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We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space."}],"issue":"1","article_type":"original","page":"35-73","publication":"Pure and Applied Analysis","citation":{"mla":"Lewin, Mathieu, et al. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis, vol. 2, no. 1, Mathematical Sciences Publishers, 2020, pp. 35–73, doi:10.2140/paa.2020.2.35.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73.","chicago":"Lewin, Mathieu, Elliott H. 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Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. 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Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology."}],"file_date_updated":"2020-07-14T12:48:09Z","type":"research_data","date_published":"2020-07-15T00:00:00Z","doi":"10.15479/AT:ISTA:8097","acknowledged_ssus":[{"_id":"LifeSc"}],"citation":{"short":"B. Kavcic, (2020).","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097.","ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097","apa":"Kavcic, B. (2020). 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Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"article_processing_charge":"No","has_accepted_license":"1","day":"15","month":"07","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254.","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.","short":"L.S. Arathoon, (2020).","mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254."},"oa":1,"doi":"10.15479/AT:ISTA:8254","date_published":"2020-08-18T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","month":"08","day":"18","_id":"8254","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","status":"public","contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","contributor_type":"data_collector","first_name":"Louise S"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Surendranadh","first_name":"Parvathy"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"David","contributor_type":"project_member","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","contributor_type":"project_member","first_name":"Melinda"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Baskett","first_name":"Carina"}],"related_material":{"record":[{"id":"11321","status":"public","relation":"later_version"},{"status":"public","relation":"later_version","id":"9192"}]},"author":[{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S","full_name":"Arathoon, Louise S"}],"oa_version":"Published Version","file":[{"file_id":"8280","relation":"main_file","date_updated":"2020-08-18T08:03:23Z","date_created":"2020-08-18T08:03:23Z","success":1,"checksum":"4f1382ed4384751b6013398c11557bf6","file_name":"Data_Rcode_MathematicaNB.zip","access_level":"open_access","creator":"dernst","file_size":5778420,"content_type":"application/x-zip-compressed"}],"date_created":"2020-08-12T12:49:23Z","date_updated":"2024-02-21T12:41:09Z","type":"research_data","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"file_date_updated":"2020-08-18T08:03:23Z"},{"status":"public","ddc":["530"],"title":"Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling","intvolume":" 32","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7541","file":[{"file_name":"2020_AdvancedMaterials_Gao.pdf","access_level":"open_access","creator":"dernst","file_size":5242880,"content_type":"application/pdf","file_id":"8782","relation":"main_file","date_updated":"2020-11-20T10:11:35Z","date_created":"2020-11-20T10:11:35Z","success":1,"checksum":"c622737dc295972065782558337124a2"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon."}],"issue":"16","article_type":"original","publication":"Advanced Materials","citation":{"ista":"Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 32(16), 1906523.","ieee":"F. Gao et al., “Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling,” Advanced Materials, vol. 32, no. 16. Wiley, 2020.","apa":"Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., … Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201906523","ama":"Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 2020;32(16). doi:10.1002/adma.201906523","chicago":"Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials. Wiley, 2020. https://doi.org/10.1002/adma.201906523.","mla":"Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials, vol. 32, no. 16, 1906523, Wiley, 2020, doi:10.1002/adma.201906523.","short":"F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang, Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros, J.-J. Zhang, Advanced Materials 32 (2020)."},"date_published":"2020-04-23T00:00:00Z","scopus_import":"1","day":"23","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication_status":"published","publisher":"Wiley","department":[{"_id":"GeKa"}],"acknowledgement":"This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010, and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000), the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union's Horizon 2020 research and innovation program under Grant Agreement #862046. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding from Xi'an Jiaotong University.","year":"2020","date_updated":"2024-02-21T12:42:12Z","date_created":"2020-02-28T09:47:00Z","volume":32,"author":[{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"full_name":"Wang, Jian-Huan","first_name":"Jian-Huan","last_name":"Wang"},{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger"},{"full_name":"Hu, Hao","last_name":"Hu","first_name":"Hao"},{"full_name":"Rančić, Marko J.","last_name":"Rančić","first_name":"Marko J."},{"first_name":"Jie-Yin","last_name":"Zhang","full_name":"Zhang, Jie-Yin"},{"full_name":"Wang, Ting","first_name":"Ting","last_name":"Wang"},{"full_name":"Yao, Yuan","last_name":"Yao","first_name":"Yuan"},{"full_name":"Wang, Gui-Lei","first_name":"Gui-Lei","last_name":"Wang"},{"first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukušić","first_name":"Lada","full_name":"Vukušić, Lada"},{"last_name":"Kloeffel","first_name":"Christoph","full_name":"Kloeffel, Christoph"},{"full_name":"Loss, Daniel","first_name":"Daniel","last_name":"Loss"},{"full_name":"Liu, Feng","first_name":"Feng","last_name":"Liu"},{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7996"},{"id":"9222","status":"public","relation":"research_data"}]},"article_number":"1906523","file_date_updated":"2020-11-20T10:11:35Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497"},{"call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000516660900001"]},"oa":1,"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.1002/adma.201906523","month":"04","publication_identifier":{"issn":["0935-9648"]}},{"keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"month":"12","day":"10","article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930.","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.","short":"B. Kavcic, (2020).","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930."},"doi":"10.15479/AT:ISTA:8930","date_published":"2020-12-10T00:00:00Z","type":"research_data","file_date_updated":"2020-12-09T15:00:19Z","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8930","year":"2020","ddc":["570"],"title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"author":[{"full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic"}],"related_material":{"record":[{"id":"8997","status":"public","relation":"used_in_publication"}]},"contributor":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","contributor_type":"supervisor","first_name":"Gašper"},{"first_name":"Tobias","contributor_type":"supervisor","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-12-09T15:04:02Z","date_updated":"2024-02-21T12:41:42Z","oa_version":"Published Version","file":[{"creator":"bkavcic","file_size":315494370,"content_type":"application/zip","file_name":"PLoSCompBiol2020_datarep.zip","access_level":"open_access","date_created":"2020-12-09T15:00:19Z","date_updated":"2020-12-09T15:00:19Z","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","file_id":"8932","relation":"main_file"}]},{"author":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1391-8377","first_name":"Anna A","last_name":"Nagy-Staron","full_name":"Nagy-Staron, Anna A"}],"related_material":{"record":[{"id":"9283","status":"public","relation":"used_in_publication"}]},"contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","last_name":"Nagy-Staron","contributor_type":"project_member"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","contributor_type":"project_member","last_name":"Tomasek"},{"first_name":"Caroline","last_name":"Caruso Carter","contributor_type":"project_member"},{"first_name":"Elisabeth","contributor_type":"project_member","last_name":"Sonnleitner"},{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic","contributor_type":"project_member"},{"first_name":"Tiago","contributor_type":"project_member","last_name":"Paixão"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","contributor_type":"project_manager"}],"date_created":"2020-12-20T10:00:26Z","date_updated":"2024-02-21T12:41:57Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"readme.txt","content_type":"text/plain","file_size":523,"creator":"bkavcic","relation":"main_file","file_id":"8952","checksum":"f57862aeee1690c7effd2b1117d40ed1","success":1,"date_updated":"2020-12-20T09:52:52Z","date_created":"2020-12-20T09:52:52Z"},{"access_level":"open_access","file_name":"GRNs Research depository.gb","creator":"bkavcic","content_type":"application/octet-stream","file_size":379228,"file_id":"8954","relation":"main_file","success":1,"checksum":"f2c6d5232ec6d551b6993991e8689e9f","date_created":"2020-12-20T22:01:44Z","date_updated":"2020-12-20T22:01:44Z"}],"_id":"8951","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-12-20T22:01:44Z","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.","lang":"eng"}],"type":"research_data","date_published":"2020-12-21T00:00:00Z","doi":"10.15479/AT:ISTA:8951","citation":{"ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","short":"A.A. Nagy-Staron, (2020)."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"day":"21","month":"12","article_processing_charge":"No","has_accepted_license":"1","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"]},{"doi":"10.15479/AT:ISTA:7383","date_published":"2020-01-28T00:00:00Z","oa":1,"citation":{"ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383.","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383.","short":"R. Grah, (2020)."},"month":"01","day":"28","has_accepted_license":"1","article_processing_charge":"No","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"author":[{"last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok"}],"related_material":{"record":[{"id":"7652","status":"public","relation":"used_in_publication"}]},"contributor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","contributor_type":"project_leader","first_name":"Calin C"}],"date_updated":"2024-02-21T12:42:31Z","date_created":"2020-01-28T10:41:49Z","file":[{"date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-28T10:39:40Z","checksum":"9d292cf5207b3829225f44c044cdb3fd","relation":"main_file","file_id":"7384","file_size":73363365,"content_type":"application/zip","creator":"rgrah","file_name":"Scripts.zip","access_level":"open_access"},{"date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-28T10:39:30Z","checksum":"4076ceab32ef588cc233802bab24c1ab","file_id":"7385","relation":"main_file","creator":"rgrah","content_type":"text/plain","file_size":962,"file_name":"READ_ME_MAIN.txt","access_level":"open_access"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7383","year":"2020","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:57Z","abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"type":"research_data"},{"type":"research_data","file_date_updated":"2021-03-10T07:31:50Z","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","ddc":["530"],"status":"public","title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","year":"2020","_id":"9222","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"9223","relation":"main_file","checksum":"41b66e195ed3dbd73077feee77b05652","date_created":"2021-03-05T17:50:45Z","date_updated":"2021-03-05T17:50:45Z","access_level":"open_access","file_name":"DOI_SiteControlledHWs.zip","creator":"gkatsaro","file_size":13317557,"content_type":"application/x-zip-compressed"},{"creator":"dernst","file_size":3515,"content_type":"text/plain","file_name":"Readme.txt","access_level":"open_access","date_updated":"2021-03-10T07:31:50Z","date_created":"2021-03-10T07:31:50Z","success":1,"checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","file_id":"9233","relation":"main_file"}],"date_created":"2021-03-05T18:00:47Z","date_updated":"2024-02-21T12:42:13Z","related_material":{"record":[{"id":"7541","relation":"used_in_publication","status":"public"}]},"contributor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","contributor_type":"research_group","last_name":"Katsaros"}],"author":[{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"has_accepted_license":"1","article_processing_charge":"No","day":"16","month":"03","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"short":"G. Katsaros, (2020).","mla":"Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.","chicago":"Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.","ama":"Katsaros G. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222","ieee":"G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling.” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9222","ista":"Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9222."},"date_published":"2020-03-16T00:00:00Z","doi":"10.15479/AT:ISTA:9222"},{"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"doi":"10.15479/AT:ISTA:8366","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"oa":1,"publication_identifier":{"isbn":["978-3-99078-010-7"],"issn":["2663-337X"]},"month":"09","date_updated":"2024-02-21T12:44:29Z","date_created":"2020-09-10T16:19:55Z","related_material":{"record":[{"status":"deleted","relation":"research_data","id":"7151"},{"id":"7262","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8562"},{"status":"public","relation":"part_of_dissertation","id":"1001"},{"status":"public","relation":"research_data","id":"8375"}]},"author":[{"full_name":"Guseinov, Ruslan","last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","year":"2020","ec_funded":1,"file_date_updated":"2020-09-16T15:11:01Z","date_published":"2020-09-21T00:00:00Z","page":"118","citation":{"apa":"Guseinov, R. (2020). Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8366","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:10.15479/AT:ISTA:8366","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8366.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","mla":"Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8366."},"has_accepted_license":"1","article_processing_charge":"No","day":"21","keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"file":[{"file_id":"8367","relation":"main_file","date_created":"2020-09-10T16:11:49Z","date_updated":"2020-09-10T16:11:49Z","success":1,"checksum":"f8da89553da36037296b0a80f14ebf50","file_name":"thesis_rguseinov.pdf","access_level":"open_access","creator":"rguseino","content_type":"application/pdf","file_size":70950442},{"file_id":"8374","relation":"source_file","date_updated":"2020-09-16T15:11:01Z","date_created":"2020-09-11T09:39:48Z","checksum":"e8fd944c960c20e0e27e6548af69121d","file_name":"thesis_source.zip","access_level":"closed","creator":"rguseino","content_type":"application/x-zip-compressed","file_size":76207597}],"oa_version":"Published Version","ddc":["000"],"title":"Computational design of curved thin shells: From glass façades to programmable matter","status":"public","_id":"8366","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop."}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-11-26T00:00:00Z","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"chicago":"Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis, Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3414685.3417843.","mla":"Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics, vol. 39, no. 6, 208, Association for Computing Machinery, 2020, doi:10.1145/3414685.3417843.","short":"K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F. Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020).","ista":"Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F, Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM Transactions on Graphics. 39(6), 208.","apa":"Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M., Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3414685.3417843","ieee":"K. Gavriil et al., “Computational design of cold bent glass façades,” ACM Transactions on Graphics, vol. 39, no. 6. Association for Computing Machinery, 2020.","ama":"Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold bent glass façades. ACM Transactions on Graphics. 2020;39(6). doi:10.1145/3414685.3417843"},"abstract":[{"lang":"eng","text":"Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.\r\nHowever, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable\r\nconfigurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface."}],"issue":"6","type":"journal_article","oa_version":"Submitted Version","file":[{"creator":"bbickel","content_type":"application/pdf","file_size":28964641,"access_level":"open_access","file_name":"coldglass.pdf","success":1,"checksum":"c7f67717ad74e670b7daeae732abe151","date_created":"2023-05-23T20:54:43Z","date_updated":"2023-05-23T20:54:43Z","file_id":"13084","relation":"main_file"}],"status":"public","title":"Computational design of cold bent glass façades","ddc":["000"],"intvolume":" 39","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8562","month":"11","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1145/3414685.3417843","isi":1,"quality_controlled":"1","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"external_id":{"isi":["000595589100048"],"arxiv":["2009.03667"]},"oa":1,"file_date_updated":"2023-05-23T20:54:43Z","ec_funded":1,"article_number":"208","date_created":"2020-09-23T11:30:02Z","date_updated":"2024-02-21T12:43:21Z","volume":39,"author":[{"last_name":"Gavriil","first_name":"Konstantinos","full_name":"Gavriil, Konstantinos"},{"full_name":"Guseinov, Ruslan","last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","last_name":"Perez Rodriguez","full_name":"Perez Rodriguez, Jesus"},{"full_name":"Pellis, Davide","last_name":"Pellis","first_name":"Davide"},{"orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","first_name":"Paul M","full_name":"Henderson, Paul M"},{"last_name":"Rist","first_name":"Florian","full_name":"Rist, Florian"},{"first_name":"Helmut","last_name":"Pottmann","full_name":"Pottmann, Helmut"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/bend-dont-break/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"8366"},{"id":"8761","status":"public","relation":"research_data"}]},"publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","acknowledgement":"We thank IST Austria’s Scientific Computing team for their support, Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding from the European Union’s\r\nHorizon 2020 research and innovation program under grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been partially supported by KAUST baseline funding.","year":"2020"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01466.","mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:10.1021/acs.nanolett.0c01466.","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.","ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206.","apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01466","ieee":"G. Katsaros et al., “Zero field splitting of heavy-hole states in quantum dots,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 2020;20(7):5201-5206. doi:10.1021/acs.nanolett.0c01466"},"publication":"Nano Letters","page":"5201-5206","article_type":"original","date_published":"2020-06-01T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits."}],"_id":"8203","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 20","ddc":["530"],"title":"Zero field splitting of heavy-hole states in quantum dots","status":"public","file":[{"file_size":3308906,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_NanoLetters_Katsaros.pdf","success":1,"date_created":"2020-08-06T09:35:37Z","date_updated":"2020-08-06T09:35:37Z","relation":"main_file","file_id":"8204"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"month":"06","external_id":{"pmid":["32479090"],"isi":["000548893200066"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046"}],"quality_controlled":"1","isi":1,"doi":"10.1021/acs.nanolett.0c01466","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"ec_funded":1,"file_date_updated":"2020-08-06T09:35:37Z","pmid":1,"year":"2020","acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","publisher":"American Chemical Society","department":[{"_id":"GeKa"}],"publication_status":"published","related_material":{"record":[{"id":"7689","status":"public","relation":"research_data"}]},"author":[{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"},{"full_name":"Kukucka, Josip","first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vukušić, Lada","first_name":"Lada","last_name":"Vukušić","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636"},{"first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"},{"first_name":"Fei","last_name":"Gao","full_name":"Gao, Fei"},{"full_name":"Wang, Ting","orcid":"0000-0002-4619-9575","last_name":"Wang","first_name":"Ting"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"},{"full_name":"Held, Karsten","last_name":"Held","first_name":"Karsten"}],"volume":20,"date_created":"2020-08-06T09:25:04Z","date_updated":"2024-02-21T12:44:01Z"},{"intvolume":" 9","status":"public","ddc":["570"],"title":"Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8740","file":[{"creator":"dernst","file_size":447669,"content_type":"application/pdf","file_name":"2020_eLife_Gridchyn.pdf","access_level":"open_access","date_updated":"2020-11-09T09:17:40Z","date_created":"2020-11-09T09:17:40Z","success":1,"checksum":"6a7b0543c440f4c000a1864e69377d95","file_id":"8749","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"In vitro work revealed that excitatory synaptic inputs to hippocampal inhibitory interneurons could undergo Hebbian, associative, or non-associative plasticity. Both behavioral and learning-dependent reorganization of these connections has also been demonstrated by measuring spike transmission probabilities in pyramidal cell-interneuron spike cross-correlations that indicate monosynaptic connections. Here we investigated the activity-dependent modification of these connections during exploratory behavior in rats by optogenetically inhibiting pyramidal cell and interneuron subpopulations. Light application and associated firing alteration of pyramidal and interneuron populations led to lasting changes in pyramidal-interneuron connection weights as indicated by spike transmission changes. Spike transmission alterations were predicted by the light-mediated changes in the number of pre- and postsynaptic spike pairing events and by firing rate changes of interneurons but not pyramidal cells. This work demonstrates the presence of activity-dependent associative and non-associative reorganization of pyramidal-interneuron connections triggered by the optogenetic modification of the firing rate and spike synchrony of cells.","lang":"eng"}],"article_type":"original","citation":{"ama":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. eLife. 2020;9. doi:10.7554/eLife.61106","ieee":"I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Gridchyn, I., Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2020). Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. 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Csicsvari, ELife 9 (2020).","mla":"Gridchyn, Igor, et al. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” ELife, vol. 9, 61106, eLife Sciences Publications, 2020, doi:10.7554/eLife.61106.","chicago":"Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.61106."},"publication":"eLife","date_published":"2020-10-05T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"05","publisher":"eLife Sciences Publications","department":[{"_id":"JoCs"}],"publication_status":"published","year":"2020","acknowledgement":"We thank Michele Nardin and Federico Stella for comments on an earlier version of the manuscript. K Deisseroth for providing the pAAV-CaMKIIα::eNpHR3.0-YFP plasmid through Addgene. E Boyden for providing AAV2/1.CaMKII::ArchT.GFP.WPRE.SV40 plasmid through Penn Vector Core. This work was supported by the Austrian Science Fund (I02072 and I03713) and a Swiss National Science Foundation grant to PS. The authors declare no conflicts of interest.","volume":9,"date_created":"2020-11-08T23:01:25Z","date_updated":"2024-02-21T12:43:40Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"8563"}]},"author":[{"full_name":"Gridchyn, Igor","last_name":"Gridchyn","first_name":"Igor","orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Philipp","last_name":"Schönenberger","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp"},{"full_name":"O'Neill, Joseph","last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"}],"article_number":"61106","file_date_updated":"2020-11-09T09:17:40Z","project":[{"name":"Interneuron plasticity during spatial learning","call_identifier":"FWF","_id":"257D4372-B435-11E9-9278-68D0E5697425","grant_number":"I2072-B27"},{"call_identifier":"FWF","name":"Interneuro Plasticity During Spatial Learning","grant_number":"I03713","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000584369000001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.61106","publication_identifier":{"eissn":["2050084X"]},"month":"10"},{"article_processing_charge":"No","has_accepted_license":"1","day":"21","month":"09","doi":"10.15479/AT:ISTA:8375","date_published":"2020-09-21T00:00:00Z","citation":{"short":"R. 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Elife.","lang":"eng"}],"type":"research_data","date_published":"2020-10-19T00:00:00Z","doi":"10.15479/AT:ISTA:8563","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"citation":{"ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563.","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563","chicago":"Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8563.","short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","mla":"Csicsvari, Jozsef L., et al. Optogenetic Alteration of Hippocampal Network Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563."},"oa":1,"article_processing_charge":"No","has_accepted_license":"1","month":"10","day":"19"},{"article_number":"237","ec_funded":1,"file_date_updated":"2020-07-14T12:47:55Z","year":"2020","department":[{"_id":"BeBi"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8366"},{"status":"public","relation":"research_data","id":"7154"}],"link":[{"url":"https://ist.ac.at/en/news/geometry-meets-time/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"full_name":"Guseinov, Ruslan","last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Connor","last_name":"McMahan","full_name":"McMahan, Connor"},{"first_name":"Jesus","last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","full_name":"Perez Rodriguez, Jesus"},{"full_name":"Daraio, Chiara","first_name":"Chiara","last_name":"Daraio"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"volume":11,"date_updated":"2024-02-21T12:45:02Z","date_created":"2020-01-13T16:54:26Z","publication_identifier":{"issn":["2041-1723"]},"month":"01","external_id":{"isi":["000511916800015"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-019-14015-2","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Advances in shape-morphing materials, such as hydrogels, shape-memory polymers and light-responsive polymers have enabled prescribing self-directed deformations of initially flat geometries. However, most proposed solutions evolve towards a target geometry without considering time-dependent actuation paths. To achieve more complex geometries and avoid self-collisions, it is critical to encode a spatial and temporal shape evolution within the initially flat shell. Recent realizations of time-dependent morphing are limited to the actuation of few, discrete hinges and cannot form doubly curved surfaces. Here, we demonstrate a method for encoding temporal shape evolution in architected shells that assume complex shapes and doubly curved geometries. The shells are non-periodic tessellations of pre-stressed contractile unit cells that soften in water at rates prescribed locally by mesostructure geometry. The ensuing midplane contraction is coupled to the formation of encoded curvatures. We propose an inverse design tool based on a data-driven model for unit cells’ temporal responses.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7262","intvolume":" 11","status":"public","title":"Programming temporal morphing of self-actuated shells","ddc":["000"],"file":[{"checksum":"7db23fef2f4cda712f17f1004116ddff","date_updated":"2020-07-14T12:47:55Z","date_created":"2020-01-15T14:35:34Z","file_id":"7336","relation":"main_file","creator":"rguseino","file_size":1315270,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_NatureComm_Guseinov.pdf"}],"oa_version":"Published Version","scopus_import":"1","keyword":["Design","Synthesis and processing","Mechanical engineering","Polymers"],"article_processing_charge":"No","has_accepted_license":"1","day":"13","citation":{"ieee":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, and B. Bickel, “Programming temporal morphing of self-actuated shells,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Guseinov, R., McMahan, C., Perez Rodriguez, J., Daraio, C., & Bickel, B. (2020). Programming temporal morphing of self-actuated shells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-14015-2","ista":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. 2020. Programming temporal morphing of self-actuated shells. Nature Communications. 11, 237.","ama":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. Programming temporal morphing of self-actuated shells. Nature Communications. 2020;11. doi:10.1038/s41467-019-14015-2","chicago":"Guseinov, Ruslan, Connor McMahan, Jesus Perez Rodriguez, Chiara Daraio, and Bernd Bickel. “Programming Temporal Morphing of Self-Actuated Shells.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-019-14015-2.","short":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, B. Bickel, Nature Communications 11 (2020).","mla":"Guseinov, Ruslan, et al. “Programming Temporal Morphing of Self-Actuated Shells.” Nature Communications, vol. 11, 237, Springer Nature, 2020, doi:10.1038/s41467-019-14015-2."},"publication":"Nature Communications","article_type":"original","date_published":"2020-01-13T00:00:00Z"},{"day":"01","month":"12","article_processing_charge":"No","has_accepted_license":"1","doi":"10.15479/AT:ISTA:14592","date_published":"2020-12-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"citation":{"ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","short":"F.K. Schur, (2020).","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592."},"oa":1,"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"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"}],"file_date_updated":"2023-12-01T10:39:59Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","type":"research_data","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"contributor":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Fäßler","first_name":"Florian"},{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","last_name":"Zens","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian KM","contributor_type":"researcher","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"8586"}]},"date_created":"2023-11-22T15:00:57Z","date_updated":"2024-02-21T12:44:48Z","file":[{"creator":"fschur","file_size":49297,"content_type":"application/zip","access_level":"open_access","file_name":"3Dprint-files_download_v2.zip","success":1,"checksum":"0108616e2a59e51879ea51299a29b091","date_updated":"2023-11-22T14:58:44Z","date_created":"2023-11-22T14:58:44Z","file_id":"14593","relation":"main_file"},{"date_updated":"2023-12-01T10:39:59Z","date_created":"2023-12-01T10:39:59Z","checksum":"4c66ddedee4d01c1c4a7978208350cfc","success":1,"relation":"main_file","file_id":"14637","file_size":641,"content_type":"text/plain","creator":"cchlebak","file_name":"readme.txt","access_level":"open_access"}],"oa_version":"Published Version","year":"2020","_id":"14592","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","department":[{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria"},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","page":"27-39","publication":"Complex Networks and their applications VIII","citation":{"mla":"Bhatia, Sumit, et al. “A Persistent Homology Perspective to the Link Prediction Problem.” Complex Networks and Their Applications VIII, vol. 881, Springer Nature, 2020, pp. 27–39, doi:10.1007/978-3-030-36687-2_3.","short":"S. Bhatia, B. Chatterjee, D. Nathani, M. Kaul, in:, Complex Networks and Their Applications VIII, Springer Nature, 2020, pp. 27–39.","chicago":"Bhatia, Sumit, Bapi Chatterjee, Deepak Nathani, and Manohar Kaul. “A Persistent Homology Perspective to the Link Prediction Problem.” In Complex Networks and Their Applications VIII, 881:27–39. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-36687-2_3.","ama":"Bhatia S, Chatterjee B, Nathani D, Kaul M. A persistent homology perspective to the link prediction problem. In: Complex Networks and Their Applications VIII. Vol 881. Springer Nature; 2020:27-39. doi:10.1007/978-3-030-36687-2_3","ista":"Bhatia S, Chatterjee B, Nathani D, Kaul M. 2020. A persistent homology perspective to the link prediction problem. Complex Networks and their applications VIII. COMPLEX: International Conference on Complex Networks and their Applications, SCI, vol. 881, 27–39.","ieee":"S. Bhatia, B. Chatterjee, D. Nathani, and M. Kaul, “A persistent homology perspective to the link prediction problem,” in Complex Networks and their applications VIII, Lisbon, Portugal, 2020, vol. 881, pp. 27–39.","apa":"Bhatia, S., Chatterjee, B., Nathani, D., & Kaul, M. (2020). A persistent homology perspective to the link prediction problem. In Complex Networks and their applications VIII (Vol. 881, pp. 27–39). Lisbon, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-36687-2_3"},"date_published":"2020-01-01T00:00:00Z","alternative_title":["SCI"],"type":"conference","abstract":[{"text":"Persistent homology is a powerful tool in Topological Data Analysis (TDA) to capture the topological properties of data succinctly at different spatial resolutions. For graphical data, the shape, and structure of the neighborhood of individual data items (nodes) are an essential means of characterizing their properties. We propose the use of persistent homology methods to capture structural and topological properties of graphs and use it to address the problem of link prediction. We achieve encouraging results on nine different real-world datasets that attest to the potential of persistent homology-based methods for network analysis.","lang":"eng"}],"ddc":["004"],"title":"A persistent homology perspective to the link prediction problem","status":"public","intvolume":" 881","_id":"7213","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"8625","date_updated":"2020-10-08T08:16:48Z","date_created":"2020-10-08T08:16:48Z","checksum":"8951f094c8c7dae9ff8db885199bc296","success":1,"file_name":"main.pdf","access_level":"open_access","file_size":310598,"content_type":"application/pdf","creator":"bchatter"}],"month":"01","publication_identifier":{"issn":["1860949X"],"isbn":["9783030366865"],"eissn":["18609503"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"oa":1,"external_id":{"isi":["000843927300003"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-12-12","start_date":"2019-12-10","location":"Lisbon, Portugal","name":"COMPLEX: International Conference on Complex Networks and their Applications"},"doi":"10.1007/978-3-030-36687-2_3","file_date_updated":"2020-10-08T08:16:48Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"year":"2020","date_updated":"2024-02-22T13:16:06Z","date_created":"2019-12-29T23:00:45Z","volume":881,"author":[{"full_name":"Bhatia, Sumit","first_name":"Sumit","last_name":"Bhatia"},{"full_name":"Chatterjee, Bapi","first_name":"Bapi","last_name":"Chatterjee","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2742-4028"},{"full_name":"Nathani, Deepak","first_name":"Deepak","last_name":"Nathani"},{"full_name":"Kaul, Manohar","first_name":"Manohar","last_name":"Kaul"}]},{"conference":{"name":"CCS: Computer and Communications Security","end_date":"2020-11-13","location":"Virtual, United States","start_date":"2020-11-09"},"doi":"10.1145/3372297.3423364","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1015"}],"oa":1,"external_id":{"isi":["000768470400104"]},"isi":1,"quality_controlled":"1","month":"10","publication_identifier":{"isbn":["978-1-4503-7089-9"]},"author":[{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"last_name":"Malkhi","first_name":"Dahlia","full_name":"Malkhi, Dahlia"},{"first_name":"Alexander","last_name":"Spiegelman","full_name":"Spiegelman, Alexander"}],"date_created":"2021-12-16T13:23:27Z","date_updated":"2024-02-22T13:10:45Z","year":"2020","acknowledgement":"We would like to thank Ittai Abraham for the discussions and guidance during the initial conception of the project, especially for HAVSS. Furthermore, we would like to thank the anonymous reviewers for pointing out the relevance of this work to MPC protocols.","publication_status":"published","department":[{"_id":"ElKo"}],"publisher":"Association for Computing Machinery","date_published":"2020-10-30T00:00:00Z","publication":"Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security","citation":{"chicago":"Kokoris Kogias, Eleftherios, Dahlia Malkhi, and Alexander Spiegelman. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, 1751–1767. Association for Computing Machinery, 2020. https://doi.org/10.1145/3372297.3423364.","short":"E. Kokoris Kogias, D. Malkhi, A. Spiegelman, in:, Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767.","mla":"Kokoris Kogias, Eleftherios, et al. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767, doi:10.1145/3372297.3423364.","ieee":"E. Kokoris Kogias, D. Malkhi, and A. Spiegelman, “Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures,” in Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Virtual, United States, 2020, pp. 1751–1767.","apa":"Kokoris Kogias, E., Malkhi, D., & Spiegelman, A. (2020). Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security (pp. 1751–1767). Virtual, United States: Association for Computing Machinery. https://doi.org/10.1145/3372297.3423364","ista":"Kokoris Kogias E, Malkhi D, Spiegelman A. 2020. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. CCS: Computer and Communications Security, 1751–1767.","ama":"Kokoris Kogias E, Malkhi D, Spiegelman A. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In: Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. Association for Computing Machinery; 2020:1751–1767. doi:10.1145/3372297.3423364"},"page":"1751–1767","day":"30","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10556","status":"public","title":"Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures","abstract":[{"text":"In this paper, we present the first Asynchronous Distributed Key Generation (ADKG) algorithm which is also the first distributed key generation algorithm that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is the number of faulty parties). As a result, using our ADKG we remove the trusted setup assumption that the most scalable consensus algorithms make. In order to create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative the open question posed by Cachin et al. [7] on how to create an Asynchronous Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+12020 IEEE Real-Time Systems Symposium, Houston, TX, USA , 2020, pp. 244–256.","apa":"Garcia Soto, M., & Prabhakar, P. (2020). Hybridization for stability verification of nonlinear switched systems. In 2020 IEEE Real-Time Systems Symposium (pp. 244–256). Houston, TX, USA : IEEE. https://doi.org/10.1109/RTSS49844.2020.00031","ama":"Garcia Soto M, Prabhakar P. Hybridization for stability verification of nonlinear switched systems. In: 2020 IEEE Real-Time Systems Symposium. IEEE; 2020:244-256. doi:10.1109/RTSS49844.2020.00031","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” In 2020 IEEE Real-Time Systems Symposium, 244–56. IEEE, 2020. https://doi.org/10.1109/RTSS49844.2020.00031.","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–56, doi:10.1109/RTSS49844.2020.00031.","short":"M. Garcia Soto, P. Prabhakar, in:, 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–256."},"publication":"2020 IEEE Real-Time Systems Symposium","abstract":[{"text":"We propose a novel hybridization method for stability analysis that over-approximates nonlinear dynamical systems by switched systems with linear inclusion dynamics. We observe that existing hybridization techniques for safety analysis that over-approximate nonlinear dynamical systems by switched affine inclusion dynamics and provide fixed approximation error, do not suffice for stability analysis. Hence, we propose a hybridization method that provides a state-dependent error which converges to zero as the state tends to the equilibrium point. The crux of our hybridization computation is an elegant recursive algorithm that uses partial derivatives of a given function to obtain upper and lower bound matrices for the over-approximating linear inclusion. We illustrate our method on some examples to demonstrate the application of the theory for stability analysis. In particular, our method is able to establish stability of a nonlinear system which does not admit a polynomial Lyapunov function.","lang":"eng"}],"type":"conference","oa_version":"Submitted Version","file":[{"date_updated":"2021-02-26T16:38:14Z","date_created":"2021-02-26T16:38:14Z","checksum":"8f97f229316c3b3a6f0cf99297aa0941","file_id":"9203","relation":"main_file","creator":"mgarcias","content_type":"application/pdf","file_size":1125794,"file_name":"main.pdf","access_level":"open_access"}],"ddc":["000"],"title":"Hybridization for stability verification of nonlinear switched systems","status":"public","_id":"9202","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eisbn":["9781728183244"],"eissn":["2576-3172"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1109/RTSS49844.2020.00031","conference":{"end_date":"2020-12-04","start_date":"2020-12-01","location":"Houston, TX, USA ","name":"RTTS: Real-Time Systems Symposium"},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000680435100021"]},"file_date_updated":"2021-02-26T16:38:14Z","date_created":"2021-02-26T16:38:24Z","date_updated":"2024-02-22T13:25:19Z","author":[{"full_name":"Garcia Soto, Miriam","first_name":"Miriam","last_name":"Garcia Soto","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2936-5719"},{"full_name":"Prabhakar, Pavithra","last_name":"Prabhakar","first_name":"Pavithra"}],"department":[{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","year":"2020","acknowledgement":"Miriam Garc´ıa Soto was partially supported by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Pavithra Prabhakar was partially supported by NSF CAREER Award No. 1552668, NSF Award No. 2008957 and ONR YIP Award No. N000141712577."},{"type":"journal_article","abstract":[{"text":"We consider systems of bosons trapped in a box, in the Gross–Pitaevskii regime. We show that low-energy states exhibit complete Bose–Einstein condensation with an optimal bound on the number of orthogonal excitations. This extends recent results obtained in Boccato et al. (Commun Math Phys 359(3):975–1026, 2018), removing the assumption of small interaction potential.","lang":"eng"}],"title":"Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime","status":"public","intvolume":" 376","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6906","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"1311-1395","publication":"Communications in Mathematical Physics","citation":{"ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 2020;376:1311-1395. doi:10.1007/s00220-019-03555-9","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 376, 1311–1395.","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime,” Communications in Mathematical Physics, vol. 376. Springer, pp. 1311–1395, 2020.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-019-03555-9","mla":"Boccato, Chiara, et al. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics, vol. 376, Springer, 2020, pp. 1311–95, doi:10.1007/s00220-019-03555-9.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Communications in Mathematical Physics 376 (2020) 1311–1395.","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics. Springer, 2020. https://doi.org/10.1007/s00220-019-03555-9."},"date_published":"2020-06-01T00:00:00Z","ec_funded":1,"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","acknowledgement":"We would like to thank P. T. Nam and R. Seiringer for several useful discussions and\r\nfor suggesting us to use the localization techniques from [9]. C. Boccato has received funding from the\r\nEuropean Research Council (ERC) under the programme Horizon 2020 (Grant Agreement 694227). B. Schlein gratefully acknowledges support from the NCCR SwissMAP and from the Swiss National Foundation of Science (Grant No. 200020_1726230) through the SNF Grant “Dynamical and energetic properties of Bose–Einstein condensates”.","year":"2020","date_updated":"2024-02-22T13:33:02Z","date_created":"2019-09-24T17:30:59Z","volume":376,"author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","last_name":"Boccato","first_name":"Chiara","full_name":"Boccato, Chiara"},{"first_name":"Christian","last_name":"Brennecke","full_name":"Brennecke, Christian"},{"first_name":"Serena","last_name":"Cenatiempo","full_name":"Cenatiempo, Serena"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"}],"month":"06","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"oa":1,"external_id":{"isi":["000536053300012"],"arxiv":["1812.03086"]},"main_file_link":[{"url":"https://arxiv.org/abs/1812.03086","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/s00220-019-03555-9"},{"date_published":"2020-04-01T00:00:00Z","publication":"International Journal of Computer Vision","citation":{"short":"R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995.","mla":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:10.1007/s11263-019-01232-x.","chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision. Springer Nature, 2020. https://doi.org/10.1007/s11263-019-01232-x.","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 2020;128(4):970-995. doi:10.1007/s11263-019-01232-x","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications,” International Journal of Computer Vision, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020.","apa":"Sun, R., & Lampert, C. (2020). KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01232-x","ista":"Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 128(4), 970–995."},"article_type":"original","page":"970-995","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2019_IJCV_Sun.pdf","creator":"dernst","file_size":1715072,"content_type":"application/pdf","file_id":"7110","relation":"main_file","checksum":"155e63edf664dcacb3bdc1c2223e606f","date_updated":"2020-07-14T12:47:45Z","date_created":"2019-11-26T10:30:02Z"}],"oa_version":"Published Version","_id":"6944","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications","ddc":["004"],"status":"public","intvolume":" 128","abstract":[{"text":"We study the problem of automatically detecting if a given multi-class classifier operates outside of its specifications (out-of-specs), i.e. on input data from a different distribution than what it was trained for. This is an important problem to solve on the road towards creating reliable computer vision systems for real-world applications, because the quality of a classifier’s predictions cannot be guaranteed if it operates out-of-specs. Previously proposed methods for out-of-specs detection make decisions on the level of single inputs. This, however, is insufficient to achieve low false positive rate and high false negative rates at the same time. In this work, we describe a new procedure named KS(conf), based on statistical reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied to the set of predicted confidence values for batches of samples. Working with batches instead of single samples allows increasing the true positive rate without negatively affecting the false positive rate, thereby overcoming a crucial limitation of single sample tests. We show by extensive experiments using a variety of convolutional network architectures and datasets that KS(conf) reliably detects out-of-specs situations even under conditions where other tests fail. It furthermore has a number of properties that make it an excellent candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with any classifier that outputs confidence scores, and requires no a priori knowledge about how the data distribution could change.","lang":"eng"}],"issue":"4","type":"journal_article","doi":"10.1007/s11263-019-01232-x","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000494406800001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"month":"04","publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]},"author":[{"first_name":"Rémy","last_name":"Sun","full_name":"Sun, Rémy"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11263-019-01262-5"}],"record":[{"relation":"earlier_version","status":"public","id":"6482"}]},"date_updated":"2024-02-22T14:57:30Z","date_created":"2019-10-14T09:14:28Z","volume":128,"year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:47:45Z","ec_funded":1},{"language":[{"iso":"eng"}],"doi":"10.1145/3371093","project":[{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1902.04744"]},"publication_identifier":{"eissn":["2475-1421"]},"month":"01","volume":4,"date_created":"2020-08-30T22:01:12Z","date_updated":"2024-02-22T15:16:45Z","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.3533633"}]},"author":[{"full_name":"Wang, Peixin","first_name":"Peixin","last_name":"Wang"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Deng, Yuxin","last_name":"Deng","first_name":"Yuxin"},{"full_name":"Xu, Ming","last_name":"Xu","first_name":"Ming"}],"publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2020","acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","file_date_updated":"2020-09-01T11:12:58Z","article_number":"25","date_published":"2020-01-01T00:00:00Z","citation":{"mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020.","chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In Proceedings of the ACM on Programming Languages, Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.","ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093","ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25.","ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM. https://doi.org/10.1145/3371093"},"publication":"Proceedings of the ACM on Programming Languages","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"date_created":"2020-09-01T11:12:58Z","date_updated":"2020-09-01T11:12:58Z","success":1,"checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","file_id":"8328","relation":"main_file","creator":"cziletti","file_size":564151,"content_type":"application/pdf","file_name":"2019_ACM_POPL_Wang.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 4","title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","ddc":["004"],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8324","issue":"POPL","abstract":[{"text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature.","lang":"eng"}],"type":"conference"},{"issue":"2","abstract":[{"lang":"eng","text":"We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 48","status":"public","title":"Correlated random matrices: Band rigidity and edge universality","_id":"6184","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-03-01T00:00:00Z","page":"963-1001","article_type":"original","citation":{"ama":"Alt J, Erdös L, Krüger TH, Schröder DJ. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 2020;48(2):963-1001. doi:10.1214/19-AOP1379","apa":"Alt, J., Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Correlated random matrices: Band rigidity and edge universality. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/19-AOP1379","ieee":"J. Alt, L. Erdös, T. H. Krüger, and D. J. Schröder, “Correlated random matrices: Band rigidity and edge universality,” Annals of Probability, vol. 48, no. 2. Institute of Mathematical Statistics, pp. 963–1001, 2020.","ista":"Alt J, Erdös L, Krüger TH, Schröder DJ. 2020. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 48(2), 963–1001.","short":"J. Alt, L. Erdös, T.H. Krüger, D.J. Schröder, Annals of Probability 48 (2020) 963–1001.","mla":"Alt, Johannes, et al. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability, vol. 48, no. 2, Institute of Mathematical Statistics, 2020, pp. 963–1001, doi:10.1214/19-AOP1379.","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Dominik J Schröder. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/19-AOP1379."},"publication":"Annals of Probability","ec_funded":1,"volume":48,"date_created":"2019-03-28T09:20:08Z","date_updated":"2024-02-22T14:34:33Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"149"},{"id":"6179","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H"},{"orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2020","publication_identifier":{"issn":["0091-1798"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1214/19-AOP1379","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.07744","open_access":"1"}],"oa":1,"external_id":{"isi":["000528269100013"],"arxiv":["1804.07744"]}},{"doi":"10.1016/j.molp.2020.02.012","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32087370"]},"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["1674-2052"]},"month":"05","author":[{"full_name":"Moulinier-Anzola, Jeanette","first_name":"Jeanette","last_name":"Moulinier-Anzola"},{"first_name":"Maximilian","last_name":"Schwihla","full_name":"Schwihla, Maximilian"},{"last_name":"De-Araújo","first_name":"Lucinda","full_name":"De-Araújo, Lucinda"},{"last_name":"Artner","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina"},{"full_name":"Jörg, Lisa","last_name":"Jörg","first_name":"Lisa"},{"first_name":"Nataliia","last_name":"Konstantinova","full_name":"Konstantinova, Nataliia"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"full_name":"Korbei, Barbara","first_name":"Barbara","last_name":"Korbei"}],"volume":13,"date_updated":"2024-02-28T12:41:52Z","date_created":"2024-02-28T08:55:56Z","pmid":1,"year":"2020","department":[{"_id":"EvBe"}],"publisher":"Elsevier","publication_status":"published","file_date_updated":"2024-02-28T12:39:56Z","date_published":"2020-05-04T00:00:00Z","citation":{"mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012.","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.","ieee":"J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” Molecular Plant, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012"},"publication":"Molecular Plant","page":"717-731","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"04","keyword":["Plant Science","Molecular Biology"],"file":[{"relation":"main_file","file_id":"15038","date_updated":"2024-02-28T12:39:56Z","date_created":"2024-02-28T12:39:56Z","checksum":"c538a5008f7827f62d17d40a3bfabe65","success":1,"file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","access_level":"open_access","file_size":3089212,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"15037","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","ddc":["580"],"status":"public","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","issue":"5","abstract":[{"lang":"eng","text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants."}],"type":"journal_article"},{"day":"02","article_processing_charge":"No","keyword":["Molecular Biology","Structural Biology"],"date_published":"2020-10-02T00:00:00Z","publication":"Journal of Molecular Biology","citation":{"short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.","chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801. doi:10.1016/j.jmb.2020.09.001","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2020.09.001","ieee":"H. V. D. Rosa et al., “Molecular recognition at septin interfaces: The switches hold the key,” Journal of Molecular Biology, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801."},"article_type":"original","page":"5784-5801","abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"issue":"21","type":"journal_article","oa_version":"Published Version","_id":"15036","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Molecular recognition at septin interfaces: The switches hold the key","intvolume":" 432","month":"10","publication_identifier":{"issn":["0022-2836"]},"doi":"10.1016/j.jmb.2020.09.001","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jmb.2020.09.001"}],"external_id":{"pmid":["32910969"]},"oa":1,"quality_controlled":"1","author":[{"first_name":"Higor Vinícius Dias","last_name":"Rosa","full_name":"Rosa, Higor Vinícius Dias"},{"last_name":"Leonardo","first_name":"Diego Antonio","full_name":"Leonardo, Diego Antonio"},{"last_name":"Brognara","first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","full_name":"Brognara, Gabriel"},{"full_name":"Brandão-Neto, José","last_name":"Brandão-Neto","first_name":"José"},{"last_name":"D'Muniz Pereira","first_name":"Humberto","full_name":"D'Muniz Pereira, Humberto"},{"full_name":"Araújo, Ana Paula Ulian","first_name":"Ana Paula Ulian","last_name":"Araújo"},{"full_name":"Garratt, Richard Charles","last_name":"Garratt","first_name":"Richard Charles"}],"date_created":"2024-02-28T08:50:34Z","date_updated":"2024-02-28T12:37:54Z","volume":432,"year":"2020","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"MaLo"}]},{"date_published":"2020-07-08T00:00:00Z","publication":"ACM Transactions on Graphics","citation":{"short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392405.","chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392405.","ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392405","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., & Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392405","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31."},"article_type":"original","day":"08","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","file":[{"success":1,"checksum":"813831ca91319d794d9748c276b24578","date_updated":"2020-11-23T09:03:19Z","date_created":"2020-11-23T09:03:19Z","file_id":"8795","relation":"main_file","creator":"dernst","file_size":14935529,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_soapfilm_submitted.pdf"}],"_id":"8384","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A model for soap film dynamics with evolving thickness","status":"public","ddc":["000"],"intvolume":" 39","abstract":[{"text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film.","lang":"eng"}],"issue":"4","type":"journal_article","doi":"10.1145/3386569.3392405","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392405"}],"oa":1,"external_id":{"isi":["000583700300004"]},"quality_controlled":"1","isi":1,"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"month":"07","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"author":[{"full_name":"Ishida, Sadashige","last_name":"Ishida","first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"},{"full_name":"Synak, Peter","first_name":"Peter","last_name":"Synak","id":"331776E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Narita, Fumiya","first_name":"Fumiya","last_name":"Narita"},{"last_name":"Hachisuka","first_name":"Toshiya","full_name":"Hachisuka, Toshiya"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-09-13T22:01:18Z","date_updated":"2024-02-28T12:57:31Z","volume":39,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","year":"2020","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"file_date_updated":"2020-11-23T09:03:19Z","ec_funded":1,"article_number":"31"},{"month":"07","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000744436200015"],"arxiv":["1912.05390"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.05390"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3350755.3400282","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","location":"Virtual Event, United States","start_date":"2020-07-15","end_date":"2020-07-17"},"ec_funded":1,"publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2020","date_updated":"2024-02-28T12:53:09Z","date_created":"2020-05-06T08:53:34Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"9541"}]},"author":[{"orcid":"0000-0002-5646-9524","last_name":"Czumaj","first_name":"Artur","full_name":"Czumaj, Artur"},{"full_name":"Davies, Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425","orcid":"0000-0002-5646-9524","first_name":"Peter","last_name":"Davies"},{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"175-185","citation":{"chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282.","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing Machinery, 2020, pp. 175–185.","ista":"Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing massively parallel computation with low space. Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on Parallelism in Algorithms and Architectures, 175–185.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” in Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Virtual Event, United States, 2020, no. 7, pp. 175–185.","apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for derandomizing massively parallel computation with low space. In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020) (pp. 175–185). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400282","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. In: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). Association for Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282"},"publication":"Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)","date_published":"2020-07-01T00:00:00Z","type":"conference","issue":"7","abstract":[{"text":"The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space.\r\n\t\r\nRecent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \\emph{significant} global progress, i.e., progress towards solving the problem for the original input graph.\r\n\t\r\nUsing this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel et al. [DISC'17].","lang":"eng"}],"title":"Graph sparsification for derandomizing massively parallel computation with low space","status":"public","_id":"7802","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint"},{"publication_identifier":{"isbn":["9781450368186"]},"month":"02","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000564476500020"]},"main_file_link":[{"url":"https://doi.org/10.1145/3332466.3374542","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3332466.3374542","conference":{"name":"PPOPP: Principles and Practice of Parallel Programming","location":"San Diego, CA, United States","start_date":"2020-02-22","end_date":"2020-02-26"},"ec_funded":1,"department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","publication_status":"published","year":"2020","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program, grant agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). ","date_created":"2020-04-05T22:00:49Z","date_updated":"2024-02-28T12:55:14Z","author":[{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A"},{"full_name":"Prokopec, Aleksandar","first_name":"Aleksandar","last_name":"Prokopec"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"scopus_import":"1","article_processing_charge":"No","day":"19","page":"276-291","citation":{"chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542.","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91, doi:10.1145/3332466.3374542.","short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","ista":"Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice of Parallel Programming, 276–291.","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 276–291.","apa":"Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542","ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:276-291. doi:10.1145/3332466.3374542"},"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","date_published":"2020-02-19T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures."}],"title":"Non-blocking interpolation search trees with doubly-logarithmic running time","status":"public","_id":"7636","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"},{"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver."}],"_id":"8385","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 39","status":"public","ddc":["000"],"title":"Homogenized yarn-level cloth","file":[{"access_level":"open_access","file_name":"2020_hylc_submitted.pdf","content_type":"application/pdf","file_size":38922662,"creator":"dernst","relation":"main_file","file_id":"8794","checksum":"cf4c1d361c3196c4bd424520a5588205","success":1,"date_updated":"2020-11-23T09:01:22Z","date_created":"2020-11-23T09:01:22Z"}],"oa_version":"Submitted Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"08","citation":{"chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392412.","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","mla":"Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392412.","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","apa":"Sperl, G., Narain, R., & Wojtan, C. (2020). Homogenized yarn-level cloth. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392412","ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48.","ama":"Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392412"},"publication":"ACM Transactions on Graphics","article_type":"original","date_published":"2020-07-08T00:00:00Z","article_number":"48","ec_funded":1,"file_date_updated":"2020-11-23T09:01:22Z","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring discussions and help with Mathematica code generation. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","year":"2020","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12358"}]},"author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Sperl","full_name":"Sperl, Georg"},{"full_name":"Narain, Rahul","first_name":"Rahul","last_name":"Narain"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"volume":39,"date_updated":"2024-02-28T12:57:47Z","date_created":"2020-09-13T22:01:18Z","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"month":"07","oa":1,"main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392412","open_access":"1"}],"external_id":{"isi":["000583700300021"]},"project":[{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"quality_controlled":"1","isi":1,"doi":"10.1145/3386569.3392412","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}]},{"doi":"10.1063/5.0005194","language":[{"iso":"eng"}],"external_id":{"isi":["000537900300001"],"arxiv":["2002.07294"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/5.0005194"}],"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["10897690"]},"month":"05","related_material":{"record":[{"id":"10759","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Pȩkalski","first_name":"J.","full_name":"Pȩkalski, J."},{"full_name":"Rzadkowski, Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419","first_name":"Wojciech","last_name":"Rzadkowski"},{"first_name":"A. Z.","last_name":"Panagiotopoulos","full_name":"Panagiotopoulos, A. Z."}],"volume":152,"date_updated":"2024-02-28T13:00:28Z","date_created":"2020-06-14T22:00:49Z","year":"2020","publisher":"AIP Publishing","department":[{"_id":"MiLe"}],"publication_status":"published","ec_funded":1,"article_number":"204905","date_published":"2020-05-29T00:00:00Z","citation":{"ama":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 2020;152(20). doi:10.1063/5.0005194","ieee":"J. Pȩkalski, W. Rzadkowski, and A. Z. Panagiotopoulos, “Shear-induced ordering in systems with competing interactions: A machine learning study,” The Journal of chemical physics, vol. 152, no. 20. AIP Publishing, 2020.","apa":"Pȩkalski, J., Rzadkowski, W., & Panagiotopoulos, A. Z. (2020). Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0005194","ista":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. 2020. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 152(20), 204905.","short":"J. Pȩkalski, W. Rzadkowski, A.Z. Panagiotopoulos, The Journal of Chemical Physics 152 (2020).","mla":"Pȩkalski, J., et al. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics, vol. 152, no. 20, 204905, AIP Publishing, 2020, doi:10.1063/5.0005194.","chicago":"Pȩkalski, J., Wojciech Rzadkowski, and A. Z. Panagiotopoulos. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005194."},"publication":"The Journal of chemical physics","article_type":"original","article_processing_charge":"No","day":"29","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7956","intvolume":" 152","title":"Shear-induced ordering in systems with competing interactions: A machine learning study","status":"public","issue":"20","abstract":[{"text":"When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.","lang":"eng"}],"type":"journal_article"},{"scopus_import":"1","publication_identifier":{"isbn":["9781450375825"]},"article_processing_charge":"No","day":"31","month":"07","page":"31-40","quality_controlled":"1","citation":{"chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” In Proceedings of the 39th Symposium on Principles of Distributed Computing, 31–40. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3406005.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40.","mla":"Baig, Mirza Ahad, et al. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40, doi:10.1145/3382734.3406005.","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived snapshots with polylogarithmic amortized step complexity,” in Proceedings of the 39th Symposium on Principles of Distributed Computing, Virtual, Italy, 2020, pp. 31–40.","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2020). Long-lived snapshots with polylogarithmic amortized step complexity. In Proceedings of the 39th Symposium on Principles of Distributed Computing (pp. 31–40). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3406005","ista":"Baig MA, Hendler D, Milani A, Travers C. 2020. Long-lived snapshots with polylogarithmic amortized step complexity. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 31–40.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived snapshots with polylogarithmic amortized step complexity. In: Proceedings of the 39th Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:31-40. doi:10.1145/3382734.3406005"},"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-02860087/document"}],"oa":1,"publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","language":[{"iso":"eng"}],"doi":"10.1145/3382734.3406005","date_published":"2020-07-31T00:00:00Z","conference":{"name":"PODC: Principles of Distributed Computing","location":"Virtual, Italy","start_date":"2020-08-03","end_date":"2020-08-07"},"type":"conference","abstract":[{"lang":"eng","text":"We present the first deterministic wait-free long-lived snapshot algorithm, using only read and write operations, that guarantees polylogarithmic amortized step complexity in all executions. This is the first non-blocking snapshot algorithm, using reads and writes only, that has sub-linear amortized step complexity in executions of arbitrary length. The key to our construction is a novel implementation of a 2-component max array object which may be of independent interest."}],"publisher":"Association for Computing Machinery","title":"Long-lived snapshots with polylogarithmic amortized step complexity","status":"public","publication_status":"published","_id":"8382","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","oa_version":"Preprint","date_created":"2020-09-13T22:01:17Z","date_updated":"2024-02-28T12:54:30Z","author":[{"full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad","last_name":"Baig"},{"last_name":"Hendler","first_name":"Danny","full_name":"Hendler, Danny"},{"full_name":"Milani, Alessia","last_name":"Milani","first_name":"Alessia"},{"first_name":"Corentin","last_name":"Travers","full_name":"Travers, Corentin"}]},{"month":"01","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"doi":"10.1103/PhysRevB.101.020504","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.02077"}],"external_id":{"isi":["000506843500001"],"arxiv":["1907.02077"]},"isi":1,"quality_controlled":"1","article_number":"020504","author":[{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"first_name":"P. L.S.","last_name":"Lopes","full_name":"Lopes, P. L.S."},{"last_name":"Hosur","first_name":"Pavan","full_name":"Hosur, Pavan"},{"full_name":"Gilbert, Matthew J.","first_name":"Matthew J.","last_name":"Gilbert"},{"full_name":"Ghaemi, Pouyan","first_name":"Pouyan","last_name":"Ghaemi"}],"date_updated":"2024-02-28T13:11:13Z","date_created":"2020-02-02T23:01:01Z","volume":101,"year":"2020","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","day":"13","article_processing_charge":"No","scopus_import":"1","date_published":"2020-01-13T00:00:00Z","publication":"Physical Review B","citation":{"chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.020504.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020).","mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:10.1103/PhysRevB.101.020504.","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” Physical Review B, vol. 101, no. 2. American Physical Society, 2020.","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., & Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.020504","ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 2020;101(2). doi:10.1103/PhysRevB.101.020504"},"article_type":"original","abstract":[{"lang":"eng","text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex."}],"issue":"2","type":"journal_article","oa_version":"Preprint","_id":"7428","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","status":"public","intvolume":" 101"},{"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1912.08334","open_access":"1"}],"external_id":{"isi":["000555104200011"],"arxiv":["1912.08334"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.102.012224","publication_identifier":{"issn":["24699926"],"eissn":["24699934"]},"month":"07","department":[{"_id":"OnHo"}],"publisher":"American Physical Society","publication_status":"published","year":"2020","acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","volume":102,"date_updated":"2024-02-28T13:11:28Z","date_created":"2020-08-30T22:01:10Z","author":[{"full_name":"Wu, Yunfan","first_name":"Yunfan","last_name":"Wu"},{"first_name":"Rajiv","last_name":"Krishnakumar","full_name":"Krishnakumar, Rajiv"},{"full_name":"Martínez-Rincón, Julián","last_name":"Martínez-Rincón","first_name":"Julián"},{"full_name":"Malia, Benjamin K.","first_name":"Benjamin K.","last_name":"Malia"},{"full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","first_name":"Onur"},{"first_name":"Mark A.","last_name":"Kasevich","full_name":"Kasevich, Mark A."}],"article_number":"012224","article_type":"original","citation":{"apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224","ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020.","ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224.","ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224.","short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224."},"publication":"Physical Review A","date_published":"2020-07-30T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"30","intvolume":" 102","title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","status":"public","_id":"8319","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated."}]},{"date_published":"2020-04-03T00:00:00Z","publication":"Proceedings of the 34th AAAI Conference on Artificial Intelligence","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i06.6531.","short":"T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.","mla":"Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06, Association for the Advancement of Artificial Intelligence, 2020, pp. 9794–801, doi:10.1609/aaai.v34i06.6531.","ieee":"T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning of risk-constrained policies in Markov decision processes,” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06. Association for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020.","apa":"Brázdil, T., Chatterjee, K., Novotný, P., & Vahala, J. (2020). Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i06.6531","ista":"Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.","ama":"Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 2020;34(06):9794-9801. doi:10.1609/aaai.v34i06.6531"},"article_type":"original","page":"9794-9801","day":"03","article_processing_charge":"No","keyword":["General Medicine"],"oa_version":"Preprint","_id":"15055","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Reinforcement learning of risk-constrained policies in Markov decision processes","intvolume":" 34","abstract":[{"lang":"eng","text":"Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states."}],"issue":"06","type":"journal_article","conference":{"end_date":"2020-02-12","location":"New York, NY, United States","start_date":"2020-02-07","name":"AAAI: Conference on Artificial Intelligence"},"doi":"10.1609/aaai.v34i06.6531","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2002.12086","open_access":"1"}],"external_id":{"arxiv":["2002.12086"]},"quality_controlled":"1","project":[{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"month":"04","publication_identifier":{"issn":["2374-3468"]},"author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Novotný","first_name":"Petr","full_name":"Novotný, Petr"},{"full_name":"Vahala, Jiří","last_name":"Vahala","first_name":"Jiří"}],"date_updated":"2024-03-04T08:30:16Z","date_created":"2024-03-04T08:07:22Z","volume":34,"acknowledgement":"Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala are supported by the Czech Science Foundation grant No. GJ19-15134Y.","year":"2020","publication_status":"published","publisher":"Association for the Advancement of Artificial Intelligence","department":[{"_id":"KrCh"}]},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-07-01T00:00:00Z","article_type":"original","publication":"Science Advances","citation":{"ista":"Park S, Artan M, Han SH, Park H-EH, Jung Y, Hwang AB, Shin WS, Kim K-T, Lee S-JV. 2020. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 6(27), aaw7824.","ieee":"S. Park et al., “VRK-1 extends life span by activation of AMPK via phosphorylation,” Science Advances, vol. 6, no. 27. American Association for the Advancement of Science, 2020.","apa":"Park, S., Artan, M., Han, S. H., Park, H.-E. H., Jung, Y., Hwang, A. B., … Lee, S.-J. V. (2020). VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw7824","ama":"Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 2020;6(27). doi:10.1126/sciadv.aaw7824","chicago":"Park, Sangsoon, Murat Artan, Seung Hyun Han, Hae-Eun H. Park, Yoonji Jung, Ara B. Hwang, Won Sik Shin, Kyong-Tai Kim, and Seung-Jae V. Lee. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.aaw7824.","mla":"Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances, vol. 6, no. 27, aaw7824, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.aaw7824.","short":"S. Park, M. Artan, S.H. Han, H.-E.H. Park, Y. Jung, A.B. Hwang, W.S. Shin, K.-T. Kim, S.-J.V. Lee, Science Advances 6 (2020)."},"abstract":[{"lang":"eng","text":"Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans."}],"issue":"27","type":"journal_article","file":[{"content_type":"application/pdf","file_size":1864415,"creator":"dernst","file_name":"2020_ScienceAdvances_Park.pdf","access_level":"open_access","date_updated":"2024-03-04T09:46:41Z","date_created":"2024-03-04T09:46:41Z","checksum":"a37157cd0de709dce5fe03f4a31cd0b6","success":1,"relation":"main_file","file_id":"15058"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"VRK-1 extends life span by activation of AMPK via phosphorylation","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15057","month":"07","publication_identifier":{"eissn":["2375-2548"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.aaw7824","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2024-03-04T09:46:41Z","article_number":"aaw7824","date_created":"2024-03-04T09:41:57Z","date_updated":"2024-03-04T09:52:09Z","volume":6,"author":[{"full_name":"Park, Sangsoon","last_name":"Park","first_name":"Sangsoon"},{"orcid":"0000-0001-8945-6992","id":"C407B586-6052-11E9-B3AE-7006E6697425","last_name":"Artan","first_name":"Murat","full_name":"Artan, Murat"},{"full_name":"Han, Seung Hyun","last_name":"Han","first_name":"Seung Hyun"},{"last_name":"Park","first_name":"Hae-Eun H.","full_name":"Park, Hae-Eun H."},{"last_name":"Jung","first_name":"Yoonji","full_name":"Jung, Yoonji"},{"full_name":"Hwang, Ara B.","first_name":"Ara B.","last_name":"Hwang"},{"last_name":"Shin","first_name":"Won Sik","full_name":"Shin, Won Sik"},{"full_name":"Kim, Kyong-Tai","last_name":"Kim","first_name":"Kyong-Tai"},{"full_name":"Lee, Seung-Jae V.","first_name":"Seung-Jae V.","last_name":"Lee"}],"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"MaDe"}],"year":"2020","acknowledgement":"This research was supported by grants NRF-2019R1A3B2067745 and NRF-2017R1A5A1015366 funded by the Korean Government (MSIT) through the National Research Foundation (NRF) of Korea to S.-J.V.L. and by grant Basic Science Research Program (No. 2019R1A2C2009440) funded by the Korean Government (MSIT) through the NRF of Korea to K.-T.K. "},{"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.191726911","open_access":"1"}],"oa":1,"external_id":{"pmid":["32848067"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.1073/pnas.1917269117","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"09","department":[{"_id":"CaBe"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","pmid":1,"acknowledgement":"We thank the staff of the macromolecular crystallography (MX) and SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss Light Source for excellent support, and the Life Sciences Facility of the Institute of Science and Technology Austria for usage of the rheometer. We thank Life Sciences editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423), Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF) Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R. ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I 2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological Macromolecules. M.B. acknowledges the University Grant Commission, India, for a senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science Engineering Research Council. ","year":"2020","volume":117,"date_updated":"2024-03-04T10:14:44Z","date_created":"2024-03-04T10:03:52Z","author":[{"full_name":"Pinotsis, Nikos","last_name":"Pinotsis","first_name":"Nikos"},{"full_name":"Zielinska, Karolina","first_name":"Karolina","last_name":"Zielinska"},{"last_name":"Babuta","first_name":"Mrigya","full_name":"Babuta, Mrigya"},{"first_name":"Joan L.","last_name":"Arolas","full_name":"Arolas, Joan L."},{"full_name":"Kostan, Julius","first_name":"Julius","last_name":"Kostan"},{"full_name":"Khan, Muhammad Bashir","last_name":"Khan","first_name":"Muhammad Bashir"},{"last_name":"Schreiner","first_name":"Claudia","full_name":"Schreiner, Claudia"},{"full_name":"Testa Salmazo, Anita P","first_name":"Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luciano","last_name":"Ciccarelli","full_name":"Ciccarelli, Luciano"},{"full_name":"Puchinger, Martin","last_name":"Puchinger","first_name":"Martin"},{"full_name":"Gkougkoulia, Eirini A.","first_name":"Eirini A.","last_name":"Gkougkoulia"},{"full_name":"Ribeiro, Euripedes de Almeida","first_name":"Euripedes de Almeida","last_name":"Ribeiro"},{"last_name":"Marlovits","first_name":"Thomas C.","full_name":"Marlovits, Thomas C."},{"first_name":"Alok","last_name":"Bhattacharya","full_name":"Bhattacharya, Alok"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"}],"page":"22101-22112","article_type":"original","citation":{"ama":"Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117","ieee":"N. Pinotsis et al., “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020.","apa":"Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M. B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1917269117","ista":"Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A, Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 117(36), 22101–22112.","short":"N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan, C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia, E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings of the National Academy of Sciences 117 (2020) 22101–22112.","mla":"Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.","chicago":"Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2020-09-08T00:00:00Z","article_processing_charge":"No","day":"08","intvolume":" 117","title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15061","oa_version":"Published Version","type":"journal_article","issue":"36","abstract":[{"text":"The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.","lang":"eng"}]},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"year":"2020","acknowledgement":"This research has been supported by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”, by Polish MNiSzW Grant No. 2621/7.PR/12/2013/2, by the Polish National Science Center under Maestro Grant No. 2014/14/A/ST1/00453 and Grant No. DEC-2013/09/N/ST6/02995. Open Access funding provided by Projekt DEAL.","date_updated":"2024-03-04T10:54:04Z","date_created":"2024-03-04T10:47:49Z","volume":4,"author":[{"full_name":"Bauer, U.","last_name":"Bauer","first_name":"U."},{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"full_name":"Jablonski, Grzegorz","last_name":"Jablonski","first_name":"Grzegorz","orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mrozek","first_name":"M.","full_name":"Mrozek, M."}],"file_date_updated":"2024-03-04T10:52:42Z","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1007/s41468-020-00058-8","month":"12","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"ddc":["500"],"status":"public","title":"Čech-Delaunay gradient flow and homology inference for self-maps","intvolume":" 4","_id":"15064","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"15065","relation":"main_file","success":1,"checksum":"eed1168b6e66cd55272c19bb7fca8a1c","date_created":"2024-03-04T10:52:42Z","date_updated":"2024-03-04T10:52:42Z","access_level":"open_access","file_name":"2020_JourApplCompTopology_Bauer.pdf","creator":"dernst","content_type":"application/pdf","file_size":851190}],"type":"journal_article","abstract":[{"lang":"eng","text":"We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspaces of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for Čech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive Čech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems."}],"issue":"4","article_type":"original","page":"455-480","publication":"Journal of Applied and Computational Topology","citation":{"ama":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 2020;4(4):455-480. doi:10.1007/s41468-020-00058-8","apa":"Bauer, U., Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2020). Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00058-8","ieee":"U. Bauer, H. Edelsbrunner, G. Jablonski, and M. Mrozek, “Čech-Delaunay gradient flow and homology inference for self-maps,” Journal of Applied and Computational Topology, vol. 4, no. 4. Springer Nature, pp. 455–480, 2020.","ista":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. 2020. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 4(4), 455–480.","short":"U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and Computational Topology 4 (2020) 455–480.","mla":"Bauer, U., et al. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology, vol. 4, no. 4, Springer Nature, 2020, pp. 455–80, doi:10.1007/s41468-020-00058-8.","chicago":"Bauer, U., Herbert Edelsbrunner, Grzegorz Jablonski, and M. Mrozek. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology. Springer Nature, 2020. https://doi.org/10.1007/s41468-020-00058-8."},"date_published":"2020-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"publication_identifier":{"issn":["2690-1005","2690-0998"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.2140/pmp.2020.1.101","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","external_id":{"arxiv":["1908.01653"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1908.01653","open_access":"1"}],"oa":1,"ec_funded":1,"volume":1,"date_created":"2024-03-04T10:27:57Z","date_updated":"2024-03-04T10:33:15Z","author":[{"full_name":"Cipolloni, Giorgio","first_name":"Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"}],"department":[{"_id":"LaEr"}],"publisher":"Mathematical Sciences Publishers","publication_status":"published","acknowledgement":"Partially supported by ERC Advanced Grant No. 338804. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 66538","year":"2020","article_processing_charge":"No","day":"16","keyword":["General Medicine"],"scopus_import":"1","date_published":"2020-11-16T00:00:00Z","page":"101-146","article_type":"original","citation":{"ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal lower bound on the least singular value of the shifted Ginibre ensemble,” Probability and Mathematical Physics, vol. 1, no. 1. Mathematical Sciences Publishers, pp. 101–146, 2020.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2020). Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2020.1.101","ista":"Cipolloni G, Erdös L, Schröder DJ. 2020. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 1(1), 101–146.","ama":"Cipolloni G, Erdös L, Schröder DJ. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 2020;1(1):101-146. doi:10.2140/pmp.2020.1.101","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/pmp.2020.1.101.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability and Mathematical Physics 1 (2020) 101–146.","mla":"Cipolloni, Giorgio, et al. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics, vol. 1, no. 1, Mathematical Sciences Publishers, 2020, pp. 101–46, doi:10.2140/pmp.2020.1.101."},"publication":"Probability and Mathematical Physics","issue":"1","abstract":[{"text":"We consider the least singular value of a large random matrix with real or complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal lower tail estimate on this singular value in the critical regime where z is around the spectral edge, thus improving the classical bound of Sankar, Spielman and Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395).","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 1","title":"Optimal lower bound on the least singular value of the shifted Ginibre ensemble","status":"public","_id":"15063","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.DISC.2020.40","conference":{"end_date":"2020-10-16","location":"Virtual","start_date":"2020-10-12","name":"DISC: Symposium on Distributed Computing"},"quality_controlled":"1","tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2005.07761"]},"oa":1,"month":"10","volume":179,"date_updated":"2024-03-05T07:13:13Z","date_created":"2024-03-05T07:09:12Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"9678"}]},"author":[{"full_name":"Brandt, Sebastian","last_name":"Brandt","first_name":"Sebastian"},{"full_name":"Keller, Barbara","last_name":"Keller","first_name":"Barbara"},{"first_name":"Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"},{"full_name":"Uitto, Jara","last_name":"Uitto","first_name":"Jara"}],"department":[{"_id":"DaAl"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2020","license":"https://creativecommons.org/licenses/by/3.0/","file_date_updated":"2024-03-05T07:08:27Z","article_number":"40","date_published":"2020-10-07T00:00:00Z","citation":{"ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Brief announcement: Efficient load-balancing through distributed token dropping. In: 34th International Symposium on Distributed Computing. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.DISC.2020.40","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2020. Brief announcement: Efficient load-balancing through distributed token dropping. 34th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 179, 40.","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2020). Brief announcement: Efficient load-balancing through distributed token dropping. In 34th International Symposium on Distributed Computing (Vol. 179). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2020.40","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement: Efficient load-balancing through distributed token dropping,” in 34th International Symposium on Distributed Computing, Virtual, 2020, vol. 179.","mla":"Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” 34th International Symposium on Distributed Computing, vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.DISC.2020.40.","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, 34th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” In 34th International Symposium on Distributed Computing, Vol. 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.DISC.2020.40."},"publication":"34th International Symposium on Distributed Computing","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","file":[{"relation":"main_file","file_id":"15075","checksum":"23e2d9321aef53092dc1e24a8ab82d72","success":1,"date_created":"2024-03-05T07:08:27Z","date_updated":"2024-03-05T07:08:27Z","access_level":"open_access","file_name":"2020_LIPIcs_Brandt.pdf","file_size":303529,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","intvolume":" 179","status":"public","ddc":["000"],"title":"Brief announcement: Efficient load-balancing through distributed token dropping","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15074","abstract":[{"lang":"eng","text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds."}],"alternative_title":["LIPIcs"],"type":"conference"},{"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"oa":1,"tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2003.09297"]},"language":[{"iso":"eng"}],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2020-07-08","location":"Saarbrücken, Germany, Virtual","end_date":"2020-07-11"},"doi":"10.4230/LIPIcs.ICALP.2020.7","month":"06","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"DaAl"}],"year":"2020","acknowledgement":"The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier\r\nversions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments.\r\nFunding: European Research Council funding award PR1042ERC01","date_updated":"2024-03-05T07:35:53Z","date_created":"2024-03-05T07:25:37Z","volume":168,"author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"first_name":"Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi"},{"full_name":"Sabour, Amirmojtaba","first_name":"Amirmojtaba","last_name":"Sabour","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67"}],"related_material":{"record":[{"id":"8286","relation":"later_version","status":"public"}]},"article_number":"7","file_date_updated":"2024-03-05T07:25:15Z","ec_funded":1,"publication":"47th International Colloquium on Automata, Languages, and Programming","citation":{"ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. In: 47th International Colloquium on Automata, Languages, and Programming. Vol 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ICALP.2020.7","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” in 47th International Colloquium on Automata, Languages, and Programming, Saarbrücken, Germany, Virtual, 2020, vol. 168.","apa":"Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2020). Dynamic averaging load balancing on cycles. In 47th International Colloquium on Automata, Languages, and Programming (Vol. 168). Saarbrücken, Germany, Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2020.7","ista":"Alistarh D-A, Nadiradze G, Sabour A. 2020. Dynamic averaging load balancing on cycles. 47th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 168, 7.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, in:, 47th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” 47th International Colloquium on Automata, Languages, and Programming, vol. 168, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ICALP.2020.7.","chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” In 47th International Colloquium on Automata, Languages, and Programming, Vol. 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ICALP.2020.7."},"date_published":"2020-06-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"No","has_accepted_license":"1","title":"Dynamic averaging load balancing on cycles","ddc":["000"],"status":"public","intvolume":" 168","_id":"15077","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"15078","checksum":"e5eb16199f4ccfd77a321977eb3f026f","success":1,"date_updated":"2024-03-05T07:25:15Z","date_created":"2024-03-05T07:25:15Z","access_level":"open_access","file_name":"2020_LIPIcs_Alistarh.pdf","content_type":"application/pdf","file_size":782987,"creator":"dernst"}],"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor.","lang":"eng"}]},{"abstract":[{"text":"Two plane drawings of geometric graphs on the same set of points are called disjoint compatible if their union is plane and they do not have an edge in common. For a given set S of 2n points two plane drawings of perfect matchings M1 and M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible if there exists a plane drawing of a spanning tree T on S which is disjoint compatible to both M1 and M2.\r\nWe show that the graph of all disjoint tree-compatible perfect geometric matchings on 2n points in convex position is connected if and only if 2n ≥ 10. Moreover, in that case the diameter\r\nof this graph is either 4 or 5, independent of n.","lang":"eng"}],"article_number":"56","type":"conference","date_updated":"2024-03-05T09:00:07Z","date_created":"2024-03-05T08:57:17Z","oa_version":"Published Version","author":[{"full_name":"Aichholzer, Oswin","first_name":"Oswin","last_name":"Aichholzer"},{"first_name":"Julia","last_name":"Obmann","full_name":"Obmann, Julia"},{"full_name":"Patak, Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83","first_name":"Pavel","last_name":"Patak"},{"first_name":"Daniel","last_name":"Perz","full_name":"Perz, Daniel"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"}],"status":"public","title":"Disjoint tree-compatible plane perfect matchings","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"UlWa"}],"_id":"15082","year":"2020","acknowledgement":"Research on this work was initiated at the 6th Austrian-Japanese-Mexican-Spanish Workshop on Discrete Geometry and continued during the 16th European Geometric Graph-Week, both held near Strobl, Austria. We are grateful to the participants for the inspiring atmosphere. We especially thank Alexander Pilz for bringing this class of problems to our attention and Birgit Vogtenhuber for inspiring discussions. D.P. is partially supported by the FWF grant I 3340-N35 (Collaborative DACH project Arrangements and Drawings). The research stay of P.P. at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement of internationalization in the field of research and development at Charles University, through the support of quality projects MSCA-IF. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 734922.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","month":"04","article_processing_charge":"No","language":[{"iso":"eng"}],"conference":{"name":"EuroCG: European Workshop on Computational Geometry","end_date":"2020-03-18","start_date":"2020-03-16","location":"Würzburg, Germany, Virtual"},"date_published":"2020-04-01T00:00:00Z","quality_controlled":"1","publication":"36th European Workshop on Computational Geometry","main_file_link":[{"url":"https://www1.pub.informatik.uni-wuerzburg.de/eurocg2020/data/uploads/papers/eurocg20_paper_56.pdf","open_access":"1"}],"oa":1,"citation":{"apa":"Aichholzer, O., Obmann, J., Patak, P., Perz, D., & Tkadlec, J. (2020). Disjoint tree-compatible plane perfect matchings. In 36th European Workshop on Computational Geometry. Würzburg, Germany, Virtual.","ieee":"O. Aichholzer, J. Obmann, P. Patak, D. Perz, and J. Tkadlec, “Disjoint tree-compatible plane perfect matchings,” in 36th European Workshop on Computational Geometry, Würzburg, Germany, Virtual, 2020.","ista":"Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. 2020. Disjoint tree-compatible plane perfect matchings. 36th European Workshop on Computational Geometry. EuroCG: European Workshop on Computational Geometry, 56.","ama":"Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. Disjoint tree-compatible plane perfect matchings. In: 36th European Workshop on Computational Geometry. ; 2020.","chicago":"Aichholzer, Oswin, Julia Obmann, Pavel Patak, Daniel Perz, and Josef Tkadlec. “Disjoint Tree-Compatible Plane Perfect Matchings.” In 36th European Workshop on Computational Geometry, 2020.","short":"O. Aichholzer, J. Obmann, P. Patak, D. Perz, J. Tkadlec, in:, 36th European Workshop on Computational Geometry, 2020.","mla":"Aichholzer, Oswin, et al. “Disjoint Tree-Compatible Plane Perfect Matchings.” 36th European Workshop on Computational Geometry, 56, 2020."}},{"language":[{"iso":"eng"}],"doi":"10.1214/20-AOS1945","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.01375"}],"oa":1,"external_id":{"isi":["000598369200021"],"arxiv":["1901.01375"]},"publication_identifier":{"eissn":["1941-7330"],"issn":["1932-6157"]},"month":"12","volume":48,"date_created":"2019-07-31T09:39:42Z","date_updated":"2024-03-06T08:28:50Z","author":[{"full_name":"Javanmard, Adel","first_name":"Adel","last_name":"Javanmard"},{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco"},{"full_name":"Montanari, Andrea","last_name":"Montanari","first_name":"Andrea"}],"publisher":"Institute of Mathematical Statistics","department":[{"_id":"MaMo"}],"publication_status":"published","year":"2020","date_published":"2020-12-11T00:00:00Z","page":"3619-3642","article_type":"original","citation":{"mla":"Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” Annals of Statistics, vol. 48, no. 6, Institute of Mathematical Statistics, 2020, pp. 3619–42, doi:10.1214/20-AOS1945.","short":"A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.","chicago":"Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” Annals of Statistics. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-AOS1945.","ama":"Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 2020;48(6):3619-3642. doi:10.1214/20-AOS1945","ista":"Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 48(6), 3619–3642.","apa":"Javanmard, A., Mondelli, M., & Montanari, A. (2020). Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/20-AOS1945","ieee":"A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural network via displacement convexity,” Annals of Statistics, vol. 48, no. 6. Institute of Mathematical Statistics, pp. 3619–3642, 2020."},"publication":"Annals of Statistics","article_processing_charge":"No","day":"11","oa_version":"Preprint","intvolume":" 48","title":"Analysis of a two-layer neural network via displacement convexity","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6748","issue":"6","abstract":[{"lang":"eng","text":"Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.\r\nHere we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge."}],"type":"journal_article"},{"month":"06","publication_identifier":{"eissn":["20545703"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000545625200001"],"arxiv":["1910.12042"]},"quality_controlled":"1","isi":1,"doi":"10.1098/rsos.200599","language":[{"iso":"eng"}],"article_number":"200599","file_date_updated":"2020-11-09T09:07:11Z","acknowledgement":"V.K. thanks the German National Academic Foundation (Studienstiftung des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork (PB.net), the Earth League’s EarthDoc program and the European Research Council Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements. This work has been performed in the context of the copan collaboration and the FutureLab on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments by N. Wunderling, J. Heitzig and M. Wiedermann.","year":"2020","publication_status":"published","publisher":"The Royal Society","department":[{"_id":"MiLe"}],"author":[{"first_name":"Ann Kristin","last_name":"Klose","full_name":"Klose, Ann Kristin"},{"full_name":"Karle, Volker","first_name":"Volker","last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","orcid":"0000-0002-6963-0129"},{"last_name":"Winkelmann","first_name":"Ricarda","full_name":"Winkelmann, Ricarda"},{"full_name":"Donges, Jonathan F.","first_name":"Jonathan F.","last_name":"Donges"}],"date_created":"2020-11-08T23:01:25Z","date_updated":"2024-03-12T12:31:30Z","volume":7,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Royal Society Open Science","citation":{"ama":"Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 2020;7(6). doi:10.1098/rsos.200599","ista":"Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 7(6), 200599.","ieee":"A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements,” Royal Society Open Science, vol. 7, no. 6. The Royal Society, 2020.","apa":"Klose, A. K., Karle, V., Winkelmann, R., & Donges, J. F. (2020). Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.200599","mla":"Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science, vol. 7, no. 6, 200599, The Royal Society, 2020, doi:10.1098/rsos.200599.","short":"A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science 7 (2020).","chicago":"Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F. Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science. The Royal Society, 2020. https://doi.org/10.1098/rsos.200599."},"article_type":"original","date_published":"2020-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In ecology, climate and other fields, (sub)systems have been identified that can transition into a qualitatively different state when a critical threshold or tipping point in a driving process is crossed. An understanding of those tipping elements is of great interest given the increasing influence of humans on the biophysical Earth system. Complex interactions exist between tipping elements, e.g. physical mechanisms connect subsystems of the climate system. Based on earlier work on such coupled nonlinear systems, we systematically assessed the qualitative long-term behaviour of interacting tipping elements. We developed an understanding of the consequences of interactions\r\non the tipping behaviour allowing for tipping cascades to emerge under certain conditions. The (narrative) application of\r\nthese qualitative results to real-world examples of interacting tipping elements indicates that tipping cascades with profound consequences may occur: the interacting Greenland ice sheet and thermohaline ocean circulation might tip before the tipping points of the isolated subsystems are crossed. The eutrophication of the first lake in a lake chain might propagate through the following lakes without a crossing of their individual critical nutrient input levels. The possibility of emerging cascading tipping dynamics calls for the development of a unified theory of interacting tipping elements and the quantitative analysis of interacting real-world tipping elements."}],"issue":"6","_id":"8741","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530","550"],"title":"Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements","status":"public","intvolume":" 7","oa_version":"Published Version","file":[{"file_name":"2020_RoyalSocOpenScience_Klose.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1611485,"file_id":"8748","relation":"main_file","date_created":"2020-11-09T09:07:11Z","date_updated":"2020-11-09T09:07:11Z","success":1,"checksum":"5505c445de373bfd836eb4d3b48b1f37"}]},{"date_published":"2020-04-28T00:00:00Z","page":"46-59","article_type":"original","citation":{"ama":"Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(1):46-59. doi:10.31263/voebm.v73i1.3491","ista":"Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59.","ieee":"D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 46–59, 2020.","apa":"Ernst, D., Novotny, G., & Schönher, E. M. (2020). (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i1.3491","mla":"Ernst, Doris, et al. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 46–59, doi:10.31263/voebm.v73i1.3491.","short":"D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 46–59.","chicago":"Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i1.3491."},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","has_accepted_license":"1","article_processing_charge":"No","day":"28","scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2024-03-12T10:12:33Z","date_created":"2020-06-17T10:50:13Z","checksum":"fee784f15a489deb7def6ccf8c5bf8c3","relation":"main_file","file_id":"7970","file_size":579291,"content_type":"application/pdf","creator":"dernst","file_name":"2020_VOEB_Ernst.pdf","access_level":"open_access"}],"popular_science":"1","intvolume":" 73","status":"public","ddc":["020"],"title":"(Core Trust) Seal your repository!","_id":"7687","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","abstract":[{"text":"A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested.","lang":"eng"},{"lang":"ger","text":" Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen (RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür wurden jenen Organisationen, die in Österreich bereits mit CTS zertifiziert sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die Entwicklung einer DINI-Zertifizierung in Österreich."}],"type":"journal_article","language":[{"iso":"ger"}],"doi":"10.31263/voebm.v73i1.3491","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["1022-2588"]},"month":"04","volume":73,"date_created":"2020-04-28T08:37:38Z","date_updated":"2024-03-12T10:12:33Z","author":[{"first_name":"Doris","last_name":"Ernst","id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2354-0195","full_name":"Ernst, Doris"},{"last_name":"Novotny","first_name":"Gertraud","full_name":"Novotny, Gertraud"},{"full_name":"Schönher, Eva Maria","last_name":"Schönher","first_name":"Eva Maria"}],"department":[{"_id":"E-Lib"}],"publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","publication_status":"published","year":"2020","file_date_updated":"2024-03-12T10:12:33Z"},{"month":"11","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.3390/ecm2020-07116","conference":{"name":"ECM: Electronic Conference on Microbiology","end_date":"2020-11-30","start_date":"2020-11-02","location":"Virtual"},"language":[{"iso":"eng"}],"file_date_updated":"2024-03-20T08:05:46Z","acknowledgement":"The work was supported by of Russian Foundation of Basic Research: grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334 for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST, Austria) for their help in obtaining the genomic sequence of strain JL01. ","year":"2020","publisher":"MDPI","department":[{"_id":"FyKo"}],"publication_status":"published","author":[{"last_name":"Oshurkova","first_name":"Viktoriia","full_name":"Oshurkova, Viktoriia"},{"last_name":"Troshina","first_name":"Olga","full_name":"Troshina, Olga"},{"first_name":"Vladimir","last_name":"Trubitsyn","full_name":"Trubitsyn, Vladimir"},{"full_name":"Ryzhmanova, Yana","first_name":"Yana","last_name":"Ryzhmanova"},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga"},{"first_name":"Viktoria","last_name":"Shcherbakova","full_name":"Shcherbakova, Viktoria"}],"date_created":"2024-03-04T11:41:31Z","date_updated":"2024-03-20T08:06:22Z","article_processing_charge":"Yes","has_accepted_license":"1","day":"02","citation":{"mla":"Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020, doi:10.3390/ecm2020-07116.","short":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V. Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020.","chicago":"Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In Proceedings of 1st International Electronic Conference on Microbiology. MDPI, 2020. https://doi.org/10.3390/ecm2020-07116.","ama":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In: Proceedings of 1st International Electronic Conference on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116","ista":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology. ECM: Electronic Conference on Microbiology.","apa":"Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O., & Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In Proceedings of 1st International Electronic Conference on Microbiology. Virtual: MDPI. https://doi.org/10.3390/ecm2020-07116","ieee":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T,” in Proceedings of 1st International Electronic Conference on Microbiology, Virtual, 2020."},"publication":"Proceedings of 1st International Electronic Conference on Microbiology","date_published":"2020-11-02T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic [1]. After long-term extensive cultivation at 15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and grew on methanol, acetate and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive. Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M.mazei was 98.5%, which is higher than the values recommended for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation of JL01 with S. associata GLS2T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative genes involved in methanochondroithin catabolism."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15071","title":"Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"date_updated":"2024-03-20T08:05:46Z","date_created":"2024-03-20T08:05:46Z","success":1,"checksum":"d1914af7811a21a4b2744eb51b5834e3","file_id":"15127","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":595543,"file_name":"2020_ECM_Oshurkova.pdf","access_level":"open_access"}]},{"abstract":[{"text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"embargo":"2021-02-28","file_id":"7538","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","relation":"main_file","checksum":"4589234fdb12b4ad72273b311723a7b4","date_updated":"2021-03-01T23:30:04Z","date_created":"2020-02-28T08:37:53Z","access_level":"open_access","file_name":"Pradeep Bhandari Thesis.pdf","creator":"pbhandari","content_type":"application/pdf","file_size":9646346},{"access_level":"closed","file_name":"Pradeep Bhandari Thesis.docx","embargo_to":"open_access","creator":"pbhandari","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":35252164,"title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file_id":"7539","relation":"source_file","checksum":"aa79490553ca0a5c9b6fbcd152e93928","date_created":"2020-02-28T08:47:14Z","date_updated":"2021-03-01T23:30:04Z"}],"oa_version":"Published Version","status":"public","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7525","has_accepted_license":"1","article_processing_charge":"No","day":"28","keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"date_published":"2020-02-28T00:00:00Z","page":"79","citation":{"ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020.","apa":"Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7525","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria.","ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525","chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525.","short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020.","mla":"Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7525."},"file_date_updated":"2021-03-01T23:30:04Z","date_updated":"2023-09-07T13:20:03Z","date_created":"2020-02-26T10:56:37Z","author":[{"full_name":"Bhandari, Pradeep","last_name":"Bhandari","first_name":"Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","publication_identifier":{"issn":["2663-337X"]},"month":"02","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7525","oa":1},{"date_published":"2020-12-01T00:00:00Z","publication":"Journal of Structural Biology","citation":{"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,” Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020.","apa":"Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633","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.","ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633","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.” Journal of Structural Biology. Elsevier, 2020. https://doi.org/10.1016/j.jsb.2020.107633.","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.” Journal of Structural Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633."},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"file":[{"file_size":7076870,"content_type":"application/pdf","creator":"dernst","file_name":"2020_JourStrucBiology_Faessler.pdf","access_level":"open_access","date_created":"2020-12-10T14:01:10Z","date_updated":"2020-12-10T14:01:10Z","checksum":"c48cbf594e84fc2f91966ffaafc0918c","success":1,"relation":"main_file","file_id":"8937"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8586","status":"public","ddc":["570"],"title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","intvolume":" 212","abstract":[{"lang":"eng","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."}],"issue":"3","type":"journal_article","doi":"10.1016/j.jsb.2020.107633","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000600997800008"]},"isi":1,"quality_controlled":"1","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"month":"12","publication_identifier":{"issn":["1047-8477"]},"author":[{"last_name":"Fäßler","first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian"},{"full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","first_name":"Bettina","last_name":"Zens"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"related_material":{"record":[{"id":"14592","status":"public","relation":"used_in_publication"},{"status":"public","relation":"dissertation_contains","id":"12491"}]},"date_created":"2020-09-29T13:24:06Z","date_updated":"2024-03-28T23:30:05Z","volume":212,"year":"2020","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.","publication_status":"published","publisher":"Elsevier","department":[{"_id":"FlSc"}],"file_date_updated":"2020-12-10T14:01:10Z","article_number":"107633"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation."}],"title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","ddc":["571","530","570"],"status":"public","_id":"8657","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":52636162,"content_type":"application/pdf","creator":"bkavcic","access_level":"open_access","file_name":"kavcicB_thesis202009.pdf","checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb","date_updated":"2021-10-07T22:30:03Z","date_created":"2020-10-15T06:41:20Z","relation":"main_file","file_id":"8663","embargo":"2021-10-06"},{"embargo_to":"open_access","file_name":"2020b.zip","access_level":"closed","file_size":321681247,"content_type":"application/zip","creator":"bkavcic","relation":"source_file","file_id":"8664","date_updated":"2021-10-07T22:30:03Z","date_created":"2020-10-15T06:41:53Z","checksum":"bb35f2352a04db19164da609f00501f3"}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"14","page":"271","citation":{"chicago":"Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.","mla":"Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.","apa":"Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657","ieee":"B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.","ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria.","ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657"},"date_published":"2020-10-14T00:00:00Z","file_date_updated":"2021-10-07T22:30:03Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"publication_status":"published","acknowledgement":"I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop.","year":"2020","date_created":"2020-10-13T16:46:14Z","date_updated":"2023-09-07T13:20:48Z","related_material":{"record":[{"id":"7673","status":"public","relation":"part_of_dissertation"},{"id":"8250","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor"}],"publication_identifier":{"isbn":["978-3-99078-011-4"],"issn":["2663-337X"]},"month":"10","oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"supervisor":[{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8657"},{"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"11196"}]},"author":[{"first_name":"Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina"},{"full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","first_name":"Olena"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"volume":105,"date_created":"2020-02-10T15:59:45Z","date_updated":"2024-03-28T23:30:07Z","pmid":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement No. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","year":"2020","publisher":"Elsevier","department":[{"_id":"PeJo"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-11-20T08:58:53Z","doi":"10.1016/j.neuron.2019.12.022","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["31928842"],"isi":["000520854700008"]},"oa":1,"project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","grant_number":"708497","call_identifier":"H2020","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","grant_number":"W01205"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0896-6273"]},"month":"03","file":[{"checksum":"3582664addf26859e86ac5bec3e01416","success":1,"date_updated":"2020-11-20T08:58:53Z","date_created":"2020-11-20T08:58:53Z","relation":"main_file","file_id":"8778","file_size":9712957,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_Neuron_BorgesMerjane.pdf"}],"oa_version":"Published Version","_id":"7473","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 105","status":"public","title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","ddc":["570"],"abstract":[{"text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses.","lang":"eng"}],"type":"journal_article","date_published":"2020-03-18T00:00:00Z","citation":{"mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron, vol. 105, Elsevier, 2020, pp. 992–1006, doi:10.1016/j.neuron.2019.12.022.","short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2019.12.022.","ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 2020;105:992-1006. doi:10.1016/j.neuron.2019.12.022","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006.","ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” Neuron, vol. 105. Elsevier, pp. 992–1006, 2020.","apa":"Borges Merjane, C., Kim, O., & Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.12.022"},"publication":"Neuron","page":"992-1006","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1"},{"month":"08","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-17734-z","quality_controlled":"1","isi":1,"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000562769300008"]},"oa":1,"file_date_updated":"2020-08-17T07:36:57Z","article_number":"4013","date_created":"2020-08-12T09:13:50Z","date_updated":"2024-03-28T23:30:08Z","volume":11,"author":[{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor","full_name":"Kavcic, Bor"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"full_name":"Bollenbach, Tobias","last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8657","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaTk"}],"year":"2020","acknowledgement":"We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K. Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support, which rendered this\r\nwork possible. B.K. thanks all members of Guet group for many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work. We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A. Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310 (to T.B.). Open access funding provided by\r\nProjekt DEAL.","day":"11","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-08-11T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ama":"Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17734-z","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).","mla":"Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z."},"abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2020_NatureComm_Kavcic.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1965672,"creator":"dernst","relation":"main_file","file_id":"8275","date_created":"2020-08-17T07:36:57Z","date_updated":"2020-08-17T07:36:57Z","checksum":"986bebb308850a55850028d3d2b5b664","success":1}],"oa_version":"Published Version","title":"Mechanisms of drug interactions between translation-inhibiting antibiotics","ddc":["570"],"status":"public","intvolume":" 11","_id":"8250","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"publication":"bioRxiv","citation":{"ama":"Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.18.047886","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","mla":"Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.18.047886."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.18.047886 "}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1101/2020.04.18.047886","date_published":"2020-04-18T00:00:00Z","day":"18","month":"04","article_processing_charge":"No","status":"public","publication_status":"published","title":"A minimal biophysical model of combined antibiotic action","department":[{"_id":"GaTk"}],"publisher":"Cold Spring Harbor Laboratory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7673","year":"2020","date_created":"2020-04-22T08:27:56Z","date_updated":"2024-03-28T23:30:08Z","oa_version":"Preprint","author":[{"full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias"}],"related_material":{"record":[{"id":"8997","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"8657"}]},"type":"preprint","abstract":[{"lang":"eng","text":"Combining drugs can improve the efficacy of treatments. However, predicting the effect of drug combinations is still challenging. The combined potency of drugs determines the drug interaction, which is classified as synergistic, additive, antagonistic, or suppressive. While probabilistic, non-mechanistic models exist, there is currently no biophysical model that can predict antibiotic interactions. Here, we present a physiologically relevant model of the combined action of antibiotics that inhibit protein synthesis by targeting the ribosome. This model captures the kinetics of antibiotic binding and transport, and uses bacterial growth laws to predict growth in the presence of antibiotic combinations. We find that this biophysical model can produce all drug interaction types except suppression. We show analytically that antibiotics which cannot bind to the ribosome simultaneously generally act as substitutes for one another, leading to additive drug interactions. Previously proposed null expectations for higher-order drug interactions follow as a limiting case of our model. We further extend the model to include the effects of direct physical or allosteric interactions between individual drugs on the ribosome. Notably, such direct interactions profoundly change the combined drug effect, depending on the kinetic parameters of the drugs used. The model makes additional predictions for the effects of resistance genes on drug interactions and for interactions between ribosome-targeting antibiotics and antibiotics with other targets. These findings enhance our understanding of the interplay between drug action and cell physiology and are a key step toward a general framework for predicting drug interactions."}]},{"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000565729700033"],"pmid":["32541049"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1073/pnas.2003346117","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"06","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","pmid":1,"year":"2020","volume":117,"date_updated":"2024-03-28T23:30:10Z","date_created":"2020-06-22T13:33:52Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9992"}],"link":[{"url":"https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926"},{"full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","first_name":"Juan C","last_name":"Montesinos López"},{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá","first_name":"Petra","full_name":"Marhavá, Petra"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"article_number":"202003346","ec_funded":1,"file_date_updated":"2020-07-14T12:48:07Z","article_type":"original","citation":{"ista":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. 2020. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 117(26), 202003346.","ieee":"L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots,” Proceedings of the National Academy of Sciences, vol. 117, no. 26. Proceedings of the National Academy of Sciences, 2020.","apa":"Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S., & Friml, J. (2020). Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2003346117","ama":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 2020;117(26). doi:10.1073/pnas.2003346117","chicago":"Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2003346117.","mla":"Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences, vol. 117, no. 26, 202003346, Proceedings of the National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.","short":"L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J. Friml, Proceedings of the National Academy of Sciences 117 (2020)."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2020-06-30T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"30","intvolume":" 117","title":"Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots","status":"public","ddc":["580"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8002","oa_version":"None","file":[{"checksum":"908b09437680181de9990915f2113aca","date_created":"2020-06-23T11:30:53Z","date_updated":"2020-07-14T12:48:07Z","relation":"main_file","file_id":"8009","content_type":"application/pdf","file_size":2407102,"creator":"dernst","access_level":"open_access","file_name":"2020_PNAS_Hoermayer.pdf"}],"type":"journal_article","issue":"26","abstract":[{"text":"Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity.","lang":"eng"}]},{"abstract":[{"text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"embargo":"2021-10-30","file_id":"7692","relation":"main_file","date_created":"2020-04-28T11:19:21Z","date_updated":"2021-10-31T23:30:05Z","checksum":"fb9a4468eb27be92690728e35c823796","file_name":"Thesis_without-signatures_PDFA.pdf","access_level":"open_access","creator":"stgingl","file_size":3268017,"content_type":"application/pdf"},{"file_size":5167703,"content_type":"application/octet-stream","creator":"stgingl","embargo_to":"open_access","file_name":"Thesis_without signatures.docx","access_level":"closed","date_updated":"2021-10-31T23:30:05Z","date_created":"2020-04-28T11:19:24Z","checksum":"f6c80ca97104a631a328cb79a2c53493","relation":"source_file","file_id":"7693"}],"oa_version":"None","title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","status":"public","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7680","day":"24","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-04-24T00:00:00Z","page":"98","citation":{"ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","apa":"Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","mla":"Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680."},"file_date_updated":"2021-10-31T23:30:05Z","date_created":"2020-04-24T16:00:51Z","date_updated":"2023-09-22T09:20:10Z","author":[{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","first_name":"Stephanie","full_name":"Kainrath, Stephanie"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1028"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"year":"2020","month":"04","publication_identifier":{"eissn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7680","oa":1},{"month":"10","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"supervisor":[{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8620","project":[{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"name":"Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","grant_number":"F07807"}],"oa":1,"file_date_updated":"2021-10-16T22:30:04Z","date_created":"2020-10-07T14:53:13Z","date_updated":"2023-09-07T13:22:14Z","author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Morandell"}],"related_material":{"record":[{"id":"7800","relation":"part_of_dissertation","status":"public"},{"id":"8131","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaNo"}],"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.","year":"2020","day":"12","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-10-12T00:00:00Z","page":"138","citation":{"chicago":"Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620.","mla":"Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620.","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.","apa":"Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620","ieee":"J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020.","ama":"Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. 2020. doi:10.15479/AT:ISTA:8620"},"abstract":[{"lang":"eng","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."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"checksum":"7ee83e42de3e5ce2fedb44dff472f75f","date_created":"2020-10-07T14:41:49Z","date_updated":"2021-10-16T22:30:04Z","embargo":"2021-10-15","file_id":"8621","relation":"main_file","creator":"jmorande","content_type":"application/pdf","file_size":16155786,"access_level":"open_access","file_name":"Jasmin_Morandell_Thesis-2020_final.pdf"},{"access_level":"closed","embargo_to":"open_access","file_name":"Jasmin_Morandell_Thesis-2020_final.zip","content_type":"application/x-zip-compressed","file_size":24344152,"creator":"jmorande","relation":"source_file","file_id":"8622","checksum":"5e0464af453734210ce7aab7b4a92e3a","date_created":"2020-10-07T14:45:07Z","date_updated":"2021-10-16T22:30:04Z"}],"oa_version":"Published Version","ddc":["610"],"title":"Illuminating the role of Cul3 in autism spectrum disorder pathogenesis","status":"public","_id":"8620","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_published":"2020-09-09T00:00:00Z","citation":{"chicago":"Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340.","mla":"Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340.","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","apa":"Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020.","ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:10.15479/AT:ISTA:8340"},"page":"242","day":"09","has_accepted_license":"1","article_processing_charge":"No","oa_version":"None","file":[{"creator":"dkampjut","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":166146359,"access_level":"closed","file_name":"ThesisFull20200908.docx","embargo_to":"open_access","checksum":"dd270baf82121eb4472ad19d77bf227c","date_created":"2020-09-08T13:32:06Z","date_updated":"2021-09-11T22:30:04Z","file_id":"8345","relation":"source_file"},{"content_type":"application/pdf","file_size":13873769,"creator":"dernst","file_name":"2020_Thesis_Kampjut.pdf","access_level":"open_access","date_updated":"2021-09-11T22:30:04Z","date_created":"2020-09-14T15:02:20Z","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c","relation":"main_file","file_id":"8393","embargo":"2021-09-10"}],"_id":"8340","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["572"],"status":"public","title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","abstract":[{"lang":"eng","text":"Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:8340","supervisor":[{"first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"month":"09","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-008-4"]},"author":[{"id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","first_name":"Domen","full_name":"Kampjut, Domen"}],"related_material":{"record":[{"id":"6848","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-07T13:26:17Z","date_created":"2020-09-07T18:42:23Z","year":"2020","acknowledgement":"I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-09-11T22:30:04Z","ec_funded":1},{"publication":"bioRxiv","citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.01.10.902064 .","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer, C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv (n.d.).","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.01.10.902064 .","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. doi:10.1101/2020.01.10.902064 ","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv, 10.1101/2020.01.10.902064 .","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer, C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.01.10.902064 ","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” bioRxiv. Cold Spring Harbor Laboratory."},"date_published":"2020-01-11T00:00:00Z","day":"11","article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"status":"public","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","_id":"7800","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","file":[{"access_level":"open_access","file_name":"2020.01.10.902064v1.full.pdf","content_type":"application/pdf","file_size":2931370,"creator":"rsix","relation":"main_file","file_id":"7801","checksum":"c6799ab5daba80efe8e2ed63c15f8c81","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-05T14:31:19Z"}],"type":"preprint","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization, Cul3 haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development, Cul3 deficiency appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutive Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due to Cul3 functions at early developmental stages.","lang":"eng"}],"project":[{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"acknowledged_ssus":[{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1101/2020.01.10.902064 ","month":"01","publication_status":"submitted","department":[{"_id":"JoDa"},{"_id":"GaNo"},{"_id":"LifeSc"}],"publisher":"Cold Spring Harbor Laboratory","year":"2020","date_updated":"2024-03-28T23:30:14Z","date_created":"2020-05-05T14:31:33Z","author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin"},{"first_name":"Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A"},{"last_name":"Basilico","first_name":"Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette"},{"full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan"},{"full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","first_name":"Armel"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"full_name":"Dobler, Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","first_name":"Zoe","last_name":"Dobler"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"9429"},{"id":"8620","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2020-07-14T12:48:03Z"},{"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2020-12-01T00:00:00Z","article_type":"original","page":"126-137","publication":"Current Opinion in Genetics and Development","citation":{"chicago":"Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms for Targeted ASD Treatments.” Current Opinion in Genetics and Development. Elsevier, 2020. https://doi.org/10.1016/j.gde.2020.06.004.","short":"B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics and Development 65 (2020) 126–137.","mla":"Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.” Current Opinion in Genetics and Development, vol. 65, no. 12, Elsevier, 2020, pp. 126–37, doi:10.1016/j.gde.2020.06.004.","apa":"Basilico, B., Morandell, J., & Novarino, G. (2020). Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2020.06.004","ieee":"B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted ASD treatments,” Current Opinion in Genetics and Development, vol. 65, no. 12. Elsevier, pp. 126–137, 2020.","ista":"Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137.","ama":"Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 2020;65(12):126-137. doi:10.1016/j.gde.2020.06.004"},"abstract":[{"lang":"eng","text":"The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes."}],"issue":"12","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_CurrentOpGenetics_Basilico.pdf","creator":"dernst","content_type":"application/pdf","file_size":1381545,"file_id":"8146","relation":"main_file","success":1,"date_created":"2020-07-22T06:47:45Z","date_updated":"2020-07-22T06:47:45Z"}],"title":"Molecular mechanisms for targeted ASD treatments","status":"public","ddc":["570"],"intvolume":" 65","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8131","month":"12","publication_identifier":{"eissn":["18790380"],"issn":["0959437X"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.gde.2020.06.004","isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"name":"Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","grant_number":"F07807"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000598918900019"],"pmid":["32659636"]},"file_date_updated":"2020-07-22T06:47:45Z","ec_funded":1,"date_created":"2020-07-19T22:00:58Z","date_updated":"2024-03-28T23:30:14Z","volume":65,"author":[{"last_name":"Basilico","first_name":"Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette"},{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Morandell"},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8620"}]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaNo"}],"year":"2020","pmid":1},{"abstract":[{"text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. ","lang":"eng"}],"issue":"7","type":"journal_article","file":[{"access_level":"open_access","file_name":"2020_JournalCellScience_Dimchev.pdf","file_size":13493302,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8435","embargo":"2020-10-10","checksum":"ba917e551acc4ece2884b751434df9ae","date_updated":"2020-10-11T22:30:02Z","date_created":"2020-09-17T14:07:51Z"}],"oa_version":"Published Version","status":"public","title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","ddc":["570"],"intvolume":" 133","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8434","day":"09","article_processing_charge":"No","has_accepted_license":"1","keyword":["Cell Biology"],"date_published":"2020-04-09T00:00:00Z","article_type":"original","publication":"Journal of Cell Science","citation":{"ieee":"G. A. Dimchev et al., “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” Journal of Cell Science, vol. 133, no. 7. The Company of Biologists, 2020.","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.239020","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 2020;133(7). doi:10.1242/jcs.239020","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.239020.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:10.1242/jcs.239020."},"file_date_updated":"2020-10-11T22:30:02Z","article_number":"jcs239020","date_created":"2020-09-17T14:00:33Z","date_updated":"2023-09-05T15:41:48Z","volume":133,"author":[{"full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","first_name":"Georgi A","last_name":"Dimchev"},{"last_name":"Amiri","first_name":"Behnam","full_name":"Amiri, Behnam"},{"full_name":"Humphries, Ashley C.","first_name":"Ashley C.","last_name":"Humphries"},{"full_name":"Schaks, Matthias","first_name":"Matthias","last_name":"Schaks"},{"last_name":"Dimchev","first_name":"Vanessa","full_name":"Dimchev, Vanessa"},{"full_name":"Stradal, Theresia E. B.","last_name":"Stradal","first_name":"Theresia E. B."},{"full_name":"Faix, Jan","first_name":"Jan","last_name":"Faix"},{"full_name":"Krause, Matthias","first_name":"Matthias","last_name":"Krause"},{"first_name":"Michael","last_name":"Way","full_name":"Way, Michael"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"}],"publication_status":"published","publisher":"The Company of Biologists","department":[{"_id":"FlSc"}],"acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","year":"2020","pmid":1,"month":"04","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"language":[{"iso":"eng"}],"doi":"10.1242/jcs.239020","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425","grant_number":"M02495"}],"external_id":{"pmid":[" 32094266"],"isi":["000534387800005"]},"oa":1},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","year":"2020","pmid":1,"date_updated":"2023-09-05T15:30:34Z","date_created":"2020-05-25T15:02:00Z","volume":38,"author":[{"full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana","last_name":"Mitiouchkina"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"full_name":"Gonzalez Somermeyer, Louisa","last_name":"Gonzalez Somermeyer","first_name":"Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nadezhda M.","last_name":"Markina","full_name":"Markina, Nadezhda M."},{"full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V.","last_name":"Chepurnyh"},{"last_name":"Guglya","first_name":"Elena B.","full_name":"Guglya, Elena B."},{"full_name":"Karataeva, Tatiana A.","first_name":"Tatiana A.","last_name":"Karataeva"},{"last_name":"Palkina","first_name":"Kseniia A.","full_name":"Palkina, Kseniia A."},{"last_name":"Shakhova","first_name":"Ekaterina S.","full_name":"Shakhova, Ekaterina S."},{"first_name":"Liliia I.","last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia I."},{"full_name":"Chekova, Sofia V.","last_name":"Chekova","first_name":"Sofia V."},{"full_name":"Tsarkova, Aleksandra S.","last_name":"Tsarkova","first_name":"Aleksandra S."},{"full_name":"Golubev, Yaroslav V.","first_name":"Yaroslav V.","last_name":"Golubev"},{"full_name":"Negrebetsky, Vadim V.","first_name":"Vadim V.","last_name":"Negrebetsky"},{"first_name":"Sergey A.","last_name":"Dolgushin","full_name":"Dolgushin, Sergey A."},{"last_name":"Shalaev","first_name":"Pavel V.","full_name":"Shalaev, Pavel V."},{"last_name":"Shlykov","first_name":"Dmitry","full_name":"Shlykov, Dmitry"},{"full_name":"Melnik, Olesya A.","last_name":"Melnik","first_name":"Olesya A."},{"first_name":"Victoria O.","last_name":"Shipunova","full_name":"Shipunova, Victoria O."},{"first_name":"Sergey M.","last_name":"Deyev","full_name":"Deyev, Sergey M."},{"first_name":"Andrey I.","last_name":"Bubyrev","full_name":"Bubyrev, Andrey I."},{"full_name":"Pushin, Alexander S.","first_name":"Alexander S.","last_name":"Pushin"},{"full_name":"Choob, Vladimir V.","last_name":"Choob","first_name":"Vladimir V."},{"last_name":"Dolgov","first_name":"Sergey V.","full_name":"Dolgov, Sergey V."},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky","first_name":"Ilia V."},{"first_name":"Karen S.","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41587-020-0578-0"}]},"file_date_updated":"2021-03-02T23:30:03Z","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"}],"oa":1,"external_id":{"pmid":["32341562"],"isi":["000529298800003"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41587-020-0500-9","month":"04","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"title":"Plants with genetically encoded autoluminescence","status":"public","ddc":["570"],"intvolume":" 38","_id":"7889","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"8316","embargo":"2021-03-01","relation":"main_file","checksum":"1b30467500ec6277229a875b06e196d0","date_updated":"2021-03-02T23:30:03Z","date_created":"2020-08-28T08:57:07Z","access_level":"open_access","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","creator":"dernst","file_size":1180086,"content_type":"application/pdf"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants.","lang":"eng"}],"article_type":"original","page":"944-946","publication":"Nature Biotechnology","citation":{"apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9","ieee":"T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020.","ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9","chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology. Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9.","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946.","mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9."},"date_published":"2020-04-27T00:00:00Z","scopus_import":"1","day":"27","article_processing_charge":"No","has_accepted_license":"1"},{"doi":"10.1101/2020.11.20.391284","date_published":"2020-11-20T00:00:00Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"SSU"}],"main_file_link":[{"url":"https://doi.org/10.1101/2020.11.20.391284","open_access":"1"}],"citation":{"short":"J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020).","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.11.20.391284.","chicago":"Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.11.20.391284.","ama":"Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. 2020. doi:10.1101/2020.11.20.391284","apa":"Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., & Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.20.391284","ieee":"J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","ista":"Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K, Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv, 10.1101/2020.11.20.391284."},"oa":1,"publication":"bioRxiv","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","grant_number":"187-2013","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension"}],"page":"41","article_processing_charge":"No","day":"20","month":"11","related_material":{"record":[{"id":"10766","relation":"later_version","status":"public"},{"id":"9623","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Slovakova, Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","last_name":"Slovakova","first_name":"Jana"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","first_name":"Silvia","last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia"},{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","last_name":"Huljev","first_name":"Karla"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"oa_version":"Preprint","date_updated":"2024-03-28T23:30:19Z","date_created":"2021-07-29T11:29:50Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9750","acknowledgement":"We would like to thank Edouard Hannezo for discussions, Shayan Shami Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript. We also thank Jack Merrin for preparing the microwells, and the Scientific Service Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC) to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie COFUND No. P_IST_EU01 to J.S.","year":"2020","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publisher":"Cold Spring Harbor Laboratory","status":"public","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion","publication_status":"published","ec_funded":1,"abstract":[{"lang":"eng","text":"Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact."}],"type":"preprint"},{"article_type":"original","citation":{"ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","apa":"Garcia Soto, M., & Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2020.100856","ieee":"M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5. Elsevier, 2020.","ama":"Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 2020;36(5). doi:10.1016/j.nahs.2020.100856","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2020. https://doi.org/10.1016/j.nahs.2020.100856.","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5, 100856, Elsevier, 2020, doi:10.1016/j.nahs.2020.100856.","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020)."},"publication":"Nonlinear Analysis: Hybrid Systems","date_published":"2020-05-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","intvolume":" 36","status":"public","title":"Abstraction based verification of stability of polyhedral switched systems","ddc":["000"],"_id":"7426","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":818774,"creator":"dernst","access_level":"open_access","file_name":"2020_NAHS_GarciaSoto.pdf","checksum":"560abfddb53f9fe921b6744f59f2cfaa","date_updated":"2022-05-16T22:30:04Z","date_created":"2020-10-21T13:16:45Z","relation":"main_file","embargo":"2022-05-15","file_id":"8688"}],"type":"journal_article","issue":"5","abstract":[{"text":"This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method.","lang":"eng"}],"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000528828600003"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.nahs.2020.100856","publication_identifier":{"issn":["1751-570X"]},"month":"05","publisher":"Elsevier","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2020","volume":36,"date_updated":"2023-08-17T14:32:54Z","date_created":"2020-02-02T23:00:59Z","author":[{"id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0003−2936−5719","first_name":"Miriam","last_name":"Garcia Soto","full_name":"Garcia Soto, Miriam"},{"full_name":"Prabhakar, Pavithra","first_name":"Pavithra","last_name":"Prabhakar"}],"article_number":"100856","file_date_updated":"2022-05-16T22:30:04Z"},{"abstract":[{"lang":"eng","text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"access_level":"open_access","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","file_size":10848175,"content_type":"application/pdf","creator":"semtenan","relation":"main_file","embargo":"2021-12-30","file_id":"8984","checksum":"ec2797ab7a6f253b35df0572b36d1b43","date_updated":"2021-12-31T23:30:04Z","date_created":"2020-12-30T15:34:01Z"},{"content_type":"application/pdf","file_size":10073648,"creator":"semtenan","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","checksum":"cc30e6608a9815414024cf548dff3b3a","date_created":"2020-12-30T15:37:36Z","date_updated":"2021-12-31T23:30:04Z","relation":"source_file","file_id":"8985"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8983","status":"public","ddc":["570"],"title":"Metabolic regulation of Drosophila macrophage tissue invasion","day":"30","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-12-30T00:00:00Z","citation":{"ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:10.15479/AT:ISTA:8983","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","apa":"Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983","mla":"Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983.","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983."},"page":"141","file_date_updated":"2021-12-31T23:30:04Z","author":[{"full_name":"Emtenani, Shamsi","last_name":"Emtenani","first_name":"Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8557","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6187"}]},"date_created":"2020-12-30T15:41:26Z","date_updated":"2023-09-07T13:24:17Z","year":"2020","acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"DaSi"}],"month":"12","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8983","degree_awarded":"PhD","supervisor":[{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"language":[{"iso":"eng"}],"oa":1},{"article_processing_charge":"No","day":"18","month":"09","citation":{"chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, n.d. https://doi.org/10.1101/2020.09.18.301481.","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, doi:10.1101/2020.09.18.301481.","ieee":"V. Belyaeva et al., “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” bioRxiv. .","apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. https://doi.org/10.1101/2020.09.18.301481","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, 10.1101/2020.09.18.301481.","ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. doi:10.1101/2020.09.18.301481"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.09.18.301481"}],"oa":1,"publication":"bioRxiv","project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638"},{"call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"},{"grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425","name":"Tissue barrier penetration is crucial for immunity and metastasis"}],"date_published":"2020-09-18T00:00:00Z","doi":"10.1101/2020.09.18.301481","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"type":"preprint","ec_funded":1,"abstract":[{"text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues.","lang":"eng"}],"_id":"8557","acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"status":"public","publication_status":"submitted","title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","related_material":{"record":[{"id":"10614","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"8983"}]},"author":[{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","last_name":"Belyaeva","full_name":"Belyaeva, Vera"},{"first_name":"Stephanie","last_name":"Wachner","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","full_name":"Wachner, Stephanie"},{"first_name":"Igor","last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor"},{"first_name":"Markus","last_name":"Linder","full_name":"Linder, Markus"},{"id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938","first_name":"Shamsi","last_name":"Emtenani","full_name":"Emtenani, Shamsi"},{"orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","first_name":"Attila","full_name":"György, Attila"},{"full_name":"Sibilia, Maria","last_name":"Sibilia","first_name":"Maria"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"}],"oa_version":"Preprint","date_created":"2020-09-23T09:36:47Z","date_updated":"2024-03-28T23:30:25Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"02","date_published":"2020-12-02T00:00:00Z","citation":{"ieee":"K. Aggarwal et al., “Enhancement of proximity induced superconductivity in planar Germanium,” arXiv. .","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity in planar Germanium. arXiv.","ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. arXiv, 2012.00322.","ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced superconductivity in planar Germanium. arXiv.","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, n.d.","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros, ArXiv (n.d.).","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, 2012.00322."},"publication":"arXiv","abstract":[{"lang":"eng","text":"Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip."}],"type":"preprint","oa_version":"Submitted Version","file":[{"checksum":"22a612e206232fa94b138b2c2f957582","date_updated":"2020-12-02T10:42:31Z","date_created":"2020-12-02T10:42:31Z","relation":"main_file","file_id":"8832","content_type":"application/pdf","file_size":1697939,"creator":"gkatsaro","access_level":"open_access","file_name":"Superconducting_2D_Ge.pdf"}],"ddc":["530"],"title":"Enhancement of proximity induced superconductivity in planar Germanium","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8831","month":"12","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511"},{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"oa":1,"external_id":{"arxiv":["2012.00322"]},"ec_funded":1,"file_date_updated":"2020-12-02T10:42:31Z","article_number":"2012.00322","date_created":"2020-12-02T10:42:53Z","date_updated":"2024-03-28T23:30:27Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"10559"},{"id":"8834","status":"public","relation":"research_data"},{"id":"10058","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Aggarwal, Kushagra","last_name":"Aggarwal","first_name":"Kushagra","orcid":"0000-0001-9985-9293","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb"},{"full_name":"Hofmann, Andrea C","first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","first_name":"Daniel","last_name":"Jirovec"},{"first_name":"Ivan","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan"},{"full_name":"Sammak, Amir","first_name":"Amir","last_name":"Sammak"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"},{"last_name":"Marti-Sanchez","first_name":"Sara","full_name":"Marti-Sanchez, Sara"},{"full_name":"Veldhorst, Menno","first_name":"Menno","last_name":"Veldhorst"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Scappucci, Giordano","last_name":"Scappucci","first_name":"Giordano"},{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"department":[{"_id":"GeKa"}],"publication_status":"submitted","year":"2020","acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. GS and MV acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO)."},{"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"month":"09","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"},{"_id":"25D32BC0-B435-11E9-9278-68D0E5697425","name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus"},{"_id":"26436750-B435-11E9-9278-68D0E5697425","grant_number":"785907","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000579945300001"]},"language":[{"iso":"eng"}],"doi":"10.3390/ijms21186737","article_number":"6737","ec_funded":1,"file_date_updated":"2020-09-21T14:08:58Z","publisher":"MDPI","department":[{"_id":"RySh"}],"publication_status":"published","year":"2020","acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","volume":21,"date_created":"2020-09-20T22:01:35Z","date_updated":"2024-03-28T23:30:31Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]},"author":[{"first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"full_name":"Bhandari, Pradeep","first_name":"Pradeep","last_name":"Bhandari","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481"},{"id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Case","first_name":"Matthew J","full_name":"Case, Matthew J"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"14","article_type":"original","citation":{"mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences, vol. 21, no. 18, 6737, MDPI, 2020, doi:10.3390/ijms21186737.","short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21186737.","ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 2020;21(18). doi:10.3390/ijms21186737","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., & Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21186737","ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” International Journal of Molecular Sciences, vol. 21, no. 18. MDPI, 2020."},"publication":"International Journal of Molecular Sciences","date_published":"2020-09-14T00:00:00Z","type":"journal_article","issue":"18","abstract":[{"text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography.","lang":"eng"}],"intvolume":" 21","ddc":["570"],"title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","status":"public","_id":"8532","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":5748456,"file_name":"2020_JournMolecSciences_Kleindienst.pdf","access_level":"open_access","date_created":"2020-09-21T14:08:58Z","date_updated":"2020-09-21T14:08:58Z","success":1,"checksum":"2e4f62f3cfe945b7391fc3070e5a289f","file_id":"8551","relation":"main_file"}]},{"doi":"10.1007/978-3-030-44914-8_5","conference":{"end_date":"2020-04-30","start_date":"2020-04-25","location":"Dublin, Ireland","name":"ESOP: Programming Languages and Systems"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000681656800005"]},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030449131"]},"month":"04","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"}],"volume":12075,"date_updated":"2024-03-28T23:30:34Z","date_created":"2020-05-10T22:00:50Z","year":"2020","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2020-07-14T12:48:03Z","date_published":"2020-04-18T00:00:00Z","citation":{"ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal and perfectly parallel algorithms for on-demand data-flow analysis,” in European Symposium on Programming, Dublin, Ireland, 2020, vol. 12075, pp. 112–140.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A. (2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In European Symposium on Programming (Vol. 12075, pp. 112–140). Dublin, Ireland: Springer Nature. https://doi.org/10.1007/978-3-030-44914-8_5","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In: European Symposium on Programming. Vol 12075. Springer Nature; 2020:112-140. doi:10.1007/978-3-030-44914-8_5","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” In European Symposium on Programming, 12075:112–40. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-44914-8_5.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European Symposium on Programming, Springer Nature, 2020, pp. 112–140.","mla":"Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” European Symposium on Programming, vol. 12075, Springer Nature, 2020, pp. 112–40, doi:10.1007/978-3-030-44914-8_5."},"publication":"European Symposium on Programming","page":"112-140","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2020_LNCS_Chatterjee.pdf","access_level":"open_access","creator":"dernst","file_size":651250,"content_type":"application/pdf","file_id":"7895","relation":"main_file","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-26T13:34:48Z","checksum":"8618b80f4cf7b39a60e61a6445ad9807"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7810","intvolume":" 12075","title":"Optimal and perfectly parallel algorithms for on-demand data-flow analysis","ddc":["000"],"status":"public","abstract":[{"text":"Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries.\r\nIn this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"]},{"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","year":"2020","date_updated":"2024-03-28T23:30:34Z","date_created":"2020-11-06T07:30:05Z","volume":12302,"author":[{"last_name":"Asadi","first_name":"Ali","full_name":"Asadi, Ali"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"},{"first_name":"Kiarash","last_name":"Mohammadi","full_name":"Mohammadi, Kiarash"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"file_date_updated":"2020-11-06T07:41:03Z","isi":1,"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"oa":1,"external_id":{"isi":["000723555700014"]},"language":[{"iso":"eng"}],"conference":{"name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2020-10-19","location":"Hanoi, Vietnam","end_date":"2020-10-23"},"doi":"10.1007/978-3-030-59152-6_14","month":"10","publication_identifier":{"isbn":["9783030591519"],"eissn":["1611-3349"],"eisbn":["9783030591526"],"issn":["0302-9743"]},"title":"Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth","status":"public","ddc":["000"],"intvolume":" 12302","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8728","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2020_LNCS_ATVA_Asadi_accepted.pdf","file_size":726648,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8729","checksum":"ae83f27e5b189d5abc2e7514f1b7e1b5","success":1,"date_created":"2020-11-06T07:41:03Z","date_updated":"2020-11-06T07:41:03Z"}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improvements. In this work, we show that treewidth can also be used to obtain faster algorithms for the quantitative problems. For an MC with n states and m transitions, we show that each of the classical quantitative objectives can be computed in O((n+m)⋅t2) time, given a tree decomposition of the MC with width t. Our results also imply a bound of O(κ⋅(n+m)⋅t2) for each objective on MDPs, where κ is the number of strategy-iteration refinements required for the given input and objective. Finally, we make an experimental evaluation of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms outperform existing well-established methods by one or more orders of magnitude.","lang":"eng"}],"page":"253-270","publication":"Automated Technology for Verification and Analysis","citation":{"ista":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. 2020. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 12302, 253–270.","apa":"Asadi, A., Chatterjee, K., Goharshady, A. K., Mohammadi, K., & Pavlogiannis, A. (2020). Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In Automated Technology for Verification and Analysis (Vol. 12302, pp. 253–270). Hanoi, Vietnam: Springer Nature. https://doi.org/10.1007/978-3-030-59152-6_14","ieee":"A. Asadi, K. Chatterjee, A. K. Goharshady, K. Mohammadi, and A. Pavlogiannis, “Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth,” in Automated Technology for Verification and Analysis, Hanoi, Vietnam, 2020, vol. 12302, pp. 253–270.","ama":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In: Automated Technology for Verification and Analysis. Vol 12302. Springer Nature; 2020:253-270. doi:10.1007/978-3-030-59152-6_14","chicago":"Asadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Kiarash Mohammadi, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” In Automated Technology for Verification and Analysis, 12302:253–70. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-59152-6_14.","mla":"Asadi, Ali, et al. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” Automated Technology for Verification and Analysis, vol. 12302, Springer Nature, 2020, pp. 253–70, doi:10.1007/978-3-030-59152-6_14.","short":"A. Asadi, K. Chatterjee, A.K. Goharshady, K. Mohammadi, A. Pavlogiannis, in:, Automated Technology for Verification and Analysis, Springer Nature, 2020, pp. 253–270."},"date_published":"2020-10-12T00:00:00Z","scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"No"},{"publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2020","date_created":"2020-07-05T22:00:45Z","date_updated":"2024-03-28T23:30:34Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"},{"full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady","first_name":"Ehsan Kafshdar"}],"publication_identifier":{"isbn":["9781450376136"]},"month":"06","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1902.04373","open_access":"1"}],"external_id":{"isi":["000614622300045"],"arxiv":["1902.04373"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3385412.3385969","conference":{"name":"PLDI: Programming Language Design and Implementation","start_date":"2020-06-15","location":"London, United Kingdom","end_date":"2020-06-20"},"type":"conference","abstract":[{"text":"We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example.","lang":"eng"}],"title":"Polynomial invariant generation for non-deterministic recursive programs","status":"public","_id":"8089","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"11","page":"672-687","citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 672–87. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385969.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–687.","mla":"Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–87, doi:10.1145/3385412.3385969.","apa":"Chatterjee, K., Fu, H., Goharshady, A. K., & Goharshady, E. K. (2020). Polynomial invariant generation for non-deterministic recursive programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 672–687). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385969","ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial invariant generation for non-deterministic recursive programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 672–687.","ista":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant generation for non-deterministic recursive programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 672–687.","ama":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation for non-deterministic recursive programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:672-687. doi:10.1145/3385412.3385969"},"publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","date_published":"2020-06-11T00:00:00Z"},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"author":[{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar"},{"last_name":"Mohammadi","first_name":"Fatemeh","full_name":"Mohammadi, Fatemeh"}],"volume":193,"date_updated":"2024-03-28T23:30:34Z","date_created":"2019-09-29T22:00:44Z","acknowledgement":"We are grateful to the anonymous reviewers for their comments, which significantly improved the present work. The research was partially supported by the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian Academy of Sciences (ÖAW).","year":"2020","department":[{"_id":"KrCh"}],"publisher":"Elsevier","publication_status":"published","article_number":"106665","doi":"10.1016/j.ress.2019.106665","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.09692"}],"external_id":{"arxiv":["1712.09692"],"isi":["000501641400050"]},"oa":1,"project":[{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["09518320"]},"month":"01","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6918","intvolume":" 193","title":"An efficient algorithm for computing network reliability in small treewidth","status":"public","abstract":[{"text":"We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem.","lang":"eng"}],"type":"journal_article","date_published":"2020-01-01T00:00:00Z","citation":{"mla":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety, vol. 193, 106665, Elsevier, 2020, doi:10.1016/j.ress.2019.106665.","short":"A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (2020).","chicago":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety. Elsevier, 2020. https://doi.org/10.1016/j.ress.2019.106665.","ama":"Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 2020;193. doi:10.1016/j.ress.2019.106665","ista":"Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665.","ieee":"A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network reliability in small treewidth,” Reliability Engineering and System Safety, vol. 193. Elsevier, 2020.","apa":"Goharshady, A. K., & Mohammadi, F. (2020). An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. Elsevier. https://doi.org/10.1016/j.ress.2019.106665"},"publication":"Reliability Engineering and System Safety","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"acknowledgement":"We are grateful to the anonymous referees and editor whose insightful comments helped to considerably improve an earlier version of this paper. The research of the first author is supported by an ERC Grant from the Institute of Science and Technology (IST).","year":"2020","publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Springer Nature","author":[{"full_name":"Shehu, Yekini","last_name":"Shehu","first_name":"Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gibali","first_name":"Aviv","full_name":"Gibali, Aviv"},{"last_name":"Sagratella","first_name":"Simone","full_name":"Sagratella, Simone"}],"date_created":"2019-12-09T21:33:44Z","date_updated":"2023-09-06T11:27:15Z","volume":184,"file_date_updated":"2021-03-16T23:30:04Z","ec_funded":1,"oa":1,"external_id":{"isi":["000511805200009"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"doi":"10.1007/s10957-019-01616-6","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0022-3239"],"eissn":["1573-2878"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7161","ddc":["518","510","515"],"status":"public","title":"Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces","intvolume":" 184","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":332641,"creator":"dernst","access_level":"open_access","file_name":"2020_JourOptimizationTheoryApplic_Shehu.pdf","checksum":"9f6dc6c6bf2b48cb3a2091a9ed5feaf2","date_created":"2020-10-12T10:40:27Z","date_updated":"2021-03-16T23:30:04Z","relation":"main_file","embargo":"2021-03-15","file_id":"8647"}],"type":"journal_article","abstract":[{"text":"In this paper, we introduce an inertial projection-type method with different updating strategies for solving quasi-variational inequalities with strongly monotone and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions, we establish different strong convergence results for the proposed algorithm. Primary numerical experiments demonstrate the potential applicability of our scheme compared with some related methods in the literature.","lang":"eng"}],"publication":"Journal of Optimization Theory and Applications","citation":{"ama":"Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6","ista":"Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 184, 877–894.","ieee":"Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces,” Journal of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894, 2020.","apa":"Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6","mla":"Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications, vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6.","short":"Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications 184 (2020) 877–894.","chicago":"Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6."},"article_type":"original","page":"877–894","date_published":"2020-03-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-04-01T00:00:00Z","article_type":"original","page":"612-625","publication":"Nature Ecology & Evolution","citation":{"chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7.","mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.","short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.","ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 4(4), 612–625.","apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7","ieee":"I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.","ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7"},"abstract":[{"lang":"eng","text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature."}],"issue":"4","type":"journal_article","oa_version":"Submitted Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":745242,"access_level":"open_access","file_name":"2020_NatureEcolEvo_Tomanek.pdf","success":1,"checksum":"ef3bbf42023e30b2c24a6278025d2040","date_updated":"2020-10-09T09:56:01Z","date_created":"2020-10-09T09:56:01Z","file_id":"8640","relation":"main_file"}],"status":"public","ddc":["570"],"title":"Gene amplification as a form of population-level gene expression regulation","intvolume":" 4","_id":"7652","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","publication_identifier":{"issn":["2397-334X"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41559-020-1132-7","quality_controlled":"1","isi":1,"project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"external_id":{"isi":["000519008300005"]},"oa":1,"file_date_updated":"2020-10-09T09:56:01Z","date_updated":"2024-03-28T23:30:37Z","date_created":"2020-04-08T15:20:53Z","volume":4,"author":[{"id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X","first_name":"Isabella","last_name":"Tomanek","full_name":"Tomanek, Isabella"},{"full_name":"Grah, Rok","last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lagator","first_name":"M.","full_name":"Lagator, M."},{"full_name":"Andersson, A. M. C.","first_name":"A. M. C.","last_name":"Andersson"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8155"},{"relation":"research_data","status":"public","id":"7383"},{"status":"public","relation":"research_data","id":"7016"},{"relation":"used_in_publication","status":"public","id":"8653"}],"link":[{"url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","relation":"press_release","description":"News on IST Homepage"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.","year":"2020"},{"page":"174","citation":{"mla":"Scarselli, Davide. New Approaches to Reduce Friction in Turbulent Pipe Flow. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7258.","short":"D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020.","chicago":"Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe Flow.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7258.","ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:10.15479/AT:ISTA:7258","ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria.","apa":"Scarselli, D. (2020). New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7258","ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020."},"date_published":"2020-01-13T00:00:00Z","day":"13","has_accepted_license":"1","article_processing_charge":"No","ddc":["532"],"status":"public","title":"New approaches to reduce friction in turbulent pipe flow","_id":"7258","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"embargo_to":"open_access","file_name":"2020_Scarselli_Thesis.zip","access_level":"closed","content_type":"application/zip","file_size":26640830,"creator":"dscarsel","relation":"source_file","file_id":"7259","date_created":"2020-01-12T15:57:14Z","date_updated":"2021-01-13T23:30:05Z","checksum":"4df1ab24e9896635106adde5a54615bf"},{"access_level":"open_access","file_name":"2020_Scarselli_Thesis.pdf","creator":"dscarsel","file_size":8515844,"content_type":"application/pdf","embargo":"2021-01-12","file_id":"7260","relation":"main_file","checksum":"48659ab98e3414293c7a721385c2fd1c","date_updated":"2021-01-13T23:30:05Z","date_created":"2020-01-12T15:56:14Z"}],"oa_version":"None","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings."}],"project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"name":"Eliminating turbulence in oil pipelines","call_identifier":"H2020","grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425"},{"_id":"25136C54-B435-11E9-9278-68D0E5697425","grant_number":"HO 4393/1-2","name":"Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents"}],"oa":1,"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7258","month":"01","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Institute of Science and Technology Austria","year":"2020","date_updated":"2023-09-15T12:20:08Z","date_created":"2020-01-12T16:07:26Z","author":[{"full_name":"Scarselli, Davide","first_name":"Davide","last_name":"Scarselli","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6228"},{"id":"6486","status":"public","relation":"part_of_dissertation"},{"id":"461","relation":"part_of_dissertation","status":"public"},{"id":"422","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2021-01-13T23:30:05Z","ec_funded":1},{"oa_version":"Published Version","file":[{"relation":"source_file","file_id":"8666","checksum":"c01d9f59794b4b70528f37637c17ad02","date_created":"2020-10-16T12:14:21Z","date_updated":"2021-10-20T22:30:03Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_ITomanek_final_201016.docx","file_size":25131884,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"itomanek"},{"date_created":"2020-10-16T12:14:21Z","date_updated":"2021-10-20T22:30:03Z","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","relation":"main_file","embargo":"2021-10-19","file_id":"8667","content_type":"application/pdf","file_size":15405675,"creator":"itomanek","file_name":"Thesis_ITomanek_final_201016.pdf","access_level":"open_access"}],"title":"The evolution of gene expression by copy number and point mutations","ddc":["576"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8653","abstract":[{"text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2020-10-13T00:00:00Z","page":"117","citation":{"chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.","mla":"Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","apa":"Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653"},"has_accepted_license":"1","article_processing_charge":"No","day":"13","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"date_created":"2020-10-13T13:02:33Z","date_updated":"2023-09-07T13:22:42Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"7652"}]},"author":[{"full_name":"Tomanek, Isabella","last_name":"Tomanek","first_name":"Isabella","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","file_date_updated":"2021-10-20T22:30:03Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"doi":"10.15479/AT:ISTA:8653","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"10"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_CurrentBiology_Tan.pdf","file_size":5360135,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8555","checksum":"16f7d51fe28f91c21e4896a2028df40b","success":1,"date_updated":"2020-09-22T09:51:28Z","date_created":"2020-09-22T09:51:28Z"}],"status":"public","title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","ddc":["580"],"intvolume":" 30","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7427","abstract":[{"text":"Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2020-02-03T00:00:00Z","article_type":"original","page":"381-395.e8","publication":"Current Biology","citation":{"chicago":"Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology. Cell Press, 2020. https://doi.org/10.1016/j.cub.2019.11.058.","mla":"Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:10.1016/j.cub.2019.11.058.","short":"S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8.","ista":"Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8.","ieee":"S. Tan et al., “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” Current Biology, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020.","apa":"Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.11.058","ama":"Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 2020;30(3):381-395.e8. doi:10.1016/j.cub.2019.11.058"},"day":"03","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_created":"2020-02-02T23:01:00Z","date_updated":"2024-03-28T23:30:38Z","volume":30,"author":[{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang"},{"id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abas","first_name":"Melinda F","full_name":"Abas, Melinda F"},{"first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783"},{"first_name":"Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Molnar, Gergely"},{"last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"first_name":"Pavel","last_name":"Lasák","full_name":"Lasák, Pavel"},{"first_name":"Ivan","last_name":"Petřík","full_name":"Petřík, Ivan"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"last_name":"Pospíšil","first_name":"Jiří","full_name":"Pospíšil, Jiří"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8822","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","publisher":"Cell Press","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"acknowledgement":"We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). ","year":"2020","pmid":1,"file_date_updated":"2020-09-22T09:51:28Z","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2019.11.058","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Long Term Fellowship","grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31956021"],"isi":["000511287900018"]},"month":"02","publication_identifier":{"issn":["09609822"]}},{"volume":226,"date_updated":"2024-03-28T23:30:38Z","date_created":"2020-02-18T10:03:47Z","related_material":{"record":[{"id":"8822","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Mazur, E","first_name":"E","last_name":"Mazur"},{"full_name":"Kulik, Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","last_name":"Kulik","first_name":"Ivan"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","first_name":"Jakub","last_name":"Hajny","full_name":"Hajny, Jakub"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests.","year":"2020","ec_funded":1,"file_date_updated":"2020-11-20T09:32:10Z","language":[{"iso":"eng"}],"doi":"10.1111/nph.16446","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development","_id":"2699E3D2-B435-11E9-9278-68D0E5697425","grant_number":"25239"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000514939700001"],"pmid":["31971254"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"month":"06","file":[{"file_id":"8781","relation":"main_file","success":1,"checksum":"17de728b0205979feb95ce663ba918c2","date_updated":"2020-11-20T09:32:10Z","date_created":"2020-11-20T09:32:10Z","access_level":"open_access","file_name":"2020_NewPhytologist_Mazur.pdf","creator":"dernst","content_type":"application/pdf","file_size":2106888}],"oa_version":"Published Version","intvolume":" 226","ddc":["580"],"title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","status":"public","_id":"7500","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"5","abstract":[{"text":"Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts.","lang":"eng"}],"type":"journal_article","date_published":"2020-06-01T00:00:00Z","page":"1375-1383","article_type":"original","citation":{"mla":"Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:10.1111/nph.16446.","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383.","chicago":"Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16446.","ama":"Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 2020;226(5):1375-1383. doi:10.1111/nph.16446","ista":"Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383.","apa":"Mazur, E., Kulik, I., Hajny, J., & Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. Wiley. https://doi.org/10.1111/nph.16446","ieee":"E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” New Phytologist, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020."},"publication":"New Phytologist","article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"file_date_updated":"2021-12-08T23:30:03Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","year":"2020","date_updated":"2023-09-19T10:39:33Z","date_created":"2020-12-01T12:38:18Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7427"},{"id":"6260","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7500"},{"relation":"part_of_dissertation","status":"public","id":"191"},{"id":"449","status":"public","relation":"part_of_dissertation"}]},"author":[{"first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub"}],"publication_identifier":{"issn":["2663-337X"]},"month":"12","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8822","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization.","lang":"eng"}],"status":"public","title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","ddc":["580"],"_id":"8822","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"8919","checksum":"210a9675af5e4c78b0b56d920ac82866","date_created":"2020-12-04T07:27:52Z","date_updated":"2021-07-16T22:30:03Z","access_level":"closed","embargo_to":"open_access","file_name":"Jakub Hajný IST Austria final_JH.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":91279806,"creator":"jhajny"},{"creator":"jhajny","file_size":68707697,"content_type":"application/pdf","access_level":"open_access","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","checksum":"1781385b4aa73eba89cc76c6172f71d2","date_updated":"2021-12-08T23:30:03Z","date_created":"2020-12-09T15:04:41Z","file_id":"8933","embargo":"2021-12-07","relation":"main_file"}],"has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"249","citation":{"mla":"Hajny, Jakub. Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822.","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020.","chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822.","ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:10.15479/AT:ISTA:8822","ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria.","apa":"Hajny, J. (2020). Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822","ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020."},"date_published":"2020-12-01T00:00:00Z"},{"abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"None","file":[{"access_level":"closed","embargo_to":"open_access","file_name":"Shayan-Thesis-Final.docx","file_size":65194814,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"sshamip","relation":"source_file","file_id":"8351","checksum":"6e47871c74f85008b9876112eb3fcfa1","date_created":"2020-09-09T11:06:27Z","date_updated":"2021-09-11T22:30:05Z"},{"creator":"sshamip","content_type":"application/pdf","file_size":23729605,"file_name":"Shayan-Thesis-Final.pdf","access_level":"open_access","date_updated":"2021-09-11T22:30:05Z","date_created":"2020-09-09T11:06:13Z","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","file_id":"8352","embargo":"2021-09-10","relation":"main_file"}],"_id":"8350","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","ddc":["570"],"day":"09","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-09-09T00:00:00Z","citation":{"chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.","mla":"Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","apa":"Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350"},"page":"107","file_date_updated":"2021-09-11T22:30:05Z","author":[{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan"}],"related_material":{"record":[{"id":"661","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6508"},{"id":"7001","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"735"}]},"date_created":"2020-09-09T11:12:10Z","date_updated":"2023-09-27T14:16:45Z","acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","year":"2020","publication_status":"published","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","month":"09","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8350","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"supervisor":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"language":[{"iso":"eng"}],"oa":1},{"month":"09","publication_identifier":{"issn":["2296-634X"]},"doi":"10.3389/fcell.2020.574382","language":[{"iso":"eng"}],"external_id":{"isi":["000577915900001"],"pmid":["33102480"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"}],"file_date_updated":"2020-09-28T13:11:17Z","ec_funded":1,"article_number":"574382","author":[{"first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"related_material":{"record":[{"id":"9962","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:41Z","date_created":"2020-09-26T06:11:07Z","volume":8,"acknowledgement":"AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Frontiers","day":"25","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2020-09-25T00:00:00Z","publication":"Frontiers in Cell and Developmental Biology","citation":{"chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology. Frontiers, 2020. https://doi.org/10.3389/fcell.2020.574382.","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology, vol. 8, no. 9, 574382, Frontiers, 2020, doi:10.3389/fcell.2020.574382.","short":"A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology 8 (2020).","ista":"Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 8(9), 574382.","apa":"Hansen, A. H., & Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2020.574382","ieee":"A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex,” Frontiers in Cell and Developmental Biology, vol. 8, no. 9. Frontiers, 2020.","ama":"Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 2020;8(9). doi:10.3389/fcell.2020.574382"},"article_type":"original","abstract":[{"lang":"eng","text":"Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future."}],"issue":"9","type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":5527139,"access_level":"open_access","file_name":"2020_Frontiers_Hansen.pdf","success":1,"checksum":"01f731824194c94c81a5da360d997073","date_created":"2020-09-28T13:11:17Z","date_updated":"2020-09-28T13:11:17Z","file_id":"8584","relation":"main_file"}],"oa_version":"Published Version","_id":"8569","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex","ddc":["570"],"intvolume":" 8"},{"type":"journal_article","issue":"159","abstract":[{"text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.","lang":"eng"}],"title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7815","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1352186,"creator":"rbeattie","access_level":"open_access","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf","checksum":"3154ea7f90b9fb45e084cd1c2770597d","date_created":"2020-05-11T08:28:38Z","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","file_id":"7816"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"08","article_type":"original","citation":{"ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. 2020;(159). doi:10.3791/61147","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., & Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. MyJove Corporation. https://doi.org/10.3791/61147","ieee":"R. J. Beattie et al., “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” Journal of Visual Experiments, no. 159. MyJove Corporation, 2020.","mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments, no. 159, e61147, MyJove Corporation, 2020, doi:10.3791/61147.","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments. MyJove Corporation, 2020. https://doi.org/10.3791/61147."},"publication":"Journal of Visual Experiments","date_published":"2020-05-08T00:00:00Z","article_number":"e61147","ec_funded":1,"file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"SiHi"}],"publisher":"MyJove Corporation","publication_status":"published","year":"2020","date_created":"2020-05-11T08:31:20Z","date_updated":"2024-03-28T23:30:42Z","related_material":{"record":[{"id":"7902","status":"public","relation":"part_of_dissertation"}]},"author":[{"orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J","full_name":"Beattie, Robert J"},{"full_name":"Streicher, Carmen","first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T"},{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras"},{"last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"publication_identifier":{"issn":["1940-087X"]},"month":"05","project":[{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF"},{"grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000546406600043"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"doi":"10.3791/61147"},{"file_date_updated":"2021-06-07T22:30:03Z","ec_funded":1,"author":[{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6830"},{"relation":"dissertation_contains","status":"public","id":"28"},{"relation":"dissertation_contains","status":"public","id":"7815"}]},"date_updated":"2023-10-18T08:45:16Z","date_created":"2020-05-29T08:27:32Z","year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"SiHi"}],"month":"06","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:7902","degree_awarded":"PhD","supervisor":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"abstract":[{"lang":"eng","text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":53134142,"creator":"xcontreras","access_level":"closed","embargo_to":"open_access","file_name":"PhDThesis_Contreras.docx","checksum":"43c172bf006c95b65992d473c7240d13","date_created":"2020-06-05T08:18:08Z","date_updated":"2021-06-07T22:30:03Z","relation":"source_file","file_id":"7927"},{"file_id":"7928","embargo":"2021-06-06","relation":"main_file","date_updated":"2021-06-07T22:30:03Z","date_created":"2020-06-05T08:18:07Z","checksum":"addfed9128271be05cae3608e03a6ec0","file_name":"PhDThesis_Contreras.pdf","access_level":"open_access","creator":"xcontreras","file_size":35117191,"content_type":"application/pdf"}],"_id":"7902","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Genetic dissection of neural development in health and disease at single cell resolution","status":"public","ddc":["570"],"day":"05","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-06-05T00:00:00Z","citation":{"ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","apa":"Contreras, X. (2020). Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7902","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7902.","mla":"Contreras, Ximena. Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7902.","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020."},"page":"214"},{"scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"No","article_type":"letter_note","publication":"The Journal of Cell Biology","citation":{"ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” The Journal of Cell Biology, vol. 219, no. 8. Rockefeller University Press, 2020.","apa":"Sixt, M. K., & Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202007029","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 2020;219(8). doi:10.1083/jcb.202007029","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.202007029.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:10.1083/jcb.202007029."},"date_published":"2020-07-22T00:00:00Z","type":"journal_article","issue":"8","title":"Zena Werb (1945-2020): Cell biology in context","ddc":["570"],"status":"public","intvolume":" 219","_id":"8190","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"8200","embargo":"2021-02-01","relation":"main_file","checksum":"30016d778d266b8e17d01094917873b8","date_created":"2020-08-04T13:11:52Z","date_updated":"2021-02-02T23:30:03Z","access_level":"open_access","file_name":"2020_JCB_Sixt.pdf","creator":"dernst","file_size":830725,"content_type":"application/pdf"}],"oa_version":"Published Version","month":"07","publication_identifier":{"eissn":["1540-8140"]},"isi":1,"external_id":{"isi":["000573631000004"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1083/jcb.202007029","article_number":"e202007029","file_date_updated":"2021-02-02T23:30:03Z","publication_status":"published","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"}],"year":"2020","date_created":"2020-08-02T22:00:57Z","date_updated":"2023-10-17T10:04:49Z","volume":219,"author":[{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Huttenlocher, Anna","first_name":"Anna","last_name":"Huttenlocher"}]},{"date_published":"2020-12-11T00:00:00Z","citation":{"chicago":"Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances. AAAS, 2020. https://doi.org/10.1126/sciadv.abc8895.","mla":"Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:10.1126/sciadv.abc8895.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020).","ista":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895.","ieee":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” Science Advances, vol. 6, no. 50. AAAS, 2020.","apa":"Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., & Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abc8895","ama":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 2020;6(50). doi:10.1126/sciadv.abc8895"},"publication":"Science Advances","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"11","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_ScienceAdvances_Zhang.pdf","creator":"dernst","file_size":10578145,"content_type":"application/pdf","file_id":"8994","relation":"main_file","success":1,"checksum":"5ac2500b191c08ef6dab5327f40ff663","date_created":"2021-01-07T12:44:33Z","date_updated":"2021-01-07T12:44:33Z"}],"_id":"8986","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 6","ddc":["580"],"title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","status":"public","issue":"50","abstract":[{"lang":"eng","text":"Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants."}],"type":"journal_article","doi":"10.1126/sciadv.abc8895","language":[{"iso":"eng"}],"external_id":{"isi":["000599903600014"],"pmid":["33310852"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["2375-2548"]},"month":"12","related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Zhang","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou"},{"full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"volume":6,"date_updated":"2024-03-28T23:30:44Z","date_created":"2021-01-03T23:01:23Z","pmid":1,"acknowledgement":"We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ","year":"2020","department":[{"_id":"JiFr"}],"publisher":"AAAS","publication_status":"published","ec_funded":1,"file_date_updated":"2021-01-07T12:44:33Z","article_number":"eabc8895"},{"article_number":"5272","file_date_updated":"2020-08-25T09:53:50Z","pmid":1,"year":"2020","acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","publisher":"MDPI","department":[{"_id":"JiFr"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"author":[{"last_name":"Chen","first_name":"Huihuang","full_name":"Chen, Huihuang"},{"first_name":"Linyi","last_name":"Lai","full_name":"Lai, Linyi"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li"},{"first_name":"Liping","last_name":"Liu","full_name":"Liu, Liping"},{"last_name":"Jakada","first_name":"Bello Hassan","full_name":"Jakada, Bello Hassan"},{"full_name":"Huang, Youmei","first_name":"Youmei","last_name":"Huang"},{"full_name":"He, Qing","first_name":"Qing","last_name":"He"},{"first_name":"Mengnan","last_name":"Chai","full_name":"Chai, Mengnan"},{"last_name":"Niu","first_name":"Xiaoping","full_name":"Niu, Xiaoping"},{"full_name":"Qin, Yuan","last_name":"Qin","first_name":"Yuan"}],"volume":21,"date_updated":"2024-03-28T23:30:44Z","date_created":"2020-08-24T06:24:03Z","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32785037"],"isi":["000565090300001"]},"quality_controlled":"1","isi":1,"doi":"10.3390/ijms21165727","language":[{"iso":"eng"}],"type":"journal_article","issue":"16","abstract":[{"lang":"eng","text":"Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. "}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8283","intvolume":" 21","status":"public","ddc":["570"],"title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","file":[{"file_name":"2020_IntMolecSciences_Chen.pdf","access_level":"open_access","file_size":5718755,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","file_id":"8292","date_updated":"2020-08-25T09:53:50Z","date_created":"2020-08-25T09:53:50Z","checksum":"03b039244e6ae80580385fd9f577e2b2","success":1}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"10","citation":{"ama":"Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727","ista":"Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272.","ieee":"H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020.","apa":"Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165727","mla":"Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727.","short":"H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020).","chicago":"Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165727."},"publication":"International Journal of Molecular Sciences","article_type":"original","date_published":"2020-08-10T00:00:00Z"},{"article_number":"jcs248062","file_date_updated":"2021-08-08T22:30:03Z","ec_funded":1,"year":"2020","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. ","pmid":1,"publication_status":"published","publisher":"The Company of Biologists","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"author":[{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","first_name":"Nataliia","last_name":"Gnyliukh"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann"},{"first_name":"Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha"},{"last_name":"Vert","first_name":"G","full_name":"Vert, G"},{"full_name":"Bednarek, SY","first_name":"SY","last_name":"Bednarek"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"}]},"date_created":"2020-07-21T08:58:19Z","date_updated":"2023-12-01T13:51:07Z","volume":133,"month":"08","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"oa":1,"external_id":{"pmid":["32616560"],"isi":["000561047900021"]},"isi":1,"quality_controlled":"1","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.1242/jcs.248062","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.","lang":"eng"}],"issue":"15","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8139","ddc":["575"],"title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","status":"public","intvolume":" 133","file":[{"date_updated":"2021-08-08T22:30:03Z","date_created":"2020-11-26T17:12:51Z","checksum":"2d11f79a0b4e0a380fb002b933da331a","relation":"main_file","file_id":"8815","embargo":"2021-08-07","file_size":15150403,"content_type":"application/pdf","creator":"ajohnson","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","day":"06","article_processing_charge":"No","has_accepted_license":"1","publication":"Journal of Cell Science","citation":{"ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062","ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062.","ieee":"A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062.","short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062."},"article_type":"original","date_published":"2020-08-06T00:00:00Z"},{"article_type":"original","citation":{"short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020).","mla":"Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications, vol. 1, no. 3, 100048, Elsevier, 2020, doi:10.1016/j.xplc.2020.100048.","chicago":"Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications. Elsevier, 2020. https://doi.org/10.1016/j.xplc.2020.100048.","ama":"Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 2020;1(3). doi:10.1016/j.xplc.2020.100048","ieee":"H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” Plant Communications, vol. 1, no. 3. Elsevier, 2020.","apa":"Semerádová, H., Montesinos López, J. C., & Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2020.100048","ista":"Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048."},"publication":"Plant Communications","date_published":"2020-05-11T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"11","intvolume":" 1","status":"public","title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","ddc":["580"],"_id":"9160","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2021-02-18T10:23:59Z","date_created":"2021-02-18T10:23:59Z","checksum":"785b266d82a94b007cf40dbbe7c4847e","success":1,"relation":"main_file","file_id":"9161","file_size":840289,"content_type":"application/pdf","creator":"dernst","file_name":"2020_PlantComm_Semeradova.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"3","abstract":[{"text":"Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development.","lang":"eng"}],"project":[{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000654052800010"],"pmid":["33367243"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.xplc.2020.100048","publication_identifier":{"issn":["2590-3462"]},"month":"05","department":[{"_id":"EvBe"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared.","year":"2020","volume":1,"date_updated":"2024-03-28T23:30:47Z","date_created":"2021-02-18T10:18:43Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10135"}]},"author":[{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova","first_name":"Hana","full_name":"Semeradova, Hana"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","first_name":"Juan C","last_name":"Montesinos López","full_name":"Montesinos López, Juan C"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"article_number":"100048","file_date_updated":"2021-02-18T10:23:59Z"},{"author":[{"first_name":"Mathew","last_name":"Yankowitz","full_name":"Yankowitz, Mathew"},{"full_name":"Chen, Shaowen","first_name":"Shaowen","last_name":"Chen"},{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy"},{"full_name":"Watanabe, K.","last_name":"Watanabe","first_name":"K."},{"full_name":"Taniguchi, T.","first_name":"T.","last_name":"Taniguchi"},{"full_name":"Graf, David","first_name":"David","last_name":"Graf"},{"full_name":"Young, Andrea F.","first_name":"Andrea F.","last_name":"Young"},{"first_name":"Cory R.","last_name":"Dean","full_name":"Dean, Cory R."},{"last_name":"Sharpe","first_name":"Aaron L.","full_name":"Sharpe, Aaron L."},{"full_name":"Fox, E.J.","last_name":"Fox","first_name":"E.J."},{"first_name":"A.W.","last_name":"Barnard","full_name":"Barnard, A.W."},{"full_name":"Finney, Joe","first_name":"Joe","last_name":"Finney"}],"date_updated":"2022-01-25T15:56:39Z","date_created":"2022-01-25T15:09:58Z","oa_version":"Published Version","volume":"03","year":"2019","_id":"10664","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"New correlated phenomena in magic-angle twisted bilayer graphene/s","publication_status":"published","status":"public","intvolume":" 3","publisher":"Simons Foundation ; University of California, Riverside","abstract":[{"lang":"eng","text":"Since the discovery of correlated insulators and superconductivity in magic-angle twisted bilayer graphene (tBLG) ([1, 2], JCCM April 2018), theorists have been excitedly pursuing the alluring mix of band topology, symmetry breaking, Mott insulators and superconductivity at play, as well as the potential relation (if any) to high-Tc physics. Now a new stream\r\nof experimental work is arriving which further enriches the story. To briefly recap Episodes 1 and 2 (JCCM April and November 2018), when two graphene layers are stacked with a small rotational mismatch θ, the resulting long-wavelength moire pattern leads to a superlattice potential which reconstructs the low energy band structure. When θ approaches the “magic-angle” θM ∼ 1 ◦, the band structure features eight nearly-flat bands which fill when the electron number per moire unit cell, n/n0, lies between −4 < n/n0 < 4. The bands can be counted as 8 = 2 × 2 × 2: for each spin (2×) and valley (2×) characteristic of monolayergraphene, tBLG has has 2× flat bands which cross at mini-Dirac points."}],"type":"journal_article","date_published":"2019-02-28T00:00:00Z","doi":"10.36471/jccm_february_2019_03","language":[{"iso":"eng"}],"publication":"Journal Club for Condensed Matter Physics","citation":{"chicago":"Yankowitz, Mathew, Shaowen Chen, Hryhoriy Polshyn, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside, 2019. https://doi.org/10.36471/jccm_february_2019_03.","mla":"Yankowitz, Mathew, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics, vol. 03, Simons Foundation ; University of California, Riverside, 2019, doi:10.36471/jccm_february_2019_03.","short":"M. Yankowitz, S. Chen, H. Polshyn, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, A.L. Sharpe, E.J. Fox, A.W. Barnard, J. Finney, Journal Club for Condensed Matter Physics 03 (2019).","ista":"Yankowitz M, Chen S, Polshyn H, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR, Sharpe AL, Fox EJ, Barnard AW, Finney J. 2019. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 03.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Watanabe, K., Taniguchi, T., Graf, D., … Finney, J. (2019). New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside. https://doi.org/10.36471/jccm_february_2019_03","ieee":"M. Yankowitz et al., “New correlated phenomena in magic-angle twisted bilayer graphene/s,” Journal Club for Condensed Matter Physics, vol. 03. Simons Foundation ; University of California, Riverside, 2019.","ama":"Yankowitz M, Chen S, Polshyn H, et al. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 2019;03. doi:10.36471/jccm_february_2019_03"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.condmatjclub.org/?p=3541"}],"article_type":"original","quality_controlled":"1","day":"28","month":"02","article_processing_charge":"No"},{"file_date_updated":"2022-05-17T06:55:49Z","author":[{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"last_name":"Abate","first_name":"Alessandro","full_name":"Abate, Alessandro"},{"first_name":"Dieky","last_name":"Adzkiya","full_name":"Adzkiya, Dieky"},{"first_name":"Anna","last_name":"Becchi","full_name":"Becchi, Anna"},{"full_name":"Bu, Lei","first_name":"Lei","last_name":"Bu"},{"full_name":"Cimatti, Alessandro","first_name":"Alessandro","last_name":"Cimatti"},{"full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","first_name":"Mirco","last_name":"Giacobbe"},{"first_name":"Alberto","last_name":"Griggio","full_name":"Griggio, Alberto"},{"first_name":"Sergio","last_name":"Mover","full_name":"Mover, Sergio"},{"full_name":"Mufid, Muhammad Syifa'ul","last_name":"Mufid","first_name":"Muhammad Syifa'ul"},{"first_name":"Idriss","last_name":"Riouak","full_name":"Riouak, Idriss"},{"full_name":"Tonetta, Stefano","first_name":"Stefano","last_name":"Tonetta"},{"first_name":"Enea","last_name":"Zaffanella","full_name":"Zaffanella, Enea"}],"date_created":"2022-03-18T12:29:23Z","date_updated":"2022-05-17T07:09:47Z","volume":61,"year":"2019","acknowledgement":"The authors gratefully acknowledge \fnancial support by the European Commission project\r\nUnCoVerCPS under grant number 643921. Lei Bu is supported by the National Natural Science\r\nFoundation of China (No.61572249).","publication_status":"published","editor":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"full_name":"Althoff, Matthias","first_name":"Matthias","last_name":"Althoff"}],"department":[{"_id":"ToHe"}],"publisher":"EasyChair","month":"05","publication_identifier":{"issn":["2398-7340"]},"conference":{"name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","end_date":"2019-04-15","location":"Montreal, Canada","start_date":"2019-04-15"},"doi":"10.29007/rjwn","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","abstract":[{"text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with piecewise constant dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this third edition, six tools have been applied to solve five different benchmark problems in the category for piecewise constant dynamics: BACH, Lyse, Hy- COMP, PHAVer/SX, PHAVerLite, and VeriSiMPL. Compared to last year, a new tool has participated (HyCOMP) and PHAVerLite has replaced PHAVer-lite. The result is a snap- shot 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 probably provide the most complete assessment of tools for the safety verification of continuous and hybrid systems with piecewise constant dynamics up to this date.","lang":"eng"}],"type":"conference","alternative_title":["EPiC Series in Computing"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"11391","checksum":"4b92e333db7b4e2349501a804dfede69","success":1,"date_created":"2022-05-17T06:55:49Z","date_updated":"2022-05-17T06:55:49Z","access_level":"open_access","file_name":"2019_EPiCs_Frehse.pdf","content_type":"application/pdf","file_size":346415,"creator":"dernst"}],"_id":"10877","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"title":"ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics","status":"public","intvolume":" 61","day":"25","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-05-25T00:00:00Z","publication":"ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems","citation":{"ama":"Frehse G, Abate A, Adzkiya D, et al. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In: Frehse G, Althoff M, eds. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. Vol 61. EasyChair; 2019:1-13. doi:10.29007/rjwn","ista":"Frehse G, Abate A, Adzkiya D, Becchi A, Bu L, Cimatti A, Giacobbe M, Griggio A, Mover S, Mufid MS, Riouak I, Tonetta S, Zaffanella E. 2019. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems, EPiC Series in Computing, vol. 61, 1–13.","ieee":"G. Frehse et al., “ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics,” in ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, Montreal, Canada, 2019, vol. 61, pp. 1–13.","apa":"Frehse, G., Abate, A., Adzkiya, D., Becchi, A., Bu, L., Cimatti, A., … Zaffanella, E. (2019). ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In G. Frehse & M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems (Vol. 61, pp. 1–13). Montreal, Canada: EasyChair. https://doi.org/10.29007/rjwn","mla":"Frehse, Goran, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, vol. 61, EasyChair, 2019, pp. 1–13, doi:10.29007/rjwn.","short":"G. Frehse, A. Abate, D. Adzkiya, A. Becchi, L. Bu, A. Cimatti, M. Giacobbe, A. Griggio, S. Mover, M.S. Mufid, I. Riouak, S. Tonetta, E. Zaffanella, in:, G. Frehse, M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, EasyChair, 2019, pp. 1–13.","chicago":"Frehse, Goran, Alessandro Abate, Dieky Adzkiya, Anna Becchi, Lei Bu, Alessandro Cimatti, Mirco Giacobbe, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” In ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, 61:1–13. EasyChair, 2019. https://doi.org/10.29007/rjwn."},"page":"1-13"},{"article_processing_charge":"No","day":"15","scopus_import":1,"date_published":"2019-09-15T00:00:00Z","page":"909–928","article_type":"original","citation":{"ieee":"N. Kalinin and M. Shkolnikov, “Tropical formulae for summation over a part of SL(2,Z),” European Journal of Mathematics, vol. 5, no. 3. Springer Nature, pp. 909–928, 2019.","apa":"Kalinin, N., & Shkolnikov, M. (2019). Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-018-0218-0","ista":"Kalinin N, Shkolnikov M. 2019. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 5(3), 909–928.","ama":"Kalinin N, Shkolnikov M. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 2019;5(3):909–928. doi:10.1007/s40879-018-0218-0","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40879-018-0218-0.","short":"N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics, vol. 5, no. 3, Springer Nature, 2019, pp. 909–928, doi:10.1007/s40879-018-0218-0."},"publication":"European Journal of Mathematics","issue":"3","type":"journal_article","oa_version":"Preprint","intvolume":" 5","title":"Tropical formulae for summation over a part of SL(2,Z)","status":"public","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"441","publication_identifier":{"issn":["2199-675X"],"eissn":["2199-6768"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/s40879-018-0218-0","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.02089"}],"oa":1,"external_id":{"arxiv":["1711.02089"]},"ec_funded":1,"publist_id":"7382","volume":5,"date_updated":"2021-01-12T07:56:46Z","date_created":"2018-12-11T11:46:29Z","author":[{"last_name":"Kalinin","first_name":"Nikita","full_name":"Kalinin, Nikita"},{"full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","first_name":"Mikhail"}],"department":[{"_id":"TaHa"}],"publisher":"Springer Nature","publication_status":"published","year":"2019"},{"quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"main_file_link":[{"url":"https://eprint.iacr.org/2016/166","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.3233/JCS-181131","month":"01","publication_identifier":{"issn":["0926227X"]},"publication_status":"published","publisher":"IOS Press","department":[{"_id":"KrPi"}],"year":"2019","date_updated":"2021-01-12T08:05:08Z","date_created":"2019-01-27T22:59:10Z","volume":27,"author":[{"full_name":"Demay, Gregory","first_name":"Gregory","last_name":"Demay"},{"full_name":"Gazi, Peter","last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maurer, Ueli","first_name":"Ueli","last_name":"Maurer"},{"full_name":"Tackmann, Bjorn","last_name":"Tackmann","first_name":"Bjorn"}],"ec_funded":1,"article_type":"original","page":"75-111","publication":"Journal of Computer Security","citation":{"chicago":"Demay, Gregory, Peter Gazi, Ueli Maurer, and Bjorn Tackmann. “Per-Session Security: Password-Based Cryptography Revisited.” Journal of Computer Security. IOS Press, 2019. https://doi.org/10.3233/JCS-181131.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, Journal of Computer Security 27 (2019) 75–111.","mla":"Demay, Gregory, et al. “Per-Session Security: Password-Based Cryptography Revisited.” Journal of Computer Security, vol. 27, no. 1, IOS Press, 2019, pp. 75–111, doi:10.3233/JCS-181131.","apa":"Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2019). Per-session security: Password-based cryptography revisited. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-181131","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Per-session security: Password-based cryptography revisited,” Journal of Computer Security, vol. 27, no. 1. IOS Press, pp. 75–111, 2019.","ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2019. Per-session security: Password-based cryptography revisited. Journal of Computer Security. 27(1), 75–111.","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Per-session security: Password-based cryptography revisited. Journal of Computer Security. 2019;27(1):75-111. doi:10.3233/JCS-181131"},"date_published":"2019-01-01T00:00:00Z","scopus_import":"1","day":"1","article_processing_charge":"No","title":"Per-session security: Password-based cryptography revisited","status":"public","intvolume":" 27","_id":"5887","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Cryptographic security is usually defined as a guarantee that holds except when a bad event with negligible probability occurs, and nothing is guaranteed in that bad case. However, in settings where such failure can happen with substantial probability, one needs to provide guarantees even for the bad case. A typical example is where a (possibly weak) password is used instead of a secure cryptographic key to protect a session, the bad event being that the adversary correctly guesses the password. In a situation with multiple such sessions, a per-session guarantee is desired: any session for which the password has not been guessed remains secure, independently of whether other sessions have been compromised. A new formalism for stating such gracefully degrading security guarantees is introduced and applied to analyze the examples of password-based message authentication and password-based encryption. While a natural per-message guarantee is achieved for authentication, the situation of password-based encryption is more delicate: a per-session confidentiality guarantee only holds against attackers for which the distribution of password-guessing effort over the sessions is known in advance. In contrast, for more general attackers without such a restriction, a strong, composable notion of security cannot be achieved."}],"issue":"1"},{"scopus_import":1,"has_accepted_license":"1","day":"01","page":"223–256","citation":{"chicago":"Dyer, Ramsay, Gert Vegter, and Mathijs Wintraecken. “Simplices Modelled on Spaces of Constant Curvature.” Journal of Computational Geometry . Carleton University, 2019. https://doi.org/10.20382/jocg.v10i1a9.","short":"R. Dyer, G. Vegter, M. Wintraecken, Journal of Computational Geometry 10 (2019) 223–256.","mla":"Dyer, Ramsay, et al. “Simplices Modelled on Spaces of Constant Curvature.” Journal of Computational Geometry , vol. 10, no. 1, Carleton University, 2019, pp. 223–256, doi:10.20382/jocg.v10i1a9.","ieee":"R. Dyer, G. Vegter, and M. Wintraecken, “Simplices modelled on spaces of constant curvature,” Journal of Computational Geometry , vol. 10, no. 1. Carleton University, pp. 223–256, 2019.","apa":"Dyer, R., Vegter, G., & Wintraecken, M. (2019). Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . Carleton University. https://doi.org/10.20382/jocg.v10i1a9","ista":"Dyer R, Vegter G, Wintraecken M. 2019. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 10(1), 223–256.","ama":"Dyer R, Vegter G, Wintraecken M. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 2019;10(1):223–256. doi:10.20382/jocg.v10i1a9"},"publication":"Journal of Computational Geometry ","date_published":"2019-07-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"We give non-degeneracy criteria for Riemannian simplices based on simplices in spaces of constant sectional curvature. It extends previous work on Riemannian simplices, where we developed Riemannian simplices with respect to Euclidean reference simplices. The criteria we give in this article are in terms of quality measures for spaces of constant curvature that we develop here. We see that simplices in spaces that have nearly constant curvature, are already non-degenerate under very weak quality demands. This is of importance because it allows for sampling of Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature.","lang":"eng"}],"intvolume":" 10","ddc":["510"],"status":"public","title":"Simplices modelled on spaces of constant curvature","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6515","oa_version":"Published Version","file":[{"file_name":"mainJournalFinal.pdf","access_level":"open_access","creator":"mwintrae","content_type":"application/pdf","file_size":2170882,"file_id":"6516","relation":"main_file","date_updated":"2020-07-14T12:47:32Z","date_created":"2019-06-03T09:30:01Z","checksum":"57b4df2f16a74eb499734ec8ee240178"}],"publication_identifier":{"issn":["1920-180X"]},"month":"07","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.20382/jocg.v10i1a9","ec_funded":1,"file_date_updated":"2020-07-14T12:47:32Z","publisher":"Carleton University","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2019","volume":10,"date_created":"2019-06-03T09:35:33Z","date_updated":"2021-01-12T08:07:50Z","author":[{"full_name":"Dyer, Ramsay","last_name":"Dyer","first_name":"Ramsay"},{"full_name":"Vegter, Gert","last_name":"Vegter","first_name":"Gert"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs"}]},{"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"article_number":"60","author":[{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"date_updated":"2021-01-12T08:07:53Z","date_created":"2019-06-06T14:12:36Z","volume":124,"year":"2019","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"month":"01","publication_identifier":{"isbn":["978-3-95977-095-8"],"issn":["1868-8969"]},"conference":{"end_date":"2019-01-12","start_date":"2019-01-10","location":"San Diego, CA, United States","name":"ITCS 2019: Innovations in Theoretical Computer Science"},"doi":"10.4230/LIPICS.ITCS.2019.60","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/627"}],"quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"abstract":[{"text":"We construct a verifiable delay function (VDF) by showing how the Rivest-Shamir-Wagner time-lock puzzle can be made publicly verifiable. Concretely, we give a statistically sound public-coin protocol to prove that a tuple (N,x,T,y) satisfies y=x2T (mod N) where the prover doesn’t know the factorization of N and its running time is dominated by solving the puzzle, that is, compute x2T, which is conjectured to require T sequential squarings. To get a VDF we make this protocol non-interactive using the Fiat-Shamir heuristic.The motivation for this work comes from the Chia blockchain design, which uses a VDF as akey ingredient. For typical parameters (T≤2 40, N= 2048), our proofs are of size around 10K B, verification cost around three RSA exponentiations and computing the proof is 8000 times faster than solving the puzzle even without any parallelism.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Published Version","file":[{"file_name":"2019_LIPIcs_Pietrzak.pdf","access_level":"open_access","file_size":558770,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6529","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-06T14:22:04Z","checksum":"f0ae1bb161431d9db3dea5ace082bfb5"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6528","ddc":["000"],"title":"Simple verifiable delay functions","status":"public","intvolume":" 124","day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"date_published":"2019-01-10T00:00:00Z","publication":"10th Innovations in Theoretical Computer Science Conference","citation":{"apa":"Pietrzak, K. Z. (2019). Simple verifiable delay functions. In 10th Innovations in Theoretical Computer Science Conference (Vol. 124). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.60","ieee":"K. Z. Pietrzak, “Simple verifiable delay functions,” in 10th Innovations in Theoretical Computer Science Conference, San Diego, CA, United States, 2019, vol. 124.","ista":"Pietrzak KZ. 2019. Simple verifiable delay functions. 10th Innovations in Theoretical Computer Science Conference. ITCS 2019: Innovations in Theoretical Computer Science, LIPIcs, vol. 124, 60.","ama":"Pietrzak KZ. Simple verifiable delay functions. In: 10th Innovations in Theoretical Computer Science Conference. Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.ITCS.2019.60","chicago":"Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” In 10th Innovations in Theoretical Computer Science Conference, Vol. 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ITCS.2019.60.","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","mla":"Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” 10th Innovations in Theoretical Computer Science Conference, vol. 124, 60, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.ITCS.2019.60."}},{"scopus_import":"1","day":"16","article_processing_charge":"No","has_accepted_license":"1","publication":"5th Indian Control Conference Proceedings","citation":{"chicago":"Kundu, Atreyee, Miriam Garcia Soto, and Pavithra Prabhakar. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” In 5th Indian Control Conference Proceedings. IEEE, 2019. https://doi.org/10.1109/INDIANCC.2019.8715598.","mla":"Kundu, Atreyee, et al. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” 5th Indian Control Conference Proceedings, 8715598, IEEE, 2019, doi:10.1109/INDIANCC.2019.8715598.","short":"A. Kundu, M. Garcia Soto, P. Prabhakar, in:, 5th Indian Control Conference Proceedings, IEEE, 2019.","ista":"Kundu A, Garcia Soto M, Prabhakar P. 2019. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. 5th Indian Control Conference Proceedings. ICC 2019 - Indian Control Conference, 8715598.","apa":"Kundu, A., Garcia Soto, M., & Prabhakar, P. (2019). Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In 5th Indian Control Conference Proceedings. Delhi, India: IEEE. https://doi.org/10.1109/INDIANCC.2019.8715598","ieee":"A. Kundu, M. Garcia Soto, and P. Prabhakar, “Formal synthesis of stabilizing controllers for periodically controlled linear switched systems,” in 5th Indian Control Conference Proceedings, Delhi, India, 2019.","ama":"Kundu A, Garcia Soto M, Prabhakar P. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In: 5th Indian Control Conference Proceedings. IEEE; 2019. doi:10.1109/INDIANCC.2019.8715598"},"date_published":"2019-05-16T00:00:00Z","type":"conference","abstract":[{"text":"In this paper, we address the problem of synthesizing periodic switching controllers for stabilizing a family of linear systems. Our broad approach consists of constructing a finite game graph based on the family of linear systems such that every winning strategy on the game graph corresponds to a stabilizing switching controller for the family of linear systems. The construction of a (finite) game graph, the synthesis of a winning strategy and the extraction of a stabilizing controller are all computationally feasible. We illustrate our method on an example.","lang":"eng"}],"ddc":["000"],"title":"Formal synthesis of stabilizing controllers for periodically controlled linear switched systems","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6565","file":[{"file_name":"2019_ICC_Kundu.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":396031,"file_id":"8687","relation":"main_file","date_created":"2020-10-21T13:13:49Z","date_updated":"2020-10-21T13:13:49Z","success":1,"checksum":"d622a91af1e427f6b1e0ba8e18a2b767"}],"oa_version":"Submitted Version","month":"05","publication_identifier":{"isbn":["978-153866246-5"]},"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2019-01-11","start_date":"2019-01-09","location":"Delhi, India","name":"ICC 2019 - Indian Control Conference"},"doi":"10.1109/INDIANCC.2019.8715598","article_number":"8715598","file_date_updated":"2020-10-21T13:13:49Z","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IEEE","year":"2019","date_created":"2019-06-17T06:57:33Z","date_updated":"2021-01-12T08:08:01Z","author":[{"full_name":"Kundu, Atreyee","last_name":"Kundu","first_name":"Atreyee"},{"orcid":"0000−0003−2936−5719","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","last_name":"Garcia Soto","first_name":"Miriam","full_name":"Garcia Soto, Miriam"},{"full_name":"Prabhakar, Pavithra","first_name":"Pavithra","last_name":"Prabhakar"}]},{"type":"conference","abstract":[{"text":"Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces in Euclidean space by piecewise flat triangular meshes with a given number of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and d is the dimension of Euclidean space. Moreover the pro-portionality constant can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In this short note, we prove the extrinsic nature of this constant for manifolds of sufficiently high codimension. We do so by constructing an family of isometric embeddings of the flat torus in Euclidean space.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"publication_status":"published","title":"The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds","status":"public","ddc":["004"],"department":[{"_id":"HeEd"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6628","year":"2019","date_updated":"2021-01-12T08:08:16Z","date_created":"2019-07-12T08:34:57Z","file":[{"checksum":"ceabd152cfa55170d57763f9c6c60a53","date_created":"2019-07-12T08:32:46Z","date_updated":"2020-07-14T12:47:34Z","file_id":"6629","relation":"main_file","creator":"mwintrae","content_type":"application/pdf","file_size":321176,"access_level":"open_access","file_name":"IntrinsicExtrinsicCCCG2019.pdf"}],"oa_version":"Submitted Version","author":[{"first_name":"Gert","last_name":"Vegter","full_name":"Vegter, Gert"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs"}],"scopus_import":1,"month":"08","day":"01","has_accepted_license":"1","quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"page":"275-279","publication":"The 31st Canadian Conference in Computational Geometry","oa":1,"citation":{"chicago":"Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff Distance of Optimal Triangulations of Manifolds.” In The 31st Canadian Conference in Computational Geometry, 275–79, 2019.","short":"G. Vegter, M. Wintraecken, in:, The 31st Canadian Conference in Computational Geometry, 2019, pp. 275–279.","mla":"Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff Distance of Optimal Triangulations of Manifolds.” The 31st Canadian Conference in Computational Geometry, 2019, pp. 275–79.","apa":"Vegter, G., & Wintraecken, M. (2019). The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. In The 31st Canadian Conference in Computational Geometry (pp. 275–279). Edmonton, Canada.","ieee":"G. Vegter and M. Wintraecken, “The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds,” in The 31st Canadian Conference in Computational Geometry, Edmonton, Canada, 2019, pp. 275–279.","ista":"Vegter G, Wintraecken M. 2019. The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. The 31st Canadian Conference in Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 275–279.","ama":"Vegter G, Wintraecken M. The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. In: The 31st Canadian Conference in Computational Geometry. ; 2019:275-279."},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-08-10","start_date":"2019-08-08","location":"Edmonton, Canada","name":"CCCG: Canadian Conference in Computational Geometry"},"date_published":"2019-08-01T00:00:00Z"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2019","volume":129,"date_created":"2019-07-17T10:36:09Z","date_updated":"2021-01-12T08:08:23Z","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Virk, Ziga","first_name":"Ziga","last_name":"Virk"},{"id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","last_name":"Wagner","full_name":"Wagner, Hubert"}],"file_date_updated":"2020-07-14T12:47:35Z","project":[{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1903.08510"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPICS.SOCG.2019.31","conference":{"end_date":"2019-06-21","start_date":"2019-06-18","location":"Portland, OR, United States","name":"SoCG 2019: Symposium on Computational Geometry"},"publication_identifier":{"isbn":["9783959771047"]},"month":"06","intvolume":" 129","ddc":["510"],"status":"public","title":"Topological data analysis in information space","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6648","file":[{"checksum":"8ec8720730d4c789bf7b06540f1c29f4","date_created":"2019-07-24T06:40:01Z","date_updated":"2020-07-14T12:47:35Z","file_id":"6666","relation":"main_file","creator":"dernst","file_size":1355179,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_LIPICS_Edelsbrunner.pdf"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory\r\nneeded for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.","lang":"eng"}],"page":"31:1-31:14","citation":{"short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14.","mla":"Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14, doi:10.4230/LIPICS.SOCG.2019.31.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data Analysis in Information Space.” In 35th International Symposium on Computational Geometry, 129:31:1-31:14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.31.","ama":"Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information space. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:31:1-31:14. doi:10.4230/LIPICS.SOCG.2019.31","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2019). Topological data analysis in information space. In 35th International Symposium on Computational Geometry (Vol. 129, p. 31:1-31:14). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.31","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information space,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 31:1-31:14.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2019. Topological data analysis in information space. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 31:1-31:14."},"publication":"35th International Symposium on Computational Geometry","date_published":"2019-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Chemical labeling of proteins with synthetic molecular probes offers the possibility to probe the functions of proteins of interest in living cells. However, the methods for covalently labeling targeted proteins using complementary peptide tag-probe pairs are still limited, irrespective of the versatility of such pairs in biological research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific covalent labeling of proteins. A broad-range evaluation of the reactivity profiles of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized and high labeling selectivity and reactivity. In particular, the labeling specificity of this pair was notably improved compared to the previously reported one. This pair was successfully utilized for the fluorescence imaging of membrane proteins on the surfaces of living cells, demonstrating its potential utility in biological research."}],"issue":"5","title":"Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins","status":"public","ddc":["570"],"intvolume":" 92","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6659","file":[{"file_size":2464903,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_BCSJ_Zenmyo.pdf","checksum":"186de511d6e0ca93f5d981e2443eb8cd","success":1,"date_updated":"2020-10-02T08:49:58Z","date_created":"2020-10-02T08:49:58Z","relation":"main_file","file_id":"8594"}],"oa_version":"Published Version","scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"995-1000","publication":"Bulletin of the Chemical Society of Japan","citation":{"short":"N. Zenmyo, H. Tokumaru, S. Uchinomiya, H. Fuchida, S. Tabata, I. Hamachi, R. Shigemoto, A. Ojida, Bulletin of the Chemical Society of Japan 92 (2019) 995–1000.","mla":"Zenmyo, Naoki, et al. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan, vol. 92, no. 5, Bulletin of the Chemical Society of Japan, 2019, pp. 995–1000, doi:10.1246/bcsj.20190034.","chicago":"Zenmyo, Naoki, Hiroki Tokumaru, Shohei Uchinomiya, Hirokazu Fuchida, Shigekazu Tabata, Itaru Hamachi, Ryuichi Shigemoto, and Akio Ojida. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan, 2019. https://doi.org/10.1246/bcsj.20190034.","ama":"Zenmyo N, Tokumaru H, Uchinomiya S, et al. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 2019;92(5):995-1000. doi:10.1246/bcsj.20190034","apa":"Zenmyo, N., Tokumaru, H., Uchinomiya, S., Fuchida, H., Tabata, S., Hamachi, I., … Ojida, A. (2019). Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan. https://doi.org/10.1246/bcsj.20190034","ieee":"N. Zenmyo et al., “Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins,” Bulletin of the Chemical Society of Japan, vol. 92, no. 5. Bulletin of the Chemical Society of Japan, pp. 995–1000, 2019.","ista":"Zenmyo N, Tokumaru H, Uchinomiya S, Fuchida H, Tabata S, Hamachi I, Shigemoto R, Ojida A. 2019. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 92(5), 995–1000."},"date_published":"2019-05-15T00:00:00Z","file_date_updated":"2020-10-02T08:49:58Z","ec_funded":1,"publication_status":"published","publisher":"Bulletin of the Chemical Society of Japan","department":[{"_id":"RySh"}],"acknowledgement":"his work was supported by the Grant-in-Aid for Scientific Research B (JSPS KAKENHI grant no. JP17H03090 to A. O.); the Scientific Research on Innovative Areas “Chemistry for Multimolecular Crowding Biosystems” (JSPS KAKENHI grant no. JP17H06349 to A. O.); and the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.). A. O. acknowledges the financial support of the Takeda Science Foundation.","year":"2019","date_updated":"2021-01-12T08:08:26Z","date_created":"2019-07-21T21:59:16Z","volume":92,"author":[{"first_name":"Naoki","last_name":"Zenmyo","full_name":"Zenmyo, Naoki"},{"last_name":"Tokumaru","first_name":"Hiroki","full_name":"Tokumaru, Hiroki"},{"first_name":"Shohei","last_name":"Uchinomiya","full_name":"Uchinomiya, Shohei"},{"full_name":"Fuchida, Hirokazu","first_name":"Hirokazu","last_name":"Fuchida"},{"full_name":"Tabata, Shigekazu","id":"4427179E-F248-11E8-B48F-1D18A9856A87","first_name":"Shigekazu","last_name":"Tabata"},{"first_name":"Itaru","last_name":"Hamachi","full_name":"Hamachi, Itaru"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"first_name":"Akio","last_name":"Ojida","full_name":"Ojida, Akio"}],"month":"05","publication_identifier":{"issn":["00092673"]},"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1246/bcsj.20190034"}]