","file_size":7835833,"creator":"dernst"}]},{"article_processing_charge":"Yes (via OA deal)","article_number":"065005","department":[{"_id":"NanoFab"}],"citation":{"ama":"Merrin J. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. <i>Physical Biology</i>. 2020;17(6). doi:<a href=\"https://doi.org/10.1088/1478-3975/abb2db\">10.1088/1478-3975/abb2db</a>","ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005.","mla":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” <i>Physical Biology</i>, vol. 17, no. 6, 065005, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.1088/1478-3975/abb2db\">10.1088/1478-3975/abb2db</a>.","short":"J. Merrin, Physical Biology 17 (2020).","chicago":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” <i>Physical Biology</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1478-3975/abb2db\">https://doi.org/10.1088/1478-3975/abb2db</a>.","apa":"Merrin, J. (2020). Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/abb2db\">https://doi.org/10.1088/1478-3975/abb2db</a>","ieee":"J. Merrin, “Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide,” <i>Physical Biology</i>, vol. 17, no. 6. IOP Publishing, 2020."},"month":"09","abstract":[{"lang":"eng","text":"Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy."}],"file":[{"file_name":"2020_PhysBio_Merrin.pdf","date_created":"2020-10-05T13:53:59Z","relation":"main_file","success":1,"file_id":"8609","content_type":"application/pdf","access_level":"open_access","checksum":"fec9bdd355ed349f09990faab20838a7","creator":"dernst","file_size":1667111,"date_updated":"2020-10-05T13:53:59Z"}],"acknowledgement":"I would especially like to thank Michael Sixt for encouraging me to think about these problems while working at home due to restrictions in place. I want to thank Nick Barton, Katka Bodova, Matthew Robinson, Simon Rella, Federico Sau, Ivan Prieto, and Pradeep Kumar for useful discussions.","scopus_import":"1","has_accepted_license":"1","external_id":{"isi":["000575539700001"]},"date_created":"2020-10-04T22:01:35Z","issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","publication_identifier":{"eissn":["14783975"]},"author":[{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","first_name":"Jack","orcid":"0000-0001-5145-4609"}],"publication_status":"published","date_published":"2020-09-23T00:00:00Z","year":"2020","file_date_updated":"2020-10-05T13:53:59Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510","570"],"status":"public","_id":"8597","intvolume":"        17","date_updated":"2023-08-22T09:53:29Z","volume":17,"oa_version":"Published Version","language":[{"iso":"eng"}],"day":"23","oa":1,"type":"journal_article","quality_controlled":"1","title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide","isi":1,"doi":"10.1088/1478-3975/abb2db","publisher":"IOP Publishing","publication":"Physical Biology"},{"quality_controlled":"1","language":[{"iso":"eng"}],"day":"06","oa":1,"type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.4230/LIPIcs.CONCUR.2020.2","publication":"31st International Conference on Concurrency Theory","title":"A survey of bidding games on graphs","ddc":["000"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)"},"status":"public","_id":"8599","intvolume":"       171","date_published":"2020-08-06T00:00:00Z","year":"2020","file_date_updated":"2020-10-05T14:13:19Z","date_updated":"2021-01-12T08:20:13Z","oa_version":"Published Version","volume":171,"date_created":"2020-10-04T22:01:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by/3.0/","conference":{"name":"CONCUR: Conference on Concurrency Theory","end_date":"2020-09-04","location":"Virtual","start_date":"2020-09-01"},"author":[{"orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724"}],"publication_status":"published","publication_identifier":{"isbn":["9783959771603"],"issn":["18688969"]},"department":[{"_id":"ToHe"}],"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>.","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>","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.","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.","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>","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>.","short":"G. Avni, T.A. Henzinger, in:, 31st International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020."},"month":"08","alternative_title":["LIPIcs"],"article_processing_charge":"No","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"article_number":"2","scopus_import":"1","file":[{"file_name":"2020_LIPIcsCONCUR_Avni.pdf","date_created":"2020-10-05T14:13:19Z","success":1,"relation":"main_file","file_id":"8611","content_type":"application/pdf","access_level":"open_access","checksum":"8f33b098e73724e0ac817f764d8e1a2d","file_size":868510,"creator":"dernst","date_updated":"2020-10-05T14:13:19Z"}],"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.","has_accepted_license":"1","abstract":[{"lang":"eng","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."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-10-04T22:01:36Z","external_id":{"arxiv":["2007.08917"]},"conference":{"location":"Virtual","start_date":"2020-09-01","end_date":"2020-09-04","name":"CONCUR: Conference on Concurrency Theory"},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop"}],"publication_status":"published","publication_identifier":{"issn":["18688969"],"isbn":["9783959771603"]},"month":"08","alternative_title":["LIPIcs"],"citation":{"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>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, 31st International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","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>.","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>","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.","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>."},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","article_number":"23","has_accepted_license":"1","scopus_import":"1","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":601231,"creator":"dernst","date_updated":"2020-10-05T14:04:25Z","checksum":"5039752f644c4b72b9361d21a5e31baf","date_created":"2020-10-05T14:04:25Z","relation":"main_file","success":1,"file_id":"8610","file_name":"2020_LIPIcsCONCUR_Chatterjee.pdf"}],"abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","oa":1,"day":"06","doi":"10.4230/LIPIcs.CONCUR.2020.23","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"31st International Conference on Concurrency Theory","title":"Multi-dimensional long-run average problems for vector addition systems with states","arxiv":1,"status":"public","ddc":["000"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)"},"_id":"8600","intvolume":"       171","date_published":"2020-08-06T00:00:00Z","file_date_updated":"2020-10-05T14:04:25Z","year":"2020","date_updated":"2021-01-12T08:20:15Z","volume":171,"oa_version":"Published Version"},{"publication":"Plant Cell","isi":1,"publisher":"American Society of Plant Biologists","doi":"10.1105/tpc.20.00384","title":"Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif","pmid":1,"quality_controlled":"1","day":"01","type":"journal_article","oa":1,"language":[{"iso":"eng"}],"volume":32,"oa_version":"Published Version","ec_funded":1,"date_updated":"2023-09-05T12:21:32Z","_id":"8607","intvolume":"        32","status":"public","year":"2020","date_published":"2020-11-01T00:00:00Z","publication_status":"published","author":[{"first_name":"D","last_name":"Liu","full_name":"Liu, D"},{"full_name":"Kumar, R","last_name":"Kumar","first_name":"R"},{"full_name":"LAN, Claus","last_name":"LAN","first_name":"Claus"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843"},{"first_name":"W","last_name":"Siao","full_name":"Siao, W"},{"first_name":"I","full_name":"Vanhoutte, I","last_name":"Vanhoutte"},{"first_name":"P","full_name":"Wang, P","last_name":"Wang"},{"first_name":"KW","last_name":"Bender","full_name":"Bender, KW"},{"full_name":"Yperman, K","last_name":"Yperman","first_name":"K"},{"full_name":"Martins, S","last_name":"Martins","first_name":"S"},{"full_name":"Zhao, X","last_name":"Zhao","first_name":"X"},{"first_name":"G","last_name":"Vert","full_name":"Vert, G"},{"last_name":"Van Damme","full_name":"Van Damme, D","first_name":"D"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"E","last_name":"Russinova","full_name":"Russinova, E"}],"publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"article_type":"original","date_created":"2020-10-05T12:45:16Z","issue":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"3598-3612","external_id":{"isi":["000600226800021"],"pmid":["32958564"]},"scopus_import":"1","main_file_link":[{"url":"https://europepmc.org/article/MED/32958564","open_access":"1"}],"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."}],"department":[{"_id":"JiFr"}],"citation":{"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>","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.","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>.","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.","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>","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>."},"month":"11","article_processing_charge":"No","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}]},{"acknowledgement":"The project was initiated in the Jan lab at UCSF. We thank Lily Jan and Yuh-Nung Jan’s generous support. We thank Liqun Luo’s lab for providing MADM-7 mice and Rolf A Brekken for VEGF-antibodies.  Drs. Yuanquan Song (UPenn), Zhaozhu Hu (JHU), Ji Hu (ShanghaiTech), Yang Xiang (U. Mass), Hao Wang (Zhejiang U.) and Ruikang Wang (U. Washington) for critical input, colleagues at Children’s Research Institute, Departments of Neuroscience, Neurology and Neurotherapeutics, Pediatrics from UT Southwestern, and colleagues from the Jan lab for discussion. Dr. Bridget Samuels, Sean Morrison (UT Southwestern), and Nannan Lu (Zhejiang U.) for critical reading. We acknowledge the assistance of the CIBR Imaging core. We also thank UT Southwestern Live Cell Imaging Facility, a Shared Resource of the Harold C. Simmons Cancer Center, supported in part by an NCI Cancer Center Support Grant, P30 CA142543K. This work is supported by CIBR funds and the American Heart Association AWRP Summer 2016 Innovative Research Grant (17IRG33410377) to W-P.G.; National Natural Science Foundation of China (No.81370031) to Z.Z.;National Key Research and Development Program of China (2016YFE0125400)to F.H.;National Natural Science Foundations of China (No. 81473202) to Y.L.; National Natural Science Foundation of China (No.31600839) and Shenzhen Science and Technology Research Program (JCYJ20170818163320865) to B.P.; National Natural Science Foundation of China (No. 31800864) and Westlake University start-up funds to J-M. J. NIH R01NS088627 to W.L.J.; NIH: R01 AG020670 and RF1AG054111 to H.Z.; R01 NS088555 to A.M.S., and European Research Council No.725780 to S.H.;W-P.G. was a recipient of Bugher-American Heart Association Dan Adams Thinking Outside the Box Award.","main_file_link":[{"url":"https://doi.org/10.1101/2020.09.15.262782","open_access":"1"}],"ec_funded":1,"date_updated":"2021-01-12T08:20:19Z","abstract":[{"lang":"eng","text":"The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal <jats:italic>in vivo</jats:italic> imaging, we reported that a substantial proportion of blood vessels in the adult brain sporadically occluded and regressed. Their regression proceeded through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels were found to be widespread in mouse, monkey and human brains. Both brief occlusions of the middle cerebral artery and lipopolysaccharide-mediated inflammation induced an increase of vessel regression. Blockage of leukocyte adhesion to endothelial cells alleviated LPS-induced vessel regression. We further revealed that blood vessel regression caused a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain."}],"oa_version":"Preprint","department":[{"_id":"SiHi"}],"citation":{"short":"X. Gao, J.-L. Li, X. Chen, B. Ci, F. Chen, N. Lu, B. Shen, L. Zheng, J.-M. Jia, Y. Yi, S. Zhang, Y.-C. Shi, K. Shi, N.E. Propson, Y. Huang, K. Poinsatte, Z. Zhang, Y. Yue, D.B. Bosco, Y. Lu, S. Yang, R.H. Adams, V. Lindner, F. Huang, L.-J. Wu, H. Zheng, F. Han, S. Hippenmeyer, A.M. Stowe, B. Peng, M. Margeta, X. Wang, Q. Liu, J. Körbelin, M. Trepel, H. Lu, B.O. Zhou, H. Zhao, W. Su, R.M. Bachoo, W. Ge, BioRxiv (n.d.).","mla":"Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.09.15.262782\">10.1101/2020.09.15.262782</a>.","ista":"Gao X, Li J-L, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J-M, Yi Y, Zhang S, Shi Y-C, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco DB, Lu Y, Yang S, Adams RH, Lindner V, Huang F, Wu L-J, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Su W, Bachoo RM, Ge W. Reduction of neuronal activity mediated by blood-vessel regression in the brain. bioRxiv, <a href=\"https://doi.org/10.1101/2020.09.15.262782\">10.1101/2020.09.15.262782</a>.","ama":"Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel regression in the brain. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.09.15.262782\">10.1101/2020.09.15.262782</a>","ieee":"X. Gao <i>et al.</i>, “Reduction of neuronal activity mediated by blood-vessel regression in the brain,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","apa":"Gao, X., Li, J.-L., Chen, X., Ci, B., Chen, F., Lu, N., … Ge, W. (n.d.). Reduction of neuronal activity mediated by blood-vessel regression in the brain. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.09.15.262782\">https://doi.org/10.1101/2020.09.15.262782</a>","chicago":"Gao, Xiaofei, Jun-Liszt Li, Xingjun Chen, Bo Ci, Fei Chen, Nannan Lu, Bo Shen, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.09.15.262782\">https://doi.org/10.1101/2020.09.15.262782</a>."},"status":"public","month":"09","_id":"8616","article_processing_charge":"No","date_published":"2020-09-15T00:00:00Z","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780"}],"year":"2020","publisher":"Cold Spring Harbor Laboratory","author":[{"first_name":"Xiaofei","full_name":"Gao, Xiaofei","last_name":"Gao"},{"last_name":"Li","full_name":"Li, Jun-Liszt","first_name":"Jun-Liszt"},{"last_name":"Chen","full_name":"Chen, Xingjun","first_name":"Xingjun"},{"first_name":"Bo","full_name":"Ci, Bo","last_name":"Ci"},{"first_name":"Fei","last_name":"Chen","full_name":"Chen, Fei"},{"first_name":"Nannan","last_name":"Lu","full_name":"Lu, Nannan"},{"last_name":"Shen","full_name":"Shen, Bo","first_name":"Bo"},{"first_name":"Lijun","full_name":"Zheng, Lijun","last_name":"Zheng"},{"last_name":"Jia","full_name":"Jia, Jie-Min","first_name":"Jie-Min"},{"last_name":"Yi","full_name":"Yi, Yating","first_name":"Yating"},{"full_name":"Zhang, Shiwen","last_name":"Zhang","first_name":"Shiwen"},{"first_name":"Ying-Chao","full_name":"Shi, Ying-Chao","last_name":"Shi"},{"first_name":"Kaibin","full_name":"Shi, Kaibin","last_name":"Shi"},{"first_name":"Nicholas E","last_name":"Propson","full_name":"Propson, Nicholas E"},{"last_name":"Huang","full_name":"Huang, Yubin","first_name":"Yubin"},{"last_name":"Poinsatte","full_name":"Poinsatte, Katherine","first_name":"Katherine"},{"first_name":"Zhaohuan","full_name":"Zhang, Zhaohuan","last_name":"Zhang"},{"first_name":"Yuanlei","full_name":"Yue, Yuanlei","last_name":"Yue"},{"first_name":"Dale B","full_name":"Bosco, Dale B","last_name":"Bosco"},{"last_name":"Lu","full_name":"Lu, Ying-mei","first_name":"Ying-mei"},{"first_name":"Shi-bing","last_name":"Yang","full_name":"Yang, Shi-bing"},{"full_name":"Adams, Ralf H.","last_name":"Adams","first_name":"Ralf H."},{"first_name":"Volkhard","full_name":"Lindner, Volkhard","last_name":"Lindner"},{"first_name":"Fen","last_name":"Huang","full_name":"Huang, Fen"},{"full_name":"Wu, Long-Jun","last_name":"Wu","first_name":"Long-Jun"},{"last_name":"Zheng","full_name":"Zheng, Hui","first_name":"Hui"},{"last_name":"Han","full_name":"Han, Feng","first_name":"Feng"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Stowe","full_name":"Stowe, Ann M.","first_name":"Ann M."},{"first_name":"Bo","last_name":"Peng","full_name":"Peng, Bo"},{"full_name":"Margeta, Marta","last_name":"Margeta","first_name":"Marta"},{"full_name":"Wang, Xiaoqun","last_name":"Wang","first_name":"Xiaoqun"},{"last_name":"Liu","full_name":"Liu, Qiang","first_name":"Qiang"},{"first_name":"Jakob","last_name":"Körbelin","full_name":"Körbelin, Jakob"},{"first_name":"Martin","full_name":"Trepel, Martin","last_name":"Trepel"},{"first_name":"Hui","last_name":"Lu","full_name":"Lu, Hui"},{"first_name":"Bo O.","full_name":"Zhou, Bo O.","last_name":"Zhou"},{"first_name":"Hu","last_name":"Zhao","full_name":"Zhao, Hu"},{"full_name":"Su, Wenzhi","last_name":"Su","first_name":"Wenzhi"},{"last_name":"Bachoo","full_name":"Bachoo, Robert M.","first_name":"Robert M."},{"full_name":"Ge, Woo-ping","last_name":"Ge","first_name":"Woo-ping"}],"doi":"10.1101/2020.09.15.262782","publication":"bioRxiv","publication_status":"submitted","title":"Reduction of neuronal activity mediated by blood-vessel regression in the brain","date_created":"2020-10-06T08:58:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"15","oa":1,"type":"preprint"},{"date_published":"2020-10-12T00:00:00Z","year":"2020","file_date_updated":"2021-10-16T22:30:04Z","ddc":["610"],"status":"public","_id":"8620","date_updated":"2024-09-10T12:04:25Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7800"},{"id":"8131","relation":"part_of_dissertation","status":"public"}]},"language":[{"iso":"eng"}],"day":"12","oa":1,"type":"dissertation","title":"Illuminating the role of Cul3 in autism spectrum disorder pathogenesis","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:8620","article_processing_charge":"No","project":[{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","grant_number":"F07807","name":"Neural stem cells in autism and epilepsy"}],"department":[{"_id":"GaNo"}],"alternative_title":["ISTA Thesis"],"month":"10","citation":{"ama":"Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8620\">10.15479/AT:ISTA:8620</a>","short":"J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis, Institute of Science and Technology Austria, 2020.","ista":"Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria.","mla":"Morandell, Jasmin. <i>Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8620\">10.15479/AT:ISTA:8620</a>.","chicago":"Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8620\">https://doi.org/10.15479/AT:ISTA:8620</a>.","ieee":"J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020.","apa":"Morandell, J. (2020). <i>Illuminating the role of Cul3 in autism spectrum disorder pathogenesis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8620\">https://doi.org/10.15479/AT:ISTA:8620</a>"},"abstract":[{"text":"The development of the human brain occurs through a tightly regulated series of dynamic and adaptive processes during prenatal and postnatal life. A disruption of this strictly orchestrated series of events can lead to a number of neurodevelopmental conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common, etiologically and phenotypically heterogeneous group of disorders sharing the core symptoms of social interaction and communication deficits and restrictive and repetitive interests and behaviors. They are estimated to affect one in 59 individuals in the U.S. and, over the last three decades, mutations in more than a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet, for the vast majority of these ASD-risk genes their role during brain development and precise molecular function still remain elusive.\r\nDe novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In the study described here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display cortical lamination abnormalities due to defective migration of post-mitotic excitatory neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal cortical organization, Cul3 heterozygous deletion is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neural cells results in atypical organization of the actin mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult mice does not induce the majority of the behavioral defects observed in constitutive Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn conclusion, our data indicate that Cul3 plays a critical role in the regulation of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral abnormalities are primarily due to dosage sensitive Cul3 functions at early brain developmental stages.","lang":"eng"}],"file":[{"file_name":"Jasmin_Morandell_Thesis-2020_final.pdf","date_created":"2020-10-07T14:41:49Z","relation":"main_file","file_id":"8621","embargo":"2021-10-15","access_level":"open_access","content_type":"application/pdf","checksum":"7ee83e42de3e5ce2fedb44dff472f75f","file_size":16155786,"creator":"jmorande","date_updated":"2021-10-16T22:30:04Z"},{"checksum":"5e0464af453734210ce7aab7b4a92e3a","file_size":24344152,"creator":"jmorande","date_updated":"2021-10-16T22:30:04Z","content_type":"application/x-zip-compressed","access_level":"closed","embargo_to":"open_access","file_name":"Jasmin_Morandell_Thesis-2020_final.zip","date_created":"2020-10-07T14:45:07Z","relation":"source_file","file_id":"8622"}],"acknowledgement":"I would like to especially thank Armel Nicolas from the Proteomics and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka, Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line maintenance and their great support.","has_accepted_license":"1","page":"138","degree_awarded":"PhD","date_created":"2020-10-07T14:53:13Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino"}],"publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin"}],"publication_status":"published"},{"date_published":"2020-10-02T00:00:00Z","year":"2020","file_date_updated":"2020-10-15T14:28:06Z","ddc":["000"],"status":"public","intvolume":"     12399","_id":"8623","date_updated":"2023-09-05T15:08:26Z","volume":12399,"oa_version":"Submitted Version","language":[{"iso":"eng"}],"day":"02","type":"conference","oa":1,"quality_controlled":"1","title":"Monitorability under assumptions","isi":1,"doi":"10.1007/978-3-030-60508-7_1","publisher":"Springer Nature","publication":"Runtime Verification","article_processing_charge":"No","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"department":[{"_id":"ToHe"}],"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>.","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>","ista":"Henzinger TA, Sarac NE. 2020. Monitorability under assumptions. Runtime Verification. RV: Runtime Verification, LNCS, vol. 12399, 3–18.","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>.","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>","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."},"alternative_title":["LNCS"],"month":"10","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"}],"scopus_import":"1","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","file":[{"file_name":"monitorability.pdf","file_id":"8665","date_created":"2020-10-15T14:28:06Z","relation":"main_file","success":1,"access_level":"open_access","content_type":"application/pdf","checksum":"00661f9b7034f52e18bf24fa552b8194","date_updated":"2020-10-15T14:28:06Z","creator":"esarac","file_size":478148}],"has_accepted_license":"1","external_id":{"isi":["000728160600001"]},"conference":{"start_date":"2020-10-06","location":"Los Angeles, CA, United States","name":"RV: Runtime Verification","end_date":"2020-10-09"},"page":"3-18","date_created":"2020-10-07T15:05:37Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030605070","9783030605087"],"issn":["0302-9743"]},"author":[{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Sarac","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E"}],"publication_status":"published"},{"day":"05","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"title":"Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits","publication":"Physical Review Letters","isi":1,"doi":"10.1103/physrevlett.125.064501","publisher":"American Physical Society","year":"2020","date_published":"2020-08-05T00:00:00Z","_id":"8634","intvolume":"       125","status":"public","oa_version":"Preprint","volume":125,"ec_funded":1,"date_updated":"2023-09-05T12:08:29Z","external_id":{"arxiv":["2008.02367"],"isi":["000555785600005"]},"keyword":["General Physics and Astronomy"],"issue":"6","date_created":"2020-10-08T17:27:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"article_type":"original","publication_status":"published","author":[{"last_name":"Suri","full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra"},{"last_name":"Kageorge","full_name":"Kageorge, Logan","first_name":"Logan"},{"last_name":"Grigoriev","full_name":"Grigoriev, Roman O.","first_name":"Roman O."},{"last_name":"Schatz","full_name":"Schatz, Michael F.","first_name":"Michael F."}],"article_number":"064501","article_processing_charge":"No","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"BjHo"}],"month":"08","citation":{"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>.","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.","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>","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>.","short":"B. Suri, L. Kageorge, R.O. Grigoriev, M.F. Schatz, Physical Review Letters 125 (2020)."},"main_file_link":[{"url":"https://arxiv.org/abs/2008.02367","open_access":"1"}],"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"}],"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."},{"date_updated":"2023-08-22T09:58:21Z","oa_version":"Published Version","volume":10,"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","_id":"8643","intvolume":"        10","date_published":"2020-10-01T00:00:00Z","year":"2020","file_date_updated":"2020-10-12T12:39:10Z","isi":1,"publisher":"Springer Nature","doi":"10.1038/s41598-020-72848-0","publication":"Scientific Reports","title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","quality_controlled":"1","language":[{"iso":"eng"}],"day":"01","type":"journal_article","oa":1,"file":[{"file_id":"8651","relation":"main_file","success":1,"date_created":"2020-10-12T12:39:10Z","file_name":"2020_ScientificReport_Deichler.pdf","date_updated":"2020-10-12T12:39:10Z","creator":"dernst","file_size":3906744,"checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","access_level":"open_access","content_type":"application/pdf"}],"scopus_import":"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.).","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."}],"department":[{"_id":"MaJö"}],"citation":{"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>","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>.","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.","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>"},"month":"10","article_processing_charge":"No","article_number":"16220","author":[{"full_name":"Deichler, Alfonso","last_name":"Deichler","first_name":"Alfonso"},{"first_name":"Denisse","full_name":"Carrasco, Denisse","last_name":"Carrasco"},{"first_name":"Luciana","full_name":"Lopez-Jury, Luciana","last_name":"Lopez-Jury"},{"first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga"},{"full_name":"Marquez, Natalia","last_name":"Marquez","first_name":"Natalia"},{"full_name":"Mpodozis, Jorge","last_name":"Mpodozis","first_name":"Jorge"},{"first_name":"Gonzalo","full_name":"Marin, Gonzalo","last_name":"Marin"}],"publication_status":"published","article_type":"original","publication_identifier":{"eissn":["20452322"]},"date_created":"2020-10-11T22:01:14Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000577142600032"]}}]