[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Hainzl, Christian, et al. “Many-Body Quantum Systems.” Oberwolfach Reports, vol. 16, no. 3, European Mathematical Society, 2020, pp. 2541–603, doi:10.4171/owr/2019/41.","ama":"Hainzl C, Schlein B, Seiringer R, Warzel S. Many-body quantum systems. Oberwolfach Reports. 2020;16(3):2541-2603. doi:10.4171/owr/2019/41","apa":"Hainzl, C., Schlein, B., Seiringer, R., & Warzel, S. (2020). Many-body quantum systems. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2019/41","short":"C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 16 (2020) 2541–2603.","ieee":"C. Hainzl, B. Schlein, R. Seiringer, and S. Warzel, “Many-body quantum systems,” Oberwolfach Reports, vol. 16, no. 3. European Mathematical Society, pp. 2541–2603, 2020.","chicago":"Hainzl, Christian, Benjamin Schlein, Robert Seiringer, and Simone Warzel. “Many-Body Quantum Systems.” Oberwolfach Reports. European Mathematical Society, 2020. https://doi.org/10.4171/owr/2019/41.","ista":"Hainzl C, Schlein B, Seiringer R, Warzel S. 2020. Many-body quantum systems. Oberwolfach Reports. 16(3), 2541–2603."},"date_updated":"2024-03-12T12:02:00Z","department":[{"_id":"RoSe"}],"title":"Many-body quantum systems","author":[{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simone","last_name":"Warzel","full_name":"Warzel, Simone"}],"article_processing_charge":"No","_id":"15072","status":"public","article_type":"original","type":"journal_article","day":"10","publication":"Oberwolfach Reports","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1660-8933"]},"year":"2020","publication_status":"published","volume":16,"doi":"10.4171/owr/2019/41","issue":"3","date_published":"2020-09-10T00:00:00Z","date_created":"2024-03-04T11:46:12Z","page":"2541-2603","oa_version":"None","abstract":[{"text":"The interaction among fundamental particles in nature leads to many interesting effects in quantum statistical mechanics; examples include superconductivity for charged systems and superfluidity in cold gases. It is a huge challenge for mathematical physics to understand the collective behavior of systems containing a large number of particles, emerging from known microscopic interactions. In this workshop we brought together researchers working on different aspects of many-body quantum mechanics to discuss recent developments, exchange ideas and propose new challenges and research directions.","lang":"eng"}],"month":"09","intvolume":" 16","publisher":"European Mathematical Society","quality_controlled":"1"},{"publication_status":"published","file":[{"creator":"dernst","date_updated":"2024-03-20T08:05:46Z","file_size":595543,"date_created":"2024-03-20T08:05:46Z","file_name":"2020_ECM_Oshurkova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d1914af7811a21a4b2744eb51b5834e3","file_id":"15127","success":1}],"language":[{"iso":"eng"}],"month":"11","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"FyKo"}],"file_date_updated":"2024-03-20T08:05:46Z","date_updated":"2024-03-20T08:06:22Z","ddc":["570"],"type":"conference","conference":{"name":"ECM: Electronic Conference on Microbiology","end_date":"2020-11-30","location":"Virtual","start_date":"2020-11-02"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"15071","doi":"10.3390/ecm2020-07116","date_published":"2020-11-02T00:00:00Z","date_created":"2024-03-04T11:41:31Z","has_accepted_license":"1","year":"2020","day":"02","publication":"Proceedings of 1st International Electronic Conference on Microbiology","quality_controlled":"1","publisher":"MDPI","oa":1,"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. ","author":[{"first_name":"Viktoriia","full_name":"Oshurkova, Viktoriia","last_name":"Oshurkova"},{"full_name":"Troshina, Olga","last_name":"Troshina","first_name":"Olga"},{"last_name":"Trubitsyn","full_name":"Trubitsyn, Vladimir","first_name":"Vladimir"},{"first_name":"Yana","full_name":"Ryzhmanova, Yana","last_name":"Ryzhmanova"},{"last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga"},{"first_name":"Viktoria","full_name":"Shcherbakova, Viktoria","last_name":"Shcherbakova"}],"article_processing_charge":"Yes","title":"Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T","citation":{"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.","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.","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.","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","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","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.","short":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V. Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"28","page":"79","date_created":"2020-02-26T10:56:37Z","doi":"10.15479/AT:ISTA:7525","date_published":"2020-02-28T00:00:00Z","citation":{"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.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","last_name":"Bhandari","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","first_name":"Pradeep"}],"title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","acknowledged_ssus":[{"_id":"EM-Fac"}],"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"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"02","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2021-02-28","file_id":"7538","checksum":"4589234fdb12b4ad72273b311723a7b4","creator":"pbhandari","file_size":9646346,"date_updated":"2021-03-01T23:30:04Z","file_name":"Pradeep Bhandari Thesis.pdf","date_created":"2020-02-28T08:37:53Z","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway"},{"file_id":"7539","checksum":"aa79490553ca0a5c9b6fbcd152e93928","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","date_created":"2020-02-28T08:47:14Z","file_name":"Pradeep Bhandari Thesis.docx","date_updated":"2021-03-01T23:30:04Z","file_size":35252164,"creator":"pbhandari"}],"_id":"7525","type":"dissertation","keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"status":"public","date_updated":"2023-09-07T13:20:03Z","supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"}],"ddc":["570"],"file_date_updated":"2021-03-01T23:30:04Z","department":[{"_id":"RySh"}]},{"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"c48cbf594e84fc2f91966ffaafc0918c","file_id":"8937","creator":"dernst","file_size":7076870,"date_updated":"2020-12-10T14:01:10Z","file_name":"2020_JourStrucBiology_Faessler.pdf","date_created":"2020-12-10T14:01:10Z"}],"publication_status":"published","publication_identifier":{"issn":["1047-8477"]},"issue":"3","volume":212,"related_material":{"record":[{"id":"14592","status":"public","relation":"used_in_publication"},{"id":"12491","status":"public","relation":"dissertation_contains"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"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."}],"intvolume":" 212","month":"12","scopus_import":"1","ddc":["570"],"date_updated":"2024-03-27T23:30:05Z","file_date_updated":"2020-12-10T14:01:10Z","department":[{"_id":"FlSc"}],"_id":"8586","keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","publication":"Journal of Structural Biology","day":"01","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-09-29T13:24:06Z","doi":"10.1016/j.jsb.2020.107633","date_published":"2020-12-01T00:00:00Z","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.","oa":1,"quality_controlled":"1","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","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.","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","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","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.","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.","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."},"title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000600997800008"]},"author":[{"first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X"},{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina","last_name":"Zens"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"article_number":"107633","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}]},{"type":"dissertation","status":"public","_id":"8657","file_date_updated":"2021-10-07T22:30:03Z","department":[{"_id":"GaTk"}],"supervisor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:20:48Z","ddc":["571","530","570"],"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7673","relation":"part_of_dissertation"},{"id":"8250","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-011-4"]},"degree_awarded":"PhD","publication_status":"published","file":[{"date_created":"2020-10-15T06:41:20Z","file_name":"kavcicB_thesis202009.pdf","date_updated":"2021-10-07T22:30:03Z","file_size":52636162,"creator":"bkavcic","file_id":"8663","checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb","embargo":"2021-10-06","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"checksum":"bb35f2352a04db19164da609f00501f3","file_id":"8664","embargo_to":"open_access","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"2020b.zip","date_created":"2020-10-15T06:41:53Z","file_size":321681247,"date_updated":"2021-10-07T22:30:03Z","creator":"bkavcic"}],"language":[{"iso":"eng"}],"author":[{"last_name":"Kavcic","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"}],"article_processing_charge":"No","title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","citation":{"ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria.","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.","ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 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","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.","ieee":"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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","oa":1,"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.","page":"271","date_published":"2020-10-14T00:00:00Z","doi":"10.15479/AT:ISTA:8657","date_created":"2020-10-13T16:46:14Z","has_accepted_license":"1","year":"2020","day":"14"},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","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.","page":"992-1006","date_created":"2020-02-10T15:59:45Z","date_published":"2020-03-18T00:00:00Z","doi":"10.1016/j.neuron.2019.12.022","year":"2020","isi":1,"has_accepted_license":"1","publication":"Neuron","day":"18","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit"}],"article_processing_charge":"No","external_id":{"isi":["000520854700008"],"pmid":["31928842"]},"author":[{"last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena","last_name":"Kim"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","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.","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","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","short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 105","month":"03","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","pmid":1,"ec_funded":1,"volume":105,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/","description":"News on IST Homepage"}],"record":[{"status":"public","id":"11196","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"issn":["0896-6273"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"3582664addf26859e86ac5bec3e01416","file_id":"8778","file_size":9712957,"date_updated":"2020-11-20T08:58:53Z","creator":"dernst","file_name":"2020_Neuron_BorgesMerjane.pdf","date_created":"2020-11-20T08:58:53Z"}],"tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","_id":"7473","department":[{"_id":"PeJo"}],"file_date_updated":"2020-11-20T08:58:53Z","date_updated":"2024-03-27T23:30:07Z","ddc":["570"]},{"date_updated":"2024-03-27T23:30:08Z","ddc":["570"],"file_date_updated":"2020-08-17T07:36:57Z","department":[{"_id":"GaTk"}],"_id":"8250","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"986bebb308850a55850028d3d2b5b664","file_id":"8275","success":1,"creator":"dernst","date_updated":"2020-08-17T07:36:57Z","file_size":1965672,"date_created":"2020-08-17T07:36:57Z","file_name":"2020_NatureComm_Kavcic.pdf"}],"language":[{"iso":"eng"}],"volume":11,"related_material":{"record":[{"id":"8657","status":"public","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","month":"08","intvolume":" 11","citation":{"ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013.","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.","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","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","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","last_name":"Kavcic"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"}],"article_processing_charge":"No","external_id":{"isi":["000562769300008"]},"title":"Mechanisms of drug interactions between translation-inhibiting antibiotics","article_number":"4013","project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"11","publication":"Nature Communications","date_published":"2020-08-11T00:00:00Z","doi":"10.1038/s41467-020-17734-z","date_created":"2020-08-12T09:13:50Z","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.","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"date_published":"2020-04-18T00:00:00Z","related_material":{"record":[{"status":"public","id":"8997","relation":"later_version"},{"status":"public","id":"8657","relation":"dissertation_contains"}]},"doi":"10.1101/2020.04.18.047886","date_created":"2020-04-22T08:27:56Z","day":"18","language":[{"iso":"eng"}],"publication":"bioRxiv","publication_status":"published","year":"2020","month":"04","publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.18.047886 "}],"oa":1,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"title":"A minimal biophysical model of combined antibiotic action","department":[{"_id":"GaTk"}],"author":[{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.","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.","ama":"Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi: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.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020)."},"date_updated":"2024-03-27T23:30:08Z","status":"public","project":[{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"type":"preprint","_id":"7673"},{"volume":117,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"9992","status":"public","relation":"dissertation_contains"}]},"issue":"26","ec_funded":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","file":[{"checksum":"908b09437680181de9990915f2113aca","file_id":"8009","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_PNAS_Hoermayer.pdf","date_created":"2020-06-23T11:30:53Z","file_size":2407102,"date_updated":"2020-07-14T12:48:07Z","creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 117","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"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"}],"oa_version":"None","pmid":1,"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:48:07Z","date_updated":"2024-03-27T23:30:11Z","ddc":["580"],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"8002","date_published":"2020-06-30T00:00:00Z","doi":"10.1073/pnas.2003346117","date_created":"2020-06-22T13:33:52Z","has_accepted_license":"1","isi":1,"year":"2020","day":"30","publication":"Proceedings of the National Academy of Sciences","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"author":[{"first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926"},{"first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López"},{"last_name":"Marhavá","full_name":"Marhavá, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yoshida","full_name":"Yoshida, Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"external_id":{"pmid":["32541049"],"isi":["000565729700033"]},"article_processing_charge":"No","title":"Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots","citation":{"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.","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.","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.","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","short":"L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J. Friml, Proceedings of the National Academy of Sciences 117 (2020).","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"}],"article_number":"202003346"},{"alternative_title":["ISTA Thesis"],"month":"04","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"}],"oa_version":"None","related_material":{"record":[{"relation":"dissertation_contains","id":"1028","status":"public"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"eissn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_size":3268017,"date_updated":"2021-10-31T23:30:05Z","creator":"stgingl","file_name":"Thesis_without-signatures_PDFA.pdf","date_created":"2020-04-28T11:19:21Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2021-10-30","checksum":"fb9a4468eb27be92690728e35c823796","file_id":"7692"},{"file_id":"7693","checksum":"f6c80ca97104a631a328cb79a2c53493","content_type":"application/octet-stream","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2020-04-28T11:19:24Z","file_name":"Thesis_without signatures.docx","date_updated":"2021-10-31T23:30:05Z","file_size":5167703,"creator":"stgingl"}],"type":"dissertation","status":"public","_id":"7680","file_date_updated":"2021-10-31T23:30:05Z","department":[{"_id":"CaGu"}],"date_updated":"2023-09-22T09:20:10Z","supervisor":[{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"oa":1,"publisher":"Institute of Science and Technology Austria","page":"98","date_created":"2020-04-24T16:00:51Z","date_published":"2020-04-24T00:00:00Z","doi":"10.15479/AT:ISTA:7680","year":"2020","has_accepted_license":"1","day":"24","article_processing_charge":"No","author":[{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"Kainrath","full_name":"Kainrath, Stephanie"}],"title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","citation":{"ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680","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","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.","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7800"},{"id":"8131","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"embargo":"2021-10-15","checksum":"7ee83e42de3e5ce2fedb44dff472f75f","file_id":"8621","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Jasmin_Morandell_Thesis-2020_final.pdf","date_created":"2020-10-07T14:41:49Z","creator":"jmorande","file_size":16155786,"date_updated":"2021-10-16T22:30:04Z"},{"file_name":"Jasmin_Morandell_Thesis-2020_final.zip","date_created":"2020-10-07T14:45:07Z","creator":"jmorande","file_size":24344152,"date_updated":"2021-10-16T22:30:04Z","checksum":"5e0464af453734210ce7aab7b4a92e3a","file_id":"8622","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"10","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"department":[{"_id":"GaNo"}],"file_date_updated":"2021-10-16T22:30:04Z","ddc":["610"],"date_updated":"2023-09-07T13:22:14Z","supervisor":[{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"status":"public","type":"dissertation","_id":"8620","date_created":"2020-10-07T14:53:13Z","date_published":"2020-10-12T00:00:00Z","doi":"10.15479/AT:ISTA:8620","page":"138","day":"12","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","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.","title":"Illuminating the role of Cul3 in autism spectrum disorder pathogenesis","article_processing_charge":"No","author":[{"first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin","last_name":"Morandell"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","ista":"Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria.","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.","ieee":"J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020.","short":"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","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"},"project":[{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"},{"name":"Neural stem cells in autism and epilepsy","grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"}]},{"title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","article_processing_charge":"No","author":[{"full_name":"Kampjut, Domen","last_name":"Kampjut","first_name":"Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","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.","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020.","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","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","ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi: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."},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-09-07T18:42:23Z","date_published":"2020-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:8340","page":"242","day":"09","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","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.","department":[{"_id":"LeSa"}],"file_date_updated":"2021-09-11T22:30:04Z","ddc":["572"],"date_updated":"2023-09-07T13:26:17Z","supervisor":[{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"status":"public","type":"dissertation","_id":"8340","ec_funded":1,"related_material":{"record":[{"status":"public","id":"6848","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"creator":"dkampjut","date_updated":"2021-09-11T22:30:04Z","file_size":166146359,"date_created":"2020-09-08T13:32:06Z","file_name":"ThesisFull20200908.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"dd270baf82121eb4472ad19d77bf227c","file_id":"8345"},{"embargo":"2021-09-10","file_id":"8393","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_Thesis_Kampjut.pdf","date_created":"2020-09-14T15:02:20Z","creator":"dernst","file_size":13873769,"date_updated":"2021-09-11T22:30:04Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-008-4"],"issn":["2663-337X"]},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"None","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."}],"acknowledged_ssus":[{"_id":"EM-Fac"}]},{"ddc":["570"],"date_updated":"2024-03-27T23:30:14Z","file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"JoDa"},{"_id":"GaNo"},{"_id":"LifeSc"}],"_id":"7800","status":"public","type":"preprint","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"file":[{"date_created":"2020-05-05T14:31:19Z","file_name":"2020.01.10.902064v1.full.pdf","creator":"rsix","date_updated":"2020-07-14T12:48:03Z","file_size":2931370,"file_id":"7801","checksum":"c6799ab5daba80efe8e2ed63c15f8c81","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"submitted","related_material":{"record":[{"status":"public","id":"9429","relation":"later_version"},{"status":"public","id":"8620","relation":"dissertation_contains"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"PreCl"}],"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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 .","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 .","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.).","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.","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 ","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 ","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 ."},"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","author":[{"last_name":"Morandell","full_name":"Morandell, Jasmin","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","full_name":"Schwarz, Lena A"},{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","last_name":"Basilico","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette"},{"first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X"},{"first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","full_name":"Nicolas, Armel"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","last_name":"Knaus","full_name":"Knaus, Lisa"},{"full_name":"Dobler, Zoe","last_name":"Dobler","first_name":"Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F"},{"last_name":"Cacci","full_name":"Cacci, Emanuele","first_name":"Emanuele"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"}],"article_processing_charge":"No","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"}],"day":"11","publication":"bioRxiv","has_accepted_license":"1","year":"2020","date_published":"2020-01-11T00:00:00Z","doi":"10.1101/2020.01.10.902064 ","date_created":"2020-05-05T14:31:33Z","publisher":"Cold Spring Harbor Laboratory","oa":1},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"doi":"10.1016/j.gde.2020.06.004","date_published":"2020-12-01T00:00:00Z","date_created":"2020-07-19T22:00:58Z","page":"126-137","day":"01","publication":"Current Opinion in Genetics and Development","has_accepted_license":"1","isi":1,"year":"2020","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07807","name":"Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"}],"title":"Molecular mechanisms for targeted ASD treatments","author":[{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette","last_name":"Basilico"},{"full_name":"Morandell, Jasmin","last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["32659636"],"isi":["000598918900019"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137.","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.","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.","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","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","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."},"month":"12","intvolume":" 65","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"volume":65,"issue":"12","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8620"}]},"ec_funded":1,"file":[{"date_created":"2020-07-22T06:47:45Z","file_name":"2020_CurrentOpGenetics_Basilico.pdf","date_updated":"2020-07-22T06:47:45Z","file_size":1381545,"creator":"dernst","file_id":"8146","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0959437X"],"eissn":["18790380"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"_id":"8131","department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-22T06:47:45Z","ddc":["570"],"date_updated":"2024-03-27T23:30:14Z"},{"_id":"8434","type":"journal_article","article_type":"original","status":"public","keyword":["Cell Biology"],"date_updated":"2023-09-05T15:41:48Z","ddc":["570"],"department":[{"_id":"FlSc"}],"file_date_updated":"2020-10-11T22:30:02Z","abstract":[{"lang":"eng","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. "}],"pmid":1,"oa_version":"Published Version","month":"04","intvolume":" 133","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"publication_status":"published","file":[{"file_id":"8435","checksum":"ba917e551acc4ece2884b751434df9ae","embargo":"2020-10-10","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-09-17T14:07:51Z","file_name":"2020_JournalCellScience_Dimchev.pdf","creator":"dernst","date_updated":"2020-10-11T22:30:02Z","file_size":13493302}],"language":[{"iso":"eng"}],"issue":"7","volume":133,"article_number":"jcs239020","project":[{"name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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.","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","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Amiri","full_name":"Amiri, Behnam","first_name":"Behnam"},{"full_name":"Humphries, Ashley C.","last_name":"Humphries","first_name":"Ashley C."},{"last_name":"Schaks","full_name":"Schaks, Matthias","first_name":"Matthias"},{"first_name":"Vanessa","last_name":"Dimchev","full_name":"Dimchev, Vanessa"},{"first_name":"Theresia E. B.","full_name":"Stradal, Theresia E. B.","last_name":"Stradal"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"first_name":"Matthias","full_name":"Krause, Matthias","last_name":"Krause"},{"last_name":"Way","full_name":"Way, Michael","first_name":"Michael"},{"first_name":"Martin","full_name":"Falcke, Martin","last_name":"Falcke"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"}],"article_processing_charge":"No","external_id":{"isi":["000534387800005"],"pmid":[" 32094266"]},"title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","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.","quality_controlled":"1","publisher":"The Company of Biologists","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"09","publication":"Journal of Cell Science","date_published":"2020-04-09T00:00:00Z","doi":"10.1242/jcs.239020","date_created":"2020-09-17T14:00:33Z"},{"scopus_import":"1","month":"04","intvolume":" 38","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","pmid":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41587-020-0578-0","relation":"erratum"}]},"volume":38,"ec_funded":1,"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"publication_status":"published","file":[{"embargo":"2021-03-01","checksum":"1b30467500ec6277229a875b06e196d0","file_id":"8316","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","date_created":"2020-08-28T08:57:07Z","file_size":1180086,"date_updated":"2021-03-02T23:30:03Z","creator":"dernst"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"7889","file_date_updated":"2021-03-02T23:30:03Z","department":[{"_id":"FyKo"}],"date_updated":"2023-09-05T15:30:34Z","ddc":["570"],"quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","page":"944-946","doi":"10.1038/s41587-020-0500-9","date_published":"2020-04-27T00:00:00Z","date_created":"2020-05-25T15:02:00Z","has_accepted_license":"1","isi":1,"year":"2020","day":"27","publication":"Nature Biotechnology","project":[{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"first_name":"Tatiana","full_name":"Mitiouchkina, Tatiana","last_name":"Mitiouchkina"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa"},{"full_name":"Markina, Nadezhda M.","last_name":"Markina","first_name":"Nadezhda M."},{"last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V."},{"last_name":"Guglya","full_name":"Guglya, Elena B.","first_name":"Elena B."},{"full_name":"Karataeva, Tatiana A.","last_name":"Karataeva","first_name":"Tatiana A."},{"first_name":"Kseniia A.","full_name":"Palkina, Kseniia A.","last_name":"Palkina"},{"full_name":"Shakhova, Ekaterina S.","last_name":"Shakhova","first_name":"Ekaterina S."},{"full_name":"Fakhranurova, Liliia I.","last_name":"Fakhranurova","first_name":"Liliia I."},{"first_name":"Sofia V.","full_name":"Chekova, Sofia V.","last_name":"Chekova"},{"last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S.","first_name":"Aleksandra S."},{"first_name":"Yaroslav V.","full_name":"Golubev, Yaroslav V.","last_name":"Golubev"},{"first_name":"Vadim V.","full_name":"Negrebetsky, Vadim V.","last_name":"Negrebetsky"},{"last_name":"Dolgushin","full_name":"Dolgushin, Sergey A.","first_name":"Sergey A."},{"full_name":"Shalaev, Pavel V.","last_name":"Shalaev","first_name":"Pavel V."},{"first_name":"Dmitry","last_name":"Shlykov","full_name":"Shlykov, Dmitry"},{"full_name":"Melnik, Olesya A.","last_name":"Melnik","first_name":"Olesya A."},{"full_name":"Shipunova, Victoria O.","last_name":"Shipunova","first_name":"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."},{"first_name":"Alexander S.","last_name":"Pushin","full_name":"Pushin, Alexander S."},{"full_name":"Choob, Vladimir V.","last_name":"Choob","first_name":"Vladimir V."},{"full_name":"Dolgov, Sergey V.","last_name":"Dolgov","first_name":"Sergey V."},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"last_name":"Yampolsky","full_name":"Yampolsky, Ilia V.","first_name":"Ilia V."},{"last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S.","first_name":"Karen S."}],"external_id":{"isi":["000529298800003"],"pmid":["32341562"]},"article_processing_charge":"No","title":"Plants with genetically encoded autoluminescence","citation":{"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.","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.","ieee":"T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"citation":{"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.","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.","short":"J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020).","ieee":"J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","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","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","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."},"date_updated":"2024-03-27T23:30:18Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Slovakova","full_name":"Slovakova, Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","first_name":"Jana"},{"first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia"},{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","last_name":"Huljev"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"_id":"9750","type":"preprint","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"187-2013","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","_id":"2521E28E-B435-11E9-9278-68D0E5697425"}],"status":"public","year":"2020","publication_status":"published","day":"20","language":[{"iso":"eng"}],"publication":"bioRxiv","page":"41","doi":"10.1101/2020.11.20.391284","related_material":{"record":[{"relation":"later_version","status":"public","id":"10766"},{"relation":"dissertation_contains","id":"9623","status":"public"}]},"date_published":"2020-11-20T00:00:00Z","date_created":"2021-07-29T11:29:50Z","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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"SSU"}],"oa_version":"Preprint","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.","publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"url":"https://doi.org/10.1101/2020.11.20.391284","open_access":"1"}],"oa":1,"month":"11"},{"date_updated":"2024-03-27T23:30:23Z","department":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"MiSi"}],"_id":"7885","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":582,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/off-road-mode-enables-mobile-cells-to-move-freely/"}],"record":[{"id":"14697","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"12401","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour."}],"oa_version":"None","scopus_import":"1","intvolume":" 582","month":"06","citation":{"ista":"Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL, de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK. 2020. Cellular locomotion using environmental topography. Nature. 582, 582–585.","chicago":"Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan, Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental Topography.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2283-z.","short":"A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez, M.K. Sixt, Nature 582 (2020) 582–585.","ieee":"A. Reversat et al., “Cellular locomotion using environmental topography,” Nature, vol. 582. Springer Nature, pp. 582–585, 2020.","ama":"Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental topography. Nature. 2020;582:582–585. doi:10.1038/s41586-020-2283-z","apa":"Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography. Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2283-z","mla":"Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.” Nature, vol. 582, Springer Nature, 2020, pp. 582–585, doi:10.1038/s41586-020-2283-z."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000532688300008"]},"author":[{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","last_name":"Gärtner","full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stopp, Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"last_name":"Tasciyan","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L","last_name":"Aguilera Servin","full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav"},{"full_name":"Piel, Matthieu","last_name":"Piel","first_name":"Matthieu"},{"last_name":"Callan-Jones","full_name":"Callan-Jones, Andrew","first_name":"Andrew"},{"first_name":"Raphael","last_name":"Voituriez","full_name":"Voituriez, Raphael"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"title":"Cellular locomotion using environmental topography","project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425","name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911"},{"call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687"}],"year":"2020","isi":1,"publication":"Nature","day":"25","page":"582–585","date_created":"2020-05-24T22:01:01Z","doi":"10.1038/s41586-020-2283-z","date_published":"2020-06-25T00:00:00Z","acknowledgement":"We thank A. Leithner and J. Renkawitz for discussion and critical reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic setups; the Bioimaging Facility of IST Austria for excellent support, as well as the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan, L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687.","quality_controlled":"1","publisher":"Springer Nature"},{"doi":"10.1016/j.nahs.2020.100856","date_published":"2020-05-01T00:00:00Z","date_created":"2020-02-02T23:00:59Z","isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Nonlinear Analysis: Hybrid Systems","quality_controlled":"1","publisher":"Elsevier","oa":1,"author":[{"last_name":"Garcia Soto","orcid":"0000−0003−2936−5719","full_name":"Garcia Soto, Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"},{"full_name":"Prabhakar, Pavithra","last_name":"Prabhakar","first_name":"Pavithra"}],"external_id":{"isi":["000528828600003"]},"article_processing_charge":"No","title":"Abstraction based verification of stability of polyhedral switched systems","citation":{"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.","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 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.","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","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","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"article_number":"100856","issue":"5","volume":36,"publication_identifier":{"issn":["1751-570X"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8688","checksum":"560abfddb53f9fe921b6744f59f2cfaa","embargo":"2022-05-15","creator":"dernst","date_updated":"2022-05-16T22:30:04Z","file_size":818774,"date_created":"2020-10-21T13:16:45Z","file_name":"2020_NAHS_GarciaSoto.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 36","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"}],"oa_version":"Submitted Version","department":[{"_id":"ToHe"}],"file_date_updated":"2022-05-16T22:30:04Z","date_updated":"2023-08-17T14:32:54Z","ddc":["000"],"type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"7426"},{"publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","page":"141","doi":"10.15479/AT:ISTA:8983","date_published":"2020-12-30T00:00:00Z","date_created":"2020-12-30T15:41:26Z","has_accepted_license":"1","year":"2020","day":"30","author":[{"first_name":"Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","full_name":"Emtenani, Shamsi","orcid":"0000-0001-6981-6938","last_name":"Emtenani"}],"article_processing_charge":"No","title":"Metabolic regulation of Drosophila macrophage tissue invasion","citation":{"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","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:10.15479/AT:ISTA:8983","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","mla":"Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"12","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"oa_version":"Published Version","related_material":{"record":[{"id":"8557","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6187"}]},"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"embargo":"2021-12-30","checksum":"ec2797ab7a6f253b35df0572b36d1b43","file_id":"8984","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","date_created":"2020-12-30T15:34:01Z","file_size":10848175,"date_updated":"2021-12-31T23:30:04Z","creator":"semtenan"},{"checksum":"cc30e6608a9815414024cf548dff3b3a","file_id":"8985","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","date_created":"2020-12-30T15:37:36Z","creator":"semtenan","file_size":10073648,"date_updated":"2021-12-31T23:30:04Z"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","_id":"8983","file_date_updated":"2021-12-31T23:30:04Z","department":[{"_id":"DaSi"}],"supervisor":[{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:24:17Z","ddc":["570"]},{"_id":"8557","type":"preprint","project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29638","name":"Drosophila TNFa´s Funktion in Immunzellen"},{"name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"24800","name":"Tissue barrier penetration is crucial for immunity and metastasis","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}],"status":"public","citation":{"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.","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.","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","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","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","ieee":"V. Belyaeva et al., “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” bioRxiv. .","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."},"date_updated":"2024-03-27T23:30:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Belyaeva","full_name":"Belyaeva, Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera"},{"full_name":"Wachner, Stephanie","last_name":"Wachner","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"},{"last_name":"Gridchyn","full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","first_name":"Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Linder","full_name":"Linder, Markus","first_name":"Markus"},{"last_name":"Emtenani","full_name":"Emtenani, Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87","first_name":"Shamsi"},{"last_name":"György","orcid":"0000-0002-1819-198X","full_name":"György, Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila"},{"first_name":"Maria","full_name":"Sibilia, Maria","last_name":"Sibilia"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"}],"title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"lang":"eng","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."}],"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.","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.09.18.301481"}],"oa":1,"month":"09","year":"2020","publication_status":"submitted","publication":"bioRxiv","language":[{"iso":"eng"}],"day":"18","date_created":"2020-09-23T09:36:47Z","ec_funded":1,"doi":"10.1101/2020.09.18.301481","related_material":{"record":[{"relation":"later_version","id":"10614","status":"public"},{"id":"8983","status":"public","relation":"dissertation_contains"}]},"date_published":"2020-09-18T00:00:00Z"},{"ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"10559","status":"public"},{"id":"8834","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"10058","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"file_size":1697939,"date_updated":"2020-12-02T10:42:31Z","creator":"gkatsaro","file_name":"Superconducting_2D_Ge.pdf","date_created":"2020-12-02T10:42:31Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"8832","checksum":"22a612e206232fa94b138b2c2f957582"}],"publication_status":"submitted","month":"12","oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"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."}],"file_date_updated":"2020-12-02T10:42:31Z","department":[{"_id":"GeKa"}],"ddc":["530"],"date_updated":"2024-03-27T23:30:26Z","status":"public","type":"preprint","_id":"8831","date_created":"2020-12-02T10:42:53Z","date_published":"2020-12-02T00:00:00Z","publication":"arXiv","day":"02","year":"2020","has_accepted_license":"1","oa":1,"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).","title":"Enhancement of proximity induced superconductivity in planar Germanium","external_id":{"arxiv":["2012.00322"]},"article_processing_charge":"No","author":[{"first_name":"Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","last_name":"Aggarwal","orcid":"0000-0001-9985-9293","full_name":"Aggarwal, Kushagra"},{"full_name":"Hofmann, Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C"},{"last_name":"Jirovec","full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez"},{"first_name":"Amir","full_name":"Sammak, Amir","last_name":"Sammak"},{"last_name":"Botifoll","full_name":"Botifoll, Marc","first_name":"Marc"},{"full_name":"Marti-Sanchez, Sara","last_name":"Marti-Sanchez","first_name":"Sara"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"full_name":"Scappucci, Giordano","last_name":"Scappucci","first_name":"Giordano"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, 2012.00322.","ieee":"K. Aggarwal et al., “Enhancement of proximity induced superconductivity in planar Germanium,” arXiv. .","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.).","ama":"Aggarwal K, Hofmann AC, Jirovec D, 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."},"project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"}],"article_number":"2012.00322"},{"publisher":"MDPI","quality_controlled":"1","oa":1,"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.","date_published":"2020-09-14T00:00:00Z","doi":"10.3390/ijms21186737","date_created":"2020-09-20T22:01:35Z","isi":1,"has_accepted_license":"1","year":"2020","day":"14","publication":"International Journal of Molecular Sciences","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","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":"25D32BC0-B435-11E9-9278-68D0E5697425","name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus"},{"grant_number":"785907","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","call_identifier":"H2020","_id":"26436750-B435-11E9-9278-68D0E5697425"}],"article_number":"6737","author":[{"last_name":"Kleindienst","full_name":"Kleindienst, David","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"last_name":"Bhandari","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Case","full_name":"Case, Matthew J","first_name":"Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fukazawa","full_name":"Fukazawa, Yugo","first_name":"Yugo"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000579945300001"]},"title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","citation":{"short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"09","intvolume":" 21","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"}],"oa_version":"Published Version","volume":21,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]},"issue":"18","ec_funded":1,"publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8551","checksum":"2e4f62f3cfe945b7391fc3070e5a289f","creator":"dernst","file_size":5748456,"date_updated":"2020-09-21T14:08:58Z","file_name":"2020_JournMolecSciences_Kleindienst.pdf","date_created":"2020-09-21T14:08:58Z"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"8532","department":[{"_id":"RySh"}],"file_date_updated":"2020-09-21T14:08:58Z","date_updated":"2024-03-27T23:30:30Z","ddc":["570"]},{"publication_status":"published","publication_identifier":{"isbn":["9783030449131"],"eissn":["16113349"],"issn":["03029743"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7895","checksum":"8618b80f4cf7b39a60e61a6445ad9807","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-26T13:34:48Z","file_name":"2020_LNCS_Chatterjee.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:03Z","file_size":651250}],"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"volume":12075,"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"}],"oa_version":"Published Version","alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 12075","month":"04","date_updated":"2024-03-27T23:30:33Z","ddc":["000"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:48:03Z","_id":"7810","conference":{"name":"ESOP: Programming Languages and Systems","location":"Dublin, Ireland","end_date":"2020-04-30","start_date":"2020-04-25"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","year":"2020","isi":1,"has_accepted_license":"1","publication":"European Symposium on Programming","day":"18","page":"112-140","date_created":"2020-05-10T22:00:50Z","doi":"10.1007/978-3-030-44914-8_5","date_published":"2020-04-18T00:00:00Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","citation":{"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.","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000681656800005"]},"article_processing_charge":"No","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"}],"title":"Optimal and perfectly parallel algorithms for on-demand data-flow analysis","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}]},{"file":[{"file_name":"2020_LNCS_ATVA_Asadi_accepted.pdf","date_created":"2020-11-06T07:41:03Z","creator":"dernst","file_size":726648,"date_updated":"2020-11-06T07:41:03Z","success":1,"file_id":"8729","checksum":"ae83f27e5b189d5abc2e7514f1b7e1b5","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783030591519"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783030591526"]},"publication_status":"published","volume":12302,"related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"oa_version":"Submitted Version","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"}],"month":"10","intvolume":" 12302","scopus_import":"1","alternative_title":["LNCS"],"ddc":["000"],"date_updated":"2024-03-27T23:30:33Z","file_date_updated":"2020-11-06T07:41:03Z","department":[{"_id":"KrCh"}],"_id":"8728","status":"public","type":"conference","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2020-10-19","end_date":"2020-10-23","location":"Hanoi, Vietnam"},"day":"12","publication":"Automated Technology for Verification and Analysis","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1007/978-3-030-59152-6_14","date_published":"2020-10-12T00:00:00Z","date_created":"2020-11-06T07:30:05Z","page":"253-270","publisher":"Springer Nature","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","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.","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."},"title":"Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth","author":[{"last_name":"Asadi","full_name":"Asadi, Ali","first_name":"Ali"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kiarash","full_name":"Mohammadi, Kiarash","last_name":"Mohammadi"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"external_id":{"isi":["000723555700014"]},"article_processing_charge":"No","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}]},{"year":"2020","isi":1,"publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","day":"11","page":"672-687","date_created":"2020-07-05T22:00:45Z","doi":"10.1145/3385412.3385969","date_published":"2020-06-11T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","citation":{"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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000614622300045"],"arxiv":["1902.04373"]},"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"},{"first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady"}],"title":"Polynomial invariant generation for non-deterministic recursive programs","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"isbn":["9781450376136"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"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"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1902.04373","open_access":"1"}],"scopus_import":"1","month":"06","date_updated":"2024-03-27T23:30:33Z","department":[{"_id":"KrCh"}],"_id":"8089","conference":{"name":"PLDI: Programming Language Design and Implementation","end_date":"2020-06-20","location":"London, United Kingdom","start_date":"2020-06-15"},"type":"conference","status":"public"},{"title":"An efficient algorithm for computing network reliability in small treewidth","article_processing_charge":"No","external_id":{"isi":["000501641400050"],"arxiv":["1712.09692"]},"author":[{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady"},{"first_name":"Fatemeh","full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665.","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.","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.","short":"A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (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","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","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."},"project":[{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"article_number":"106665","date_created":"2019-09-29T22:00:44Z","doi":"10.1016/j.ress.2019.106665","date_published":"2020-01-01T00:00:00Z","publication":"Reliability Engineering and System Safety","day":"01","year":"2020","isi":1,"oa":1,"quality_controlled":"1","publisher":"Elsevier","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).","department":[{"_id":"KrCh"}],"date_updated":"2024-03-27T23:30:33Z","status":"public","type":"journal_article","article_type":"original","_id":"6918","related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"volume":193,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["09518320"]},"intvolume":" 193","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1712.09692","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","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"}]},{"department":[{"_id":"VlKo"}],"file_date_updated":"2021-03-16T23:30:04Z","date_updated":"2023-09-06T11:27:15Z","ddc":["518","510","515"],"article_type":"original","type":"journal_article","status":"public","_id":"7161","ec_funded":1,"volume":184,"publication_status":"published","publication_identifier":{"eissn":["1573-2878"],"issn":["0022-3239"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8647","checksum":"9f6dc6c6bf2b48cb3a2091a9ed5feaf2","embargo":"2021-03-15","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-12T10:40:27Z","file_name":"2020_JourOptimizationTheoryApplic_Shehu.pdf","creator":"dernst","date_updated":"2021-03-16T23:30:04Z","file_size":332641}],"scopus_import":"1","intvolume":" 184","month":"03","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","article_processing_charge":"No","external_id":{"isi":["000511805200009"]},"author":[{"first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu"},{"last_name":"Gibali","full_name":"Gibali, Aviv","first_name":"Aviv"},{"last_name":"Sagratella","full_name":"Sagratella, Simone","first_name":"Simone"}],"title":"Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces","citation":{"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","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","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.","short":"Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications 184 (2020) 877–894.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"page":"877–894","date_created":"2019-12-09T21:33:44Z","doi":"10.1007/s10957-019-01616-6","date_published":"2020-03-01T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Journal of Optimization Theory and Applications","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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)."},{"date_created":"2020-04-08T15:20:53Z","date_published":"2020-04-01T00:00:00Z","doi":"10.1038/s41559-020-1132-7","page":"612-625","publication":"Nature Ecology & Evolution","day":"01","year":"2020","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.","title":"Gene amplification as a form of population-level gene expression regulation","external_id":{"isi":["000519008300005"]},"article_processing_charge":"No","author":[{"full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","last_name":"Tomanek","first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87"},{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"},{"full_name":"Lagator, M.","last_name":"Lagator","first_name":"M."},{"first_name":"A. M. C.","last_name":"Andersson","full_name":"Andersson, A. M. C."},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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","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.","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."},"project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"volume":4,"related_material":{"record":[{"status":"public","id":"8155","relation":"dissertation_contains"},{"status":"public","id":"7383","relation":"research_data"},{"id":"7016","status":"public","relation":"research_data"},{"id":"8653","status":"public","relation":"used_in_publication"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","description":"News on IST Homepage"}]},"issue":"4","language":[{"iso":"eng"}],"file":[{"file_name":"2020_NatureEcolEvo_Tomanek.pdf","date_created":"2020-10-09T09:56:01Z","file_size":745242,"date_updated":"2020-10-09T09:56:01Z","creator":"dernst","success":1,"file_id":"8640","checksum":"ef3bbf42023e30b2c24a6278025d2040","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["2397-334X"]},"intvolume":" 4","month":"04","scopus_import":"1","oa_version":"Submitted Version","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."}],"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2020-10-09T09:56:01Z","ddc":["570"],"date_updated":"2024-03-27T23:30:36Z","status":"public","type":"journal_article","article_type":"original","_id":"7652"},{"project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"name":"Eliminating turbulence in oil pipelines","grant_number":"737549","call_identifier":"H2020","_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"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria.","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.","ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020.","ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:10.15479/AT:ISTA:7258","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"},"title":"New approaches to reduce friction in turbulent pipe flow","author":[{"full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","last_name":"Scarselli","first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"13","has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:7258","date_published":"2020-01-13T00:00:00Z","date_created":"2020-01-12T16:07:26Z","page":"174","_id":"7258","status":"public","type":"dissertation","ddc":["532"],"supervisor":[{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"date_updated":"2023-09-15T12:20:08Z","department":[{"_id":"BjHo"}],"file_date_updated":"2021-01-13T23:30:05Z","oa_version":"None","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."}],"month":"01","alternative_title":["ISTA Thesis"],"file":[{"checksum":"4df1ab24e9896635106adde5a54615bf","file_id":"7259","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip","file_name":"2020_Scarselli_Thesis.zip","date_created":"2020-01-12T15:57:14Z","creator":"dscarsel","file_size":26640830,"date_updated":"2021-01-13T23:30:05Z"},{"embargo":"2021-01-12","file_id":"7260","checksum":"48659ab98e3414293c7a721385c2fd1c","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_Scarselli_Thesis.pdf","date_created":"2020-01-12T15:56:14Z","file_size":8515844,"date_updated":"2021-01-13T23:30:05Z","creator":"dscarsel"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"6228","relation":"part_of_dissertation"},{"status":"public","id":"6486","relation":"part_of_dissertation"},{"status":"public","id":"461","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"422"}]},"ec_funded":1},{"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"8666","checksum":"c01d9f59794b4b70528f37637c17ad02","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Thesis_ITomanek_final_201016.docx","date_created":"2020-10-16T12:14:21Z","file_size":25131884,"date_updated":"2021-10-20T22:30:03Z","creator":"itomanek"},{"creator":"itomanek","date_updated":"2021-10-20T22:30:03Z","file_size":15405675,"date_created":"2020-10-16T12:14:21Z","file_name":"Thesis_ITomanek_final_201016.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8667","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","embargo":"2021-10-19"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"7652","status":"public"}]},"abstract":[{"lang":"eng","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. "}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"date_updated":"2023-09-07T13:22:42Z","ddc":["576"],"file_date_updated":"2021-10-20T22:30:03Z","department":[{"_id":"CaGu"}],"_id":"8653","type":"dissertation","status":"public","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"has_accepted_license":"1","year":"2020","day":"13","page":"117","doi":"10.15479/AT:ISTA:8653","date_published":"2020-10-13T00:00:00Z","date_created":"2020-10-13T13:02:33Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653","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.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","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.","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","last_name":"Tomanek","orcid":"0000-0001-6197-363X","full_name":"Tomanek, Isabella"}],"article_processing_charge":"No","title":"The evolution of gene expression by copy number and point mutations"},{"publication":"Current Biology","day":"03","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-02-02T23:01:00Z","date_published":"2020-02-03T00:00:00Z","doi":"10.1016/j.cub.2019.11.058","page":"381-395.e8","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). ","oa":1,"quality_controlled":"1","publisher":"Cell Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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.","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."},"title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","article_processing_charge":"No","external_id":{"isi":["000511287900018"],"pmid":["31956021"]},"author":[{"last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda F","full_name":"Abas, Melinda F","last_name":"Abas"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"Molnar, Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely"},{"last_name":"Hajny","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pavel","last_name":"Lasák","full_name":"Lasák, Pavel"},{"last_name":"Petřík","full_name":"Petřík, Ivan","first_name":"Ivan"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"first_name":"Jiří","full_name":"Pospíšil, Jiří","last_name":"Pospíšil"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"723-2015","name":"Long Term Fellowship","_id":"256FEF10-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-09-22T09:51:28Z","file_size":5360135,"date_created":"2020-09-22T09:51:28Z","file_name":"2020_CurrentBiology_Tan.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"16f7d51fe28f91c21e4896a2028df40b","file_id":"8555","success":1}],"publication_status":"published","publication_identifier":{"issn":["09609822"]},"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"8822","status":"public"}]},"volume":30,"issue":"3","pmid":1,"oa_version":"Published Version","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"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"intvolume":" 30","month":"02","scopus_import":"1","ddc":["580"],"date_updated":"2024-03-27T23:30:37Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file_date_updated":"2020-09-22T09:51:28Z","_id":"7427","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article"},{"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"2699E3D2-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development"}],"title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","author":[{"first_name":"E","full_name":"Mazur, E","last_name":"Mazur"},{"full_name":"Kulik, Ivan","last_name":"Kulik","first_name":"Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB"},{"orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","last_name":"Hajny","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"external_id":{"isi":["000514939700001"],"pmid":["31971254"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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","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.","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383."},"publisher":"Wiley","quality_controlled":"1","oa":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.","doi":"10.1111/nph.16446","date_published":"2020-06-01T00:00:00Z","date_created":"2020-02-18T10:03:47Z","page":"1375-1383","day":"01","publication":"New Phytologist","has_accepted_license":"1","isi":1,"year":"2020","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7500","file_date_updated":"2020-11-20T09:32:10Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2024-03-27T23:30:37Z","month":"06","intvolume":" 226","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8822"}]},"volume":226,"issue":"5","ec_funded":1,"file":[{"date_created":"2020-11-20T09:32:10Z","file_name":"2020_NewPhytologist_Mazur.pdf","date_updated":"2020-11-20T09:32:10Z","file_size":2106888,"creator":"dernst","file_id":"8781","checksum":"17de728b0205979feb95ce663ba918c2","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"publication_status":"published"},{"author":[{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"}],"article_processing_charge":"No","title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","citation":{"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.","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.","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","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"249","doi":"10.15479/AT:ISTA:8822","date_published":"2020-12-01T00:00:00Z","date_created":"2020-12-01T12:38:18Z","has_accepted_license":"1","year":"2020","day":"01","publisher":"Institute of Science and Technology Austria","oa":1,"department":[{"_id":"JiFr"}],"file_date_updated":"2021-12-08T23:30:03Z","supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"date_updated":"2023-09-19T10:39:33Z","ddc":["580"],"type":"dissertation","status":"public","_id":"8822","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7427"},{"id":"6260","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7500","status":"public"},{"id":"191","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"449"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_id":"8919","checksum":"210a9675af5e4c78b0b56d920ac82866","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Jakub Hajný IST Austria final_JH.docx","date_created":"2020-12-04T07:27:52Z","creator":"jhajny","file_size":91279806,"date_updated":"2021-07-16T22:30:03Z"},{"embargo":"2021-12-07","file_id":"8933","checksum":"1781385b4aa73eba89cc76c6172f71d2","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","date_created":"2020-12-09T15:04:41Z","creator":"jhajny","file_size":68707697,"date_updated":"2021-12-08T23:30:03Z"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"12","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version"},{"oa_version":"None","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"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.","lang":"eng"}],"month":"09","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"creator":"sshamip","date_updated":"2021-09-11T22:30:05Z","file_size":65194814,"date_created":"2020-09-09T11:06:27Z","file_name":"Shayan-Thesis-Final.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"8351","checksum":"6e47871c74f85008b9876112eb3fcfa1"},{"embargo":"2021-09-10","file_id":"8352","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Shayan-Thesis-Final.pdf","date_created":"2020-09-09T11:06:13Z","creator":"sshamip","file_size":23729605,"date_updated":"2021-09-11T22:30:05Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"661","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6508","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7001"},{"id":"735","status":"public","relation":"part_of_dissertation"}]},"_id":"8350","status":"public","type":"dissertation","ddc":["570"],"date_updated":"2023-09-27T14:16:45Z","supervisor":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-09-11T22:30:05Z","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"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.","oa":1,"publisher":"Institute of Science and Technology Austria","day":"09","year":"2020","has_accepted_license":"1","date_created":"2020-09-09T11:12:10Z","doi":"10.15479/AT:ISTA:8350","date_published":"2020-09-09T00:00:00Z","page":"107","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","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.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","short":"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"},"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","article_processing_charge":"No","author":[{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","full_name":"Shamipour, Shayan"}]},{"date_created":"2020-09-26T06:11:07Z","date_published":"2020-09-25T00:00:00Z","doi":"10.3389/fcell.2020.574382","publication":"Frontiers in Cell and Developmental Biology","day":"25","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Frontiers","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.","title":"Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["33102480"],"isi":["000577915900001"]},"author":[{"first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","last_name":"Hansen"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology 8 (2020).","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.","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.","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.","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."},"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"}],"article_number":"574382","ec_funded":1,"issue":"9","related_material":{"record":[{"status":"public","id":"9962","relation":"dissertation_contains"}]},"volume":8,"language":[{"iso":"eng"}],"file":[{"checksum":"01f731824194c94c81a5da360d997073","file_id":"8584","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-09-28T13:11:17Z","file_name":"2020_Frontiers_Hansen.pdf","creator":"dernst","date_updated":"2020-09-28T13:11:17Z","file_size":5527139}],"publication_status":"published","publication_identifier":{"issn":["2296-634X"]},"intvolume":" 8","month":"09","scopus_import":"1","pmid":1,"oa_version":"Published Version","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."}],"file_date_updated":"2020-09-28T13:11:17Z","department":[{"_id":"SiHi"}],"ddc":["570"],"date_updated":"2024-03-27T23:30:40Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"8569"},{"_id":"7815","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2024-03-27T23:30:41Z","file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"SiHi"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"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"}],"month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"3154ea7f90b9fb45e084cd1c2770597d","file_id":"7816","creator":"rbeattie","date_updated":"2020-07-14T12:48:03Z","file_size":1352186,"date_created":"2020-05-11T08:28:38Z","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf"}],"publication_status":"published","publication_identifier":{"issn":["1940-087X"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7902"}]},"issue":"159","article_number":"e61147","project":[{"call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416"},{"name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","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","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","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.","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.","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."},"title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","article_processing_charge":"No","external_id":{"isi":["000546406600043"]},"author":[{"last_name":"Beattie","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cheung","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras"},{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"quality_controlled":"1","publisher":"MyJove Corporation","publication":"Journal of Visual Experiments","day":"08","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-05-11T08:31:20Z","doi":"10.3791/61147","date_published":"2020-05-08T00:00:00Z"},{"publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2020","day":"05","page":"214","doi":"10.15479/AT:ISTA:7902","date_published":"2020-06-05T00:00:00Z","date_created":"2020-05-29T08:27:32Z","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"citation":{"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.","ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020.","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902","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","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.","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Genetic dissection of neural development in health and disease at single cell resolution","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_id":"7927","checksum":"43c172bf006c95b65992d473c7240d13","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"PhDThesis_Contreras.docx","date_created":"2020-06-05T08:18:08Z","file_size":53134142,"date_updated":"2021-06-07T22:30:03Z","creator":"xcontreras"},{"embargo":"2021-06-06","checksum":"addfed9128271be05cae3608e03a6ec0","file_id":"7928","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"PhDThesis_Contreras.pdf","date_created":"2020-06-05T08:18:07Z","file_size":35117191,"date_updated":"2021-06-07T22:30:03Z","creator":"xcontreras"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6830"},{"relation":"dissertation_contains","id":"28","status":"public"},{"relation":"dissertation_contains","id":"7815","status":"public"}]},"ec_funded":1,"_id":"7902","type":"dissertation","status":"public","supervisor":[{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"date_updated":"2023-10-18T08:45:16Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2021-06-07T22:30:03Z"},{"_id":"8190","article_type":"letter_note","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","date_updated":"2023-10-17T10:04:49Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2021-02-02T23:30:03Z","oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 219","publication_identifier":{"eissn":["1540-8140"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2021-02-01","checksum":"30016d778d266b8e17d01094917873b8","file_id":"8200","file_size":830725,"date_updated":"2021-02-02T23:30:03Z","creator":"dernst","file_name":"2020_JCB_Sixt.pdf","date_created":"2020-08-04T13:11:52Z"}],"language":[{"iso":"eng"}],"volume":219,"issue":"8","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","article_number":"e202007029","citation":{"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.","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","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.","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","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","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","last_name":"Huttenlocher","full_name":"Huttenlocher, Anna"}],"external_id":{"isi":["000573631000004"]},"article_processing_charge":"No","title":"Zena Werb (1945-2020): Cell biology in context","publisher":"Rockefeller University Press","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"22","publication":"The Journal of Cell Biology","date_published":"2020-07-22T00:00:00Z","doi":"10.1083/jcb.202007029","date_created":"2020-08-02T22:00:57Z"},{"citation":{"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.","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.","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","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.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li"},{"first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"external_id":{"pmid":["33310852"],"isi":["000599903600014"]},"article_processing_charge":"No","title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","article_number":"eabc8895","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"_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","grant_number":"25351"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"11","publication":"Science Advances","doi":"10.1126/sciadv.abc8895","date_published":"2020-12-11T00:00:00Z","date_created":"2021-01-03T23:01:23Z","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. ","publisher":"AAAS","quality_controlled":"1","oa":1,"date_updated":"2024-03-27T23:30:43Z","ddc":["580"],"department":[{"_id":"JiFr"}],"file_date_updated":"2021-01-07T12:44:33Z","_id":"8986","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","file":[{"success":1,"checksum":"5ac2500b191c08ef6dab5327f40ff663","file_id":"8994","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_ScienceAdvances_Zhang.pdf","date_created":"2021-01-07T12:44:33Z","creator":"dernst","file_size":10578145,"date_updated":"2021-01-07T12:44:33Z"}],"language":[{"iso":"eng"}],"issue":"50","related_material":{"record":[{"status":"public","id":"10083","relation":"dissertation_contains"}]},"volume":6,"ec_funded":1,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"12","intvolume":" 6"},{"pmid":1,"oa_version":"Published Version","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. "}],"month":"08","intvolume":" 21","scopus_import":"1","file":[{"file_name":"2020_IntMolecSciences_Chen.pdf","date_created":"2020-08-25T09:53:50Z","creator":"cziletti","file_size":5718755,"date_updated":"2020-08-25T09:53:50Z","success":1,"file_id":"8292","checksum":"03b039244e6ae80580385fd9f577e2b2","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"publication_status":"published","issue":"16","volume":21,"related_material":{"record":[{"relation":"dissertation_contains","id":"10083","status":"public"}]},"_id":"8283","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2024-03-27T23:30:43Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-08-25T09:53:50Z","acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","publisher":"MDPI","quality_controlled":"1","oa":1,"day":"10","publication":"International Journal of Molecular Sciences","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.3390/ijms21165727","date_published":"2020-08-10T00:00:00Z","date_created":"2020-08-24T06:24:03Z","article_number":"5272","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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","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","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.","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."},"title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","author":[{"full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang"},{"full_name":"Lai, Linyi","last_name":"Lai","first_name":"Linyi"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Liu","full_name":"Liu, Liping","first_name":"Liping"},{"last_name":"Jakada","full_name":"Jakada, Bello Hassan","first_name":"Bello Hassan"},{"full_name":"Huang, Youmei","last_name":"Huang","first_name":"Youmei"},{"first_name":"Qing","full_name":"He, Qing","last_name":"He"},{"full_name":"Chai, Mengnan","last_name":"Chai","first_name":"Mengnan"},{"first_name":"Xiaoping","full_name":"Niu, Xiaoping","last_name":"Niu"},{"first_name":"Yuan","full_name":"Qin, Yuan","last_name":"Qin"}],"article_processing_charge":"No","external_id":{"isi":["000565090300001"],"pmid":["32785037"]}},{"publication":"Journal of Cell Science","day":"06","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-07-21T08:58:19Z","date_published":"2020-08-06T00:00:00Z","doi":"10.1242/jcs.248062","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. ","oa":1,"publisher":"The Company of Biologists","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","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."},"title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","external_id":{"isi":["000561047900021"],"pmid":["32616560"]},"article_processing_charge":"No","author":[{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vert, G","last_name":"Vert","first_name":"G"},{"first_name":"SY","last_name":"Bednarek","full_name":"Bednarek, SY"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"article_number":"jcs248062","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"language":[{"iso":"eng"}],"file":[{"file_id":"8815","checksum":"2d11f79a0b4e0a380fb002b933da331a","embargo":"2021-08-07","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-11-26T17:12:51Z","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","creator":"ajohnson","date_updated":"2021-08-08T22:30:03Z","file_size":15150403}],"publication_status":"published","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"ec_funded":1,"issue":"15","related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"}]},"volume":133,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"intvolume":" 133","month":"08","scopus_import":"1","ddc":["575"],"date_updated":"2023-12-01T13:51:07Z","file_date_updated":"2021-08-08T22:30:03Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"_id":"8139","status":"public","type":"journal_article","article_type":"original"},{"issue":"3","related_material":{"record":[{"status":"public","id":"10135","relation":"dissertation_contains"}]},"volume":1,"publication_identifier":{"issn":["2590-3462"]},"publication_status":"published","file":[{"creator":"dernst","file_size":840289,"date_updated":"2021-02-18T10:23:59Z","file_name":"2020_PlantComm_Semeradova.pdf","date_created":"2021-02-18T10:23:59Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"785b266d82a94b007cf40dbbe7c4847e","file_id":"9161"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 1","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"EvBe"}],"file_date_updated":"2021-02-18T10:23:59Z","date_updated":"2024-03-27T23:30:46Z","ddc":["580"],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"9160","doi":"10.1016/j.xplc.2020.100048","date_published":"2020-05-11T00:00:00Z","date_created":"2021-02-18T10:18:43Z","isi":1,"has_accepted_license":"1","year":"2020","day":"11","publication":"Plant Communications","publisher":"Elsevier","quality_controlled":"1","oa":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.","author":[{"last_name":"Semeradova","full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana"},{"full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"article_processing_charge":"No","external_id":{"pmid":["33367243"],"isi":["000654052800010"]},"title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","citation":{"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.","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","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.","short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"article_number":"100048"},{"publication_identifier":{"issn":["2398-7340"]},"publication_status":"published","file":[{"date_created":"2022-05-17T06:55:49Z","file_name":"2019_EPiCs_Frehse.pdf","date_updated":"2022-05-17T06:55:49Z","file_size":346415,"creator":"dernst","file_id":"11391","checksum":"4b92e333db7b4e2349501a804dfede69","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":61,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","alternative_title":["EPiC Series in Computing"],"scopus_import":"1","month":"05","intvolume":" 61","date_updated":"2022-05-17T07:09:47Z","ddc":["000"],"file_date_updated":"2022-05-17T06:55:49Z","department":[{"_id":"ToHe"}],"_id":"10877","type":"conference","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"},"status":"public","has_accepted_license":"1","year":"2019","day":"25","publication":"ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems","page":"1-13","doi":"10.29007/rjwn","date_published":"2019-05-25T00:00:00Z","date_created":"2022-03-18T12:29:23Z","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).","quality_controlled":"1","publisher":"EasyChair","oa":1,"citation":{"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.","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.","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.","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Goran","full_name":"Frehse, Goran","last_name":"Frehse"},{"first_name":"Alessandro","last_name":"Abate","full_name":"Abate, Alessandro"},{"full_name":"Adzkiya, Dieky","last_name":"Adzkiya","first_name":"Dieky"},{"last_name":"Becchi","full_name":"Becchi, Anna","first_name":"Anna"},{"first_name":"Lei","last_name":"Bu","full_name":"Bu, Lei"},{"full_name":"Cimatti, Alessandro","last_name":"Cimatti","first_name":"Alessandro"},{"first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","last_name":"Giacobbe","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco"},{"first_name":"Alberto","full_name":"Griggio, Alberto","last_name":"Griggio"},{"last_name":"Mover","full_name":"Mover, Sergio","first_name":"Sergio"},{"first_name":"Muhammad Syifa'ul","full_name":"Mufid, Muhammad Syifa'ul","last_name":"Mufid"},{"last_name":"Riouak","full_name":"Riouak, Idriss","first_name":"Idriss"},{"first_name":"Stefano","full_name":"Tonetta, Stefano","last_name":"Tonetta"},{"last_name":"Zaffanella","full_name":"Zaffanella, Enea","first_name":"Enea"}],"article_processing_charge":"No","editor":[{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"full_name":"Althoff, Matthias","last_name":"Althoff","first_name":"Matthias"}],"title":"ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics"},{"date_updated":"2021-01-12T07:56:46Z","department":[{"_id":"TaHa"}],"_id":"441","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2199-6768"],"issn":["2199-675X"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"3","volume":5,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1711.02089","open_access":"1"}],"scopus_import":1,"intvolume":" 5","month":"09","citation":{"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.","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.","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","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","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.","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."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","external_id":{"arxiv":["1711.02089"]},"article_processing_charge":"No","publist_id":"7382","author":[{"last_name":"Kalinin","full_name":"Kalinin, Nikita","first_name":"Nikita"},{"first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov"}],"title":"Tropical formulae for summation over a part of SL(2,Z)","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2019","publication":"European Journal of Mathematics","day":"15","page":"909–928","date_created":"2018-12-11T11:46:29Z","date_published":"2019-09-15T00:00:00Z","doi":"10.1007/s40879-018-0218-0","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"department":[{"_id":"CaHe"}],"editor":[{"first_name":"Alexander","last_name":"Hergovich","full_name":"Hergovich, Alexander"}],"title":"Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids","author":[{"first_name":"Yoichi","full_name":"Asaoka, Yoichi","last_name":"Asaoka"},{"last_name":"Morita","full_name":"Morita, Hitoshi","first_name":"Hitoshi"},{"full_name":"Furumoto, Hiroko","last_name":"Furumoto","first_name":"Hiroko"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Furutani-Seiki, Makoto","last_name":"Furutani-Seiki","first_name":"Makoto"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki, “Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,” in The hippo pathway, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp. 167–181.","short":"Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki, in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181.","ama":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich A, ed. The Hippo Pathway. Vol 1893. Methods in Molecular Biology. Springer; 2019:167-181. doi:10.1007/978-1-4939-8910-2_14","apa":"Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., & Furutani-Seiki, M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In A. Hergovich (Ed.), The hippo pathway (Vol. 1893, pp. 167–181). Springer. https://doi.org/10.1007/978-1-4939-8910-2_14","mla":"Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” The Hippo Pathway, edited by Alexander Hergovich, vol. 1893, Springer, 2019, pp. 167–81, doi:10.1007/978-1-4939-8910-2_14.","ista":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The hippo pathway. MIMB, vol. 1893, 167–181.","chicago":"Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg, and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” In The Hippo Pathway, edited by Alexander Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. https://doi.org/10.1007/978-1-4939-8910-2_14."},"date_updated":"2021-01-12T08:03:30Z","status":"public","type":"book_chapter","_id":"5793","series_title":"Methods in Molecular Biology","volume":1893,"date_published":"2019-01-01T00:00:00Z","doi":"10.1007/978-1-4939-8910-2_14","date_created":"2019-01-06T22:59:11Z","page":"167-181","day":"01","language":[{"iso":"eng"}],"publication":"The hippo pathway","publication_identifier":{"isbn":["978-1-4939-8909-6"]},"year":"2019","publication_status":"published","month":"01","intvolume":" 1893","publisher":"Springer","quality_controlled":"1","scopus_import":1,"alternative_title":["MIMB"],"oa_version":"None","abstract":[{"text":"The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis.","lang":"eng"}]},{"_id":"5887","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T08:05:08Z","department":[{"_id":"KrPi"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2016/166","open_access":"1"}],"scopus_import":"1","intvolume":" 27","month":"01","publication_status":"published","publication_identifier":{"issn":["0926227X"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"1","volume":27,"project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"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.","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.","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.","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.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, Journal of Computer Security 27 (2019) 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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Demay, Gregory","last_name":"Demay","first_name":"Gregory"},{"first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","last_name":"Gazi","full_name":"Gazi, Peter"},{"first_name":"Ueli","full_name":"Maurer, Ueli","last_name":"Maurer"},{"last_name":"Tackmann","full_name":"Tackmann, Bjorn","first_name":"Bjorn"}],"title":"Per-session security: Password-based cryptography revisited","oa":1,"publisher":"IOS Press","quality_controlled":"1","year":"2019","publication":"Journal of Computer Security","day":"1","page":"75-111","date_created":"2019-01-27T22:59:10Z","doi":"10.3233/JCS-181131","date_published":"2019-01-01T00:00:00Z"},{"oa":1,"quality_controlled":"1","publisher":"Carleton University","date_created":"2019-06-03T09:35:33Z","date_published":"2019-07-01T00:00:00Z","doi":"10.20382/jocg.v10i1a9","page":"223–256","publication":"Journal of Computational Geometry ","day":"01","year":"2019","has_accepted_license":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Simplices modelled on spaces of constant curvature","author":[{"first_name":"Ramsay","last_name":"Dyer","full_name":"Dyer, Ramsay"},{"full_name":"Vegter, Gert","last_name":"Vegter","first_name":"Gert"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"R. Dyer, G. Vegter, M. Wintraecken, Journal of Computational Geometry 10 (2019) 223–256.","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","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","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.","ista":"Dyer R, Vegter G, Wintraecken M. 2019. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 10(1), 223–256."},"intvolume":" 10","month":"07","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"ec_funded":1,"issue":"1","volume":10,"language":[{"iso":"eng"}],"file":[{"date_created":"2019-06-03T09:30:01Z","file_name":"mainJournalFinal.pdf","date_updated":"2020-07-14T12:47:32Z","file_size":2170882,"creator":"mwintrae","checksum":"57b4df2f16a74eb499734ec8ee240178","file_id":"6516","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["1920-180X"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"6515","file_date_updated":"2020-07-14T12:47:32Z","department":[{"_id":"HeEd"}],"ddc":["510"],"date_updated":"2021-01-12T08:07:50Z"},{"day":"10","publication":"10th Innovations in Theoretical Computer Science Conference","has_accepted_license":"1","year":"2019","doi":"10.4230/LIPICS.ITCS.2019.60","date_published":"2019-01-10T00:00:00Z","date_created":"2019-06-06T14:12:36Z","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","ieee":"K. Z. Pietrzak, “Simple verifiable delay functions,” in 10th Innovations in Theoretical Computer Science Conference, San Diego, CA, United States, 2019, vol. 124."},"title":"Simple verifiable delay functions","author":[{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","article_number":"60","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6529","checksum":"f0ae1bb161431d9db3dea5ace082bfb5","creator":"dernst","file_size":558770,"date_updated":"2020-07-14T12:47:33Z","file_name":"2019_LIPIcs_Pietrzak.pdf","date_created":"2019-06-06T14:22:04Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-95977-095-8"],"issn":["1868-8969"]},"publication_status":"published","volume":124,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"01","intvolume":" 124","scopus_import":1,"alternative_title":["LIPIcs"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/627"}],"ddc":["000"],"date_updated":"2021-01-12T08:07:53Z","department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:47:33Z","_id":"6528","status":"public","type":"conference","conference":{"name":"ITCS 2019: Innovations in Theoretical Computer Science","end_date":"2019-01-12","location":"San Diego, CA, United States","start_date":"2019-01-10"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"author":[{"last_name":"Kundu","full_name":"Kundu, Atreyee","first_name":"Atreyee"},{"last_name":"Garcia Soto","full_name":"Garcia Soto, Miriam","orcid":"0000−0003−2936−5719","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"},{"last_name":"Prabhakar","full_name":"Prabhakar, Pavithra","first_name":"Pavithra"}],"article_processing_charge":"No","title":"Formal synthesis of stabilizing controllers for periodically controlled linear switched systems","citation":{"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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"article_number":"8715598","date_published":"2019-05-16T00:00:00Z","doi":"10.1109/INDIANCC.2019.8715598","date_created":"2019-06-17T06:57:33Z","has_accepted_license":"1","year":"2019","day":"16","publication":"5th Indian Control Conference Proceedings","publisher":"IEEE","quality_controlled":"1","oa":1,"file_date_updated":"2020-10-21T13:13:49Z","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T08:08:01Z","ddc":["000"],"type":"conference","conference":{"start_date":"2019-01-09","location":"Delhi, India","end_date":"2019-01-11","name":"ICC 2019 - Indian Control Conference"},"status":"public","_id":"6565","publication_identifier":{"isbn":["978-153866246-5"]},"publication_status":"published","file":[{"file_name":"2019_ICC_Kundu.pdf","date_created":"2020-10-21T13:13:49Z","file_size":396031,"date_updated":"2020-10-21T13:13:49Z","creator":"dernst","success":1,"file_id":"8687","checksum":"d622a91af1e427f6b1e0ba8e18a2b767","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","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"}],"oa_version":"Submitted Version"},{"_id":"6628","status":"public","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"conference":{"end_date":"2019-08-10","location":"Edmonton, Canada","start_date":"2019-08-08","name":"CCCG: Canadian Conference in Computational Geometry"},"type":"conference","ddc":["004"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:08:16Z","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.","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.","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.","short":"G. Vegter, M. Wintraecken, in:, The 31st Canadian Conference in Computational Geometry, 2019, pp. 275–279.","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.","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.","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."},"department":[{"_id":"HeEd"}],"title":"The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds","file_date_updated":"2020-07-14T12:47:34Z","author":[{"full_name":"Vegter, Gert","last_name":"Vegter","first_name":"Gert"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs"}],"oa_version":"Submitted Version","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"}],"month":"08","oa":1,"quality_controlled":"1","scopus_import":1,"language":[{"iso":"eng"}],"publication":"The 31st Canadian Conference in Computational Geometry","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"ceabd152cfa55170d57763f9c6c60a53","file_id":"6629","creator":"mwintrae","file_size":321176,"date_updated":"2020-07-14T12:47:34Z","file_name":"IntrinsicExtrinsicCCCG2019.pdf","date_created":"2019-07-12T08:32:46Z"}],"day":"01","publication_status":"published","year":"2019","has_accepted_license":"1","date_created":"2019-07-12T08:34:57Z","ec_funded":1,"date_published":"2019-08-01T00:00:00Z","page":"275-279"},{"project":[{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","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.","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.","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."},"title":"Topological data analysis in information space","external_id":{"arxiv":["1903.08510"]},"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"Ziga","last_name":"Virk","full_name":"Virk, Ziga"},{"id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","last_name":"Wagner","full_name":"Wagner, Hubert"}],"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"35th International Symposium on Computational Geometry","day":"01","year":"2019","has_accepted_license":"1","date_created":"2019-07-17T10:36:09Z","doi":"10.4230/LIPICS.SOCG.2019.31","date_published":"2019-06-01T00:00:00Z","page":"31:1-31:14","_id":"6648","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"SoCG 2019: Symposium on Computational Geometry","start_date":"2019-06-18","end_date":"2019-06-21","location":"Portland, OR, United States"},"type":"conference","ddc":["510"],"date_updated":"2021-01-12T08:08:23Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:47:35Z","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 129","month":"06","alternative_title":["LIPIcs"],"scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:35Z","file_size":1355179,"creator":"dernst","date_created":"2019-07-24T06:40:01Z","file_name":"2019_LIPICS_Edelsbrunner.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"8ec8720730d4c789bf7b06540f1c29f4","file_id":"6666"}],"publication_status":"published","publication_identifier":{"isbn":["9783959771047"]},"volume":129},{"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"186de511d6e0ca93f5d981e2443eb8cd","file_id":"8594","success":1,"creator":"dernst","date_updated":"2020-10-02T08:49:58Z","file_size":2464903,"date_created":"2020-10-02T08:49:58Z","file_name":"2019_BCSJ_Zenmyo.pdf"}],"publication_status":"published","publication_identifier":{"issn":["00092673"]},"ec_funded":1,"issue":"5","volume":92,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 92","month":"05","scopus_import":"1","ddc":["570"],"date_updated":"2021-01-12T08:08:26Z","file_date_updated":"2020-10-02T08:49:58Z","department":[{"_id":"RySh"}],"_id":"6659","status":"public","article_type":"original","type":"journal_article","publication":"Bulletin of the Chemical Society of Japan","day":"15","year":"2019","has_accepted_license":"1","date_created":"2019-07-21T21:59:16Z","doi":"10.1246/bcsj.20190034","date_published":"2019-05-15T00:00:00Z","page":"995-1000","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.","oa":1,"publisher":"Bulletin of the Chemical Society of Japan","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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."},"title":"Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins","article_processing_charge":"No","author":[{"last_name":"Zenmyo","full_name":"Zenmyo, Naoki","first_name":"Naoki"},{"first_name":"Hiroki","full_name":"Tokumaru, Hiroki","last_name":"Tokumaru"},{"first_name":"Shohei","last_name":"Uchinomiya","full_name":"Uchinomiya, Shohei"},{"last_name":"Fuchida","full_name":"Fuchida, Hirokazu","first_name":"Hirokazu"},{"id":"4427179E-F248-11E8-B48F-1D18A9856A87","first_name":"Shigekazu","full_name":"Tabata, Shigekazu","last_name":"Tabata"},{"first_name":"Itaru","last_name":"Hamachi","full_name":"Hamachi, Itaru"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"last_name":"Ojida","full_name":"Ojida, Akio","first_name":"Akio"}],"project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” In 46th International Colloquium on Automata, Languages and Programming, 132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.77.","ista":"Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th International Colloquium on Automata, Languages and Programming. ICALP 2019: International Colloquim on Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12.","mla":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” 46th International Colloquium on Automata, Languages and Programming, vol. 132, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:10.4230/LIPICS.ICALP.2019.77.","ieee":"V. Kolmogorov, “Testing the complexity of a valued CSP language,” in 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, 2019, vol. 132, p. 77:1-77:12.","short":"V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12.","apa":"Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In 46th International Colloquium on Automata, Languages and Programming (Vol. 132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2019.77","ama":"Kolmogorov V. Testing the complexity of a valued CSP language. In: 46th International Colloquium on Automata, Languages and Programming. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:10.4230/LIPICS.ICALP.2019.77"},"title":"Testing the complexity of a valued CSP language","external_id":{"arxiv":["1803.02289"]},"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"publication":"46th International Colloquium on Automata, Languages and Programming","day":"01","year":"2019","has_accepted_license":"1","date_created":"2019-07-29T12:23:29Z","doi":"10.4230/LIPICS.ICALP.2019.77","date_published":"2019-07-01T00:00:00Z","page":"77:1-77:12","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","ddc":["000"],"date_updated":"2021-01-12T08:08:40Z","department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:47:38Z","_id":"6725","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2019-07-08","end_date":"2019-07-12","location":"Patras, Greece","name":"ICALP 2019: International Colloquim on Automata, Languages and Programming"},"type":"conference","language":[{"iso":"eng"}],"file":[{"file_name":"2019_LIPICS_Kolmogorov.pdf","date_created":"2019-07-31T07:01:45Z","file_size":575475,"date_updated":"2020-07-14T12:47:38Z","creator":"dernst","checksum":"f5ebee8eec6ae09e30365578ee63a492","file_id":"6738","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-109-2"]},"ec_funded":1,"volume":132,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language. \r\nRecent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds."}],"intvolume":" 132","month":"07","scopus_import":1,"alternative_title":["LIPIcs"]},{"project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Walter, Michael. “Sampling the Integers with Low Relative Error.” In Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann, A Nitaj, and T Rachidi, 11627:157–80. LNCS. Cham: Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23696-0_9.","ista":"Walter M. 2019.Sampling the integers with low relative error. In: Progress in Cryptology – AFRICACRYPT 2019. vol. 11627, 157–180.","mla":"Walter, Michael. “Sampling the Integers with Low Relative Error.” Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann et al., vol. 11627, Springer Nature, 2019, pp. 157–80, doi:10.1007/978-3-030-23696-0_9.","ieee":"M. Walter, “Sampling the integers with low relative error,” in Progress in Cryptology – AFRICACRYPT 2019, vol. 11627, J. Buchmann, A. Nitaj, and T. Rachidi, Eds. Cham: Springer Nature, 2019, pp. 157–180.","short":"M. Walter, in:, J. Buchmann, A. Nitaj, T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019, Springer Nature, Cham, 2019, pp. 157–180.","apa":"Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann, A. Nitaj, & T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019 (Vol. 11627, pp. 157–180). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-23696-0_9","ama":"Walter M. Sampling the integers with low relative error. In: Buchmann J, Nitaj A, Rachidi T, eds. Progress in Cryptology – AFRICACRYPT 2019. Vol 11627. LNCS. Cham: Springer Nature; 2019:157-180. doi:10.1007/978-3-030-23696-0_9"},"title":"Sampling the integers with low relative error","editor":[{"first_name":"J","full_name":"Buchmann, J","last_name":"Buchmann"},{"last_name":"Nitaj","full_name":"Nitaj, A","first_name":"A"},{"last_name":"Rachidi","full_name":"Rachidi, T","first_name":"T"}],"article_processing_charge":"No","author":[{"first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","last_name":"Walter"}],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Progress in Cryptology – AFRICACRYPT 2019","day":"29","year":"2019","date_created":"2019-07-29T12:25:31Z","date_published":"2019-06-29T00:00:00Z","doi":"10.1007/978-3-030-23696-0_9","page":"157-180","series_title":"LNCS","_id":"6726","status":"public","conference":{"start_date":"2019-07-09","end_date":"2019-07-11","location":"Rabat, Morocco","name":"AFRICACRYPT: International Conference on Cryptology in Africa"},"type":"book_chapter","date_updated":"2023-02-23T12:50:15Z","department":[{"_id":"KrPi"}],"oa_version":"Preprint","abstract":[{"text":"Randomness is an essential part of any secure cryptosystem, but many constructions rely on distributions that are not uniform. This is particularly true for lattice based cryptosystems, which more often than not make use of discrete Gaussian distributions over the integers. For practical purposes it is crucial to evaluate the impact that approximation errors have on the security of a scheme to provide the best possible trade-off between security and performance. Recent years have seen surprising results allowing to use relatively low precision while maintaining high levels of security. A key insight in these results is that sampling a distribution with low relative error can provide very strong security guarantees. Since floating point numbers provide guarantees on the relative approximation error, they seem a suitable tool in this setting, but it is not obvious which sampling algorithms can actually profit from them. While previous works have shown that inversion sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES 2014; Prest, ASIACRYPT 2017), other works have called into question if this is possible for other sampling techniques (Zheng et al., Eprint report 2018/309). In this work, we consider all sampling algorithms that are popular in the cryptographic setting and analyze the relationship of floating point precision and the resulting relative error. We show that all of the algorithms either natively achieve a low relative error or can be adapted to do so.","lang":"eng"}],"intvolume":" 11627","place":"Cham","month":"06","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/068"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["978-3-0302-3695-3"],"eisbn":["978-3-0302-3696-0"]},"ec_funded":1,"volume":11627},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported. "}],"intvolume":" 67","month":"11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.09203"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1053587X"]},"volume":67,"issue":"22","_id":"6750","status":"public","article_type":"original","type":"journal_article","date_updated":"2021-01-12T08:08:51Z","department":[{"_id":"MaMo"}],"oa":1,"publisher":"IEEE","quality_controlled":"1","publication":"IEEE Transactions on Signal Processing","day":"15","year":"2019","date_created":"2019-07-31T09:51:14Z","date_published":"2019-11-15T00:00:00Z","doi":"10.1109/TSP.2019.2944738","article_number":"8854897","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"chicago":"Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing. IEEE, 2019. https://doi.org/10.1109/TSP.2019.2944738.","ista":"Hashemi SA, Condo C, Mondelli M, Gross WJ. 2019. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 67(22), 8854897.","mla":"Hashemi, Seyyed Ali, et al. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing, vol. 67, no. 22, 8854897, IEEE, 2019, doi:10.1109/TSP.2019.2944738.","ama":"Hashemi SA, Condo C, Mondelli M, Gross WJ. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 2019;67(22). doi:10.1109/TSP.2019.2944738","apa":"Hashemi, S. A., Condo, C., Mondelli, M., & Gross, W. J. (2019). Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2019.2944738","ieee":"S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast polar decoders,” IEEE Transactions on Signal Processing, vol. 67, no. 22. IEEE, 2019.","short":"S.A. Hashemi, C. Condo, M. Mondelli, W.J. Gross, IEEE Transactions on Signal Processing 67 (2019)."},"title":"Rate-flexible fast polar decoders","external_id":{"arxiv":["1903.09203"]},"article_processing_charge":"No","author":[{"first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi"},{"first_name":"Carlo","full_name":"Condo, Carlo","last_name":"Condo"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"},{"first_name":"Warren J","last_name":"Gross","full_name":"Gross, Warren J"}]},{"article_number":"P3.17","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 26(3), P3.17.","chicago":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2019. https://doi.org/10.37236/8096.","apa":"Jelínek, V., & Töpfer, M. (2019). On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/8096","ama":"Jelínek V, Töpfer M. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 2019;26(3). doi:10.37236/8096","ieee":"V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” Electronic Journal of Combinatorics, vol. 26, no. 3. Electronic Journal of Combinatorics, 2019.","short":"V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019).","mla":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics, vol. 26, no. 3, P3.17, Electronic Journal of Combinatorics, 2019, doi:10.37236/8096."},"title":"On grounded L-graphs and their relatives","author":[{"first_name":"Vít","full_name":"Jelínek, Vít","last_name":"Jelínek"},{"full_name":"Töpfer, Martin","last_name":"Töpfer","first_name":"Martin","id":"4B865388-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1808.04148"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Electronic Journal of Combinatorics","oa":1,"day":"19","publication":"Electronic Journal of Combinatorics","has_accepted_license":"1","year":"2019","date_published":"2019-07-19T00:00:00Z","doi":"10.37236/8096","date_created":"2019-08-04T21:59:20Z","_id":"6759","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_updated":"2022-03-18T12:32:02Z","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:47:39Z","oa_version":"Published Version","abstract":[{"text":"We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns. \r\nWe also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions.","lang":"eng"}],"month":"07","intvolume":" 26","scopus_import":"1","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:39Z","file_size":533697,"date_created":"2019-08-05T06:46:55Z","file_name":"2019_eJourCombinatorics_Jelinek.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6764","checksum":"20fc366fc6683ef0b074a019b73a663a"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10778926"]},"publication_status":"published","volume":26,"issue":"3","ec_funded":1},{"project":[{"call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"},{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Avni, Guy, et al. “Bidding Games on Markov Decision Processes.” Proceedings of the 13th International Conference of Reachability Problems, vol. 11674, Springer, 2019, pp. 1–12, doi:10.1007/978-3-030-30806-3_1.","ama":"Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. Bidding games on Markov decision processes. In: Proceedings of the 13th International Conference of Reachability Problems. Vol 11674. Springer; 2019:1-12. doi:10.1007/978-3-030-30806-3_1","apa":"Avni, G., Henzinger, T. A., Ibsen-Jensen, R., & Novotny, P. (2019). Bidding games on Markov decision processes. In Proceedings of the 13th International Conference of Reachability Problems (Vol. 11674, pp. 1–12). Brussels, Belgium: Springer. https://doi.org/10.1007/978-3-030-30806-3_1","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, P. Novotny, in:, Proceedings of the 13th International Conference of Reachability Problems, Springer, 2019, pp. 1–12.","ieee":"G. Avni, T. A. Henzinger, R. Ibsen-Jensen, and P. Novotny, “Bidding games on Markov decision processes,” in Proceedings of the 13th International Conference of Reachability Problems, Brussels, Belgium, 2019, vol. 11674, pp. 1–12.","chicago":"Avni, Guy, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Petr Novotny. “Bidding Games on Markov Decision Processes.” In Proceedings of the 13th International Conference of Reachability Problems, 11674:1–12. Springer, 2019. https://doi.org/10.1007/978-3-030-30806-3_1.","ista":"Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. 2019. Bidding games on Markov decision processes. Proceedings of the 13th International Conference of Reachability Problems. RP: Reachability Problems, LNCS, vol. 11674, 1–12."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"full_name":"Novotny, Petr","last_name":"Novotny","first_name":"Petr"}],"title":"Bidding games on Markov decision processes","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2019","has_accepted_license":"1","publication":" Proceedings of the 13th International Conference of Reachability Problems","day":"06","page":"1-12","date_created":"2019-08-19T07:58:10Z","date_published":"2019-09-06T00:00:00Z","doi":"10.1007/978-3-030-30806-3_1","_id":"6822","conference":{"name":"RP: Reachability Problems","start_date":"2019-09-11","location":"Brussels, Belgium","end_date":"2019-09-13"},"type":"conference","status":"public","date_updated":"2021-01-12T08:09:12Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:41Z","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the qualitative winner or quantitative payoff of the game. In bidding games, in each turn, we hold an auction between the two players to determine which player moves the token. Bidding games have largely been studied with concrete bidding mechanisms that are variants of a first-price auction: in each turn both players simultaneously submit bids, the higher\r\nbidder moves the token, and pays his bid to the lower bidder in Richman bidding, to the bank in poorman bidding, and in taxman bidding, the bid is split between the other player and the bank according to a predefined constant factor. Bidding games are deterministic games. They have an intriguing connection with a fragment of stochastic games called \r\n randomturn games. We study, for the first time, a combination of bidding games with probabilistic behavior; namely, we study bidding games that are played on Markov decision processes, where the players bid for the right to choose the next action, which determines the probability distribution according to which the next vertex is chosen. We study parity and meanpayoff bidding games on MDPs and extend results from the deterministic bidding setting to the probabilistic one.","lang":"eng"}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":1,"intvolume":" 11674","month":"09","publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["978-303030805-6"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"45ebbc709af2b247d28c7c293c01504b","file_id":"6823","creator":"gavni","date_updated":"2020-07-14T12:47:41Z","file_size":436635,"date_created":"2019-08-19T07:56:40Z","file_name":"prob.pdf"}],"volume":11674},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The fundamental model-checking problem, given as input a model and a specification, asks for the algorithmic verification of whether the model satisfies the specification. Two classical models for reactive systems are graphs and Markov decision processes (MDPs). A basic specification formalism in the verification of reactive systems is the strong fairness (aka Streett) objective, where given different types of requests and corresponding grants, the requirement is that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All omega-regular objectives can be expressed as Streett objectives and hence they are canonical in verification. Consider graphs/MDPs with n vertices, m edges, and a Streett objectives with k pairs, and let b denote the size of the description of the Streett objective for the sets of requests and grants. The current best-known algorithm for the problem requires time O(min(n^2, m sqrt{m log n}) + b log n). In this work we present randomized near-linear time algorithms, with expected running time O~(m + b), where the O~ notation hides poly-log factors. Our randomized algorithms are near-linear in the size of the input, and hence optimal up to poly-log factors. "}],"intvolume":" 140","month":"08","alternative_title":["LIPIcs"],"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2019_LIPIcs_Chatterjee.pdf","date_created":"2019-10-01T08:20:30Z","file_size":730112,"date_updated":"2020-07-14T12:47:43Z","creator":"kschuh","file_id":"6922","checksum":"e1f0e4061212454574f34a1368d018ec","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","ec_funded":1,"volume":140,"_id":"6887","status":"public","conference":{"name":"CONCUR: International Conference on Concurrency Theory","start_date":"2019-08-27","location":"Amsterdam, Netherlands","end_date":"2019-08-30"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","ddc":["000"],"date_updated":"2022-08-12T10:54:34Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:43Z","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","publication":"Leibniz International Proceedings in Informatics","day":"01","year":"2019","has_accepted_license":"1","date_created":"2019-09-18T08:07:58Z","doi":"10.4230/LIPICS.CONCUR.2019.7","date_published":"2019-08-01T00:00:00Z","article_number":"7","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Chatterjee, Krishnendu, et al. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” Leibniz International Proceedings in Informatics, vol. 140, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.7.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Near-linear time algorithms for Streett objectives in graphs and MDPs,” in Leibniz International Proceedings in Informatics, Amsterdam, Netherlands, 2019, vol. 140.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2019). Near-linear time algorithms for Streett objectives in graphs and MDPs. In Leibniz International Proceedings in Informatics (Vol. 140). Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.7","ama":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Near-linear time algorithms for Streett objectives in graphs and MDPs. In: Leibniz International Proceedings in Informatics. Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.7","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” In Leibniz International Proceedings in Informatics, Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.7.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2019. Near-linear time algorithms for Streett objectives in graphs and MDPs. Leibniz International Proceedings in Informatics. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 7."},"title":"Near-linear time algorithms for Streett objectives in graphs and MDPs","article_processing_charge":"No","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dvorák","full_name":"Dvorák, Wolfgang","first_name":"Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}]},{"file_date_updated":"2020-10-08T17:30:38Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2021-01-12T08:09:28Z","status":"public","conference":{"name":"ICRA: International Conference on Robotics and Automation","start_date":"2019-05-20","end_date":"2019-05-24","location":"Montreal, QC, Canada"},"type":"conference","_id":"6888","volume":"2019-May","language":[{"iso":"eng"}],"file":[{"file_name":"2019_ICRA_Lechner.pdf","date_created":"2020-10-08T17:30:38Z","creator":"dernst","file_size":3265107,"date_updated":"2020-10-08T17:30:38Z","success":1,"file_id":"8636","checksum":"f5545a6b60c3ffd01feb3613f81d03b6","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"isbn":["9781538660270"]},"month":"05","scopus_import":"1","alternative_title":["ICRA"],"oa_version":"Submitted Version","abstract":[{"text":"In this paper, we design novel liquid time-constant recurrent neural networks for robotic control, inspired by the brain of the nematode, C. elegans. In the worm's nervous system, neurons communicate through nonlinear time-varying synaptic links established amongst them by their particular wiring structure. This property enables neurons to express liquid time-constants dynamics and therefore allows the network to originate complex behaviors with a small number of neurons. We identify neuron-pair communication motifs as design operators and use them to configure compact neuronal network structures to govern sequential robotic tasks. The networks are systematically designed to map the environmental observations to motor actions, by their hierarchical topology from sensory neurons, through recurrently-wired interneurons, to motor neurons. The networks are then parametrized in a supervised-learning scheme by a search-based algorithm. We demonstrate that obtained networks realize interpretable dynamics. We evaluate their performance in controlling mobile and arm robots, and compare their attributes to other artificial neural network-based control agents. Finally, we experimentally show their superior resilience to environmental noise, compared to the existing machine learning-based methods.","lang":"eng"}],"title":"Designing worm-inspired neural networks for interpretable robotic control","article_processing_charge":"No","author":[{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"first_name":"Manuel","full_name":"Zimmer, Manuel","last_name":"Zimmer"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Radu","full_name":"Grosu, Radu","last_name":"Grosu"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Lechner, Mathias, et al. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” Proceedings - IEEE International Conference on Robotics and Automation, vol. 2019–May, 8793840, IEEE, 2019, doi:10.1109/icra.2019.8793840.","apa":"Lechner, M., Hasani, R., Zimmer, M., Henzinger, T. A., & Grosu, R. (2019). Designing worm-inspired neural networks for interpretable robotic control. In Proceedings - IEEE International Conference on Robotics and Automation (Vol. 2019–May). Montreal, QC, Canada: IEEE. https://doi.org/10.1109/icra.2019.8793840","ama":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. Designing worm-inspired neural networks for interpretable robotic control. In: Proceedings - IEEE International Conference on Robotics and Automation. Vol 2019-May. IEEE; 2019. doi:10.1109/icra.2019.8793840","short":"M. Lechner, R. Hasani, M. Zimmer, T.A. Henzinger, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2019.","ieee":"M. Lechner, R. Hasani, M. Zimmer, T. A. Henzinger, and R. Grosu, “Designing worm-inspired neural networks for interpretable robotic control,” in Proceedings - IEEE International Conference on Robotics and Automation, Montreal, QC, Canada, 2019, vol. 2019–May.","chicago":"Lechner, Mathias, Ramin Hasani, Manuel Zimmer, Thomas A Henzinger, and Radu Grosu. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” In Proceedings - IEEE International Conference on Robotics and Automation, Vol. 2019–May. IEEE, 2019. https://doi.org/10.1109/icra.2019.8793840.","ista":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. 2019. Designing worm-inspired neural networks for interpretable robotic control. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, vol. 2019–May, 8793840."},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"article_number":"8793840","date_created":"2019-09-18T08:09:51Z","date_published":"2019-05-01T00:00:00Z","doi":"10.1109/icra.2019.8793840","publication":"Proceedings - IEEE International Conference on Robotics and Automation","day":"01","year":"2019","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"IEEE"},{"status":"public","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"conference":{"end_date":"2019-08-30","location":"Amsterdam, Netherlands","start_date":"2019-08-27","name":"CONCUR: International Conference on Concurrency Theory"},"type":"conference","_id":"6886","file_date_updated":"2020-07-14T12:47:43Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2022-01-26T08:27:10Z","intvolume":" 140","month":"08","scopus_import":"1","alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets. "}],"volume":140,"language":[{"iso":"eng"}],"file":[{"file_name":"2019_LIPIcs_Aghajohari.pdf","date_created":"2019-09-27T12:21:38Z","creator":"kschuh","file_size":741425,"date_updated":"2020-07-14T12:47:43Z","file_id":"6915","checksum":"4df6d3575c506edb17215adada03cc8e","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","project":[{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"20","title":"Determinacy in discrete-bidding infinite-duration games","article_processing_charge":"No","external_id":{"arxiv":["1905.03588"]},"author":[{"last_name":"Aghajohari","full_name":"Aghajohari, Milad","first_name":"Milad"},{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.20","apa":"Aghajohari, M., Avni, G., & Henzinger, T. A. (2019). Determinacy in discrete-bidding infinite-duration games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.20","ieee":"M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","short":"M. Aghajohari, G. Avni, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","mla":"Aghajohari, Milad, et al. Determinacy in Discrete-Bidding Infinite-Duration Games. Vol. 140, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.20.","ista":"Aghajohari M, Avni G, Henzinger TA. 2019. Determinacy in discrete-bidding infinite-duration games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 20.","chicago":"Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.20."},"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","date_created":"2019-09-18T08:06:58Z","date_published":"2019-08-01T00:00:00Z","doi":"10.4230/LIPICS.CONCUR.2019.20","day":"01","year":"2019","has_accepted_license":"1"},{"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"date_published":"2019-08-01T00:00:00Z","doi":"10.4230/LIPICS.CONCUR.2019.27","date_created":"2019-09-18T08:06:14Z","has_accepted_license":"1","year":"2019","day":"01","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"}],"article_number":"27","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"}],"title":"Long-run average behavior of vector addition systems with states","citation":{"short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Long-run average behavior of vector addition systems with states,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","ama":"Chatterjee K, Henzinger TA, Otop J. Long-run average behavior of vector addition systems with states. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.27","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2019). Long-run average behavior of vector addition systems with states (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.27","mla":"Chatterjee, Krishnendu, et al. Long-Run Average Behavior of Vector Addition Systems with States. Vol. 140, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.27.","ista":"Chatterjee K, Henzinger TA, Otop J. 2019. Long-run average behavior of vector addition systems with states. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 27.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Long-Run Average Behavior of Vector Addition Systems with States,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.27."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"alternative_title":["LIPIcs"],"month":"08","intvolume":" 140","abstract":[{"lang":"eng","text":"A vector addition system with states (VASS) consists of a finite set of states and counters. A configuration is a state and a value for each counter; a transition changes the state and each counter is incremented, decremented, or left unchanged. While qualitative properties such as state and configuration reachability have been studied for VASS, we consider the long-run average cost of infinite computations of VASS. The cost of a configuration is for each state, a linear combination of the counter values. In the special case of uniform cost functions, the linear combination is the same for all states. The (regular) long-run emptiness problem is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped) computation such that the long-run average value of the cost function does not exceed the threshold. For uniform cost functions, we show that the regular long-run emptiness problem is (a) decidable in polynomial time for integer-valued VASS, and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative counters). For general cost functions, we show that the problem is (c) NP-complete for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most interesting result is for (c) integer-valued VASS with general cost functions, where we establish a connection between the regular long-run emptiness problem and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness problem is equally hard as the regular problem in all cases except (c), where it remains open. "}],"oa_version":"Published Version","volume":140,"publication_status":"published","file":[{"creator":"kschuh","file_size":538120,"date_updated":"2020-07-14T12:47:43Z","file_name":"2019_LIPIcs_Chatterjee.pdf","date_created":"2019-09-27T12:09:35Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6914","checksum":"4985e26e1572d1575d64d38acabd71d6"}],"language":[{"iso":"eng"}],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CONCUR: International Conference on Concurrency Theory","start_date":"2019-08-27","location":"Amsterdam, Netherlands","end_date":"2019-08-30"},"status":"public","_id":"6885","file_date_updated":"2020-07-14T12:47:43Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2021-01-12T08:09:27Z","ddc":["000"]},{"citation":{"chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.6.","ista":"Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic Parity Games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 6.","mla":"Chatterjee, Krishnendu, and Nir Piterman. Combinations of Qualitative Winning for Stochastic Parity Games. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.6.","ieee":"K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic Parity Games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","short":"K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","apa":"Chatterjee, K., & Piterman, N. (2019). Combinations of Qualitative Winning for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.6","ama":"Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.6"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Piterman","full_name":"Piterman, Nir","first_name":"Nir"}],"title":"Combinations of Qualitative Winning for Stochastic Parity Games","article_number":"6","project":[{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"has_accepted_license":"1","year":"2019","day":"01","date_published":"2019-08-01T00:00:00Z","doi":"10.4230/LIPICS.CONCUR.2019.6","date_created":"2019-09-18T08:11:43Z","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"date_updated":"2021-01-12T08:09:28Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:43Z","department":[{"_id":"KrCh"}],"_id":"6889","type":"conference","conference":{"location":"Amsterdam, Netherlands","end_date":"2019-08-30","start_date":"2019-08-27","name":"CONCUR: International Conference on Concurrency Theory"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"file_id":"6923","checksum":"7b2ecfd4d9d02360308c0ca986fc10a7","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_LIPIcs_Chatterjee.pdf","date_created":"2019-10-01T08:49:45Z","file_size":509163,"date_updated":"2020-07-14T12:47:43Z","creator":"kschuh"}],"language":[{"iso":"eng"}],"volume":140,"abstract":[{"text":"We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":1,"month":"08","intvolume":" 140"},{"_id":"6931","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Budapest, Hungary","end_date":"2019-10-18","start_date":"2019-10-14","name":"DISC: International Symposium on Distributed Computing"},"status":"public","keyword":["consensus","approximate agreement","Byzantine faults","chordal graphs","lattice agreement"],"date_updated":"2021-01-12T08:09:38Z","ddc":["004"],"file_date_updated":"2020-07-14T12:47:44Z","department":[{"_id":"DaAl"}],"abstract":[{"text":"Consider a distributed system with n processors out of which f can be Byzantine faulty. In the\r\napproximate agreement task, each processor i receives an input value xi and has to decide on an\r\noutput value yi such that\r\n1. the output values are in the convex hull of the non-faulty processors’ input values,\r\n2. the output values are within distance d of each other.\r\n\r\n\r\nClassically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.\r\nIn this work, we study the task in a discrete setting, where input values with some structure\r\nexpressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to\r\noutput vertices that are within distance d of each other in G, but still remain in the graph-induced\r\nconvex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with\r\na deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,\r\nwe show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,\r\nwhere ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a\r\nvariant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact\r\nvariants of these and related tasks over a large class of combinatorial structures.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 146","publication_identifier":{"eisbn":["978-3-95977-126-9"]},"publication_status":"published","file":[{"file_name":"LIPIcs-DISC-2019-29.pdf","date_created":"2019-10-08T12:47:19Z","file_size":639378,"date_updated":"2020-07-14T12:47:44Z","creator":"jrybicki","checksum":"2d2202f90c6ac991e50876451627c4b5","file_id":"6934","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":146,"ec_funded":1,"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Nowak T, Rybicki J. 2019. Byzantine approximate agreement on graphs. 33rd International Symposium on Distributed Computing. DISC: International Symposium on Distributed Computing, LIPIcs, vol. 146, 29:1--29:17.","chicago":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” In 33rd International Symposium on Distributed Computing, 146:29:1--29:17. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.DISC.2019.29.","short":"T. Nowak, J. Rybicki, in:, 33rd International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17.","ieee":"T. Nowak and J. Rybicki, “Byzantine approximate agreement on graphs,” in 33rd International Symposium on Distributed Computing, Budapest, Hungary, 2019, vol. 146, p. 29:1--29:17.","ama":"Nowak T, Rybicki J. Byzantine approximate agreement on graphs. In: 33rd International Symposium on Distributed Computing. Vol 146. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:29:1--29:17. doi:10.4230/LIPICS.DISC.2019.29","apa":"Nowak, T., & Rybicki, J. (2019). Byzantine approximate agreement on graphs. In 33rd International Symposium on Distributed Computing (Vol. 146, p. 29:1--29:17). Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.DISC.2019.29","mla":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” 33rd International Symposium on Distributed Computing, vol. 146, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17, doi:10.4230/LIPICS.DISC.2019.29."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Thomas","full_name":"Nowak, Thomas","last_name":"Nowak"},{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki"}],"external_id":{"arxiv":["1908.02743"]},"article_processing_charge":"No","title":"Byzantine approximate agreement on graphs","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"has_accepted_license":"1","year":"2019","publication":"33rd International Symposium on Distributed Computing","page":"29:1--29:17","doi":"10.4230/LIPICS.DISC.2019.29","date_published":"2019-01-01T00:00:00Z","date_created":"2019-10-08T12:41:38Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:19Z","citation":{"ista":"Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. 2019. Response characterization for auditing cell dynamics in long short-term memory networks. Proceedings of the International Joint Conference on Neural Networks. IJCNN: International Joint Conference on Neural Networks, 8851954.","chicago":"Hasani, Ramin, Alexander Amini, Mathias Lechner, Felix Naser, Radu Grosu, and Daniela Rus. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” In Proceedings of the International Joint Conference on Neural Networks. IEEE, 2019. https://doi.org/10.1109/ijcnn.2019.8851954.","ieee":"R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, and D. Rus, “Response characterization for auditing cell dynamics in long short-term memory networks,” in Proceedings of the International Joint Conference on Neural Networks, Budapest, Hungary, 2019.","short":"R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, D. Rus, in:, Proceedings of the International Joint Conference on Neural Networks, IEEE, 2019.","apa":"Hasani, R., Amini, A., Lechner, M., Naser, F., Grosu, R., & Rus, D. (2019). Response characterization for auditing cell dynamics in long short-term memory networks. In Proceedings of the International Joint Conference on Neural Networks. Budapest, Hungary: IEEE. https://doi.org/10.1109/ijcnn.2019.8851954","ama":"Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. Response characterization for auditing cell dynamics in long short-term memory networks. In: Proceedings of the International Joint Conference on Neural Networks. IEEE; 2019. doi:10.1109/ijcnn.2019.8851954","mla":"Hasani, Ramin, et al. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” Proceedings of the International Joint Conference on Neural Networks, 8851954, IEEE, 2019, doi:10.1109/ijcnn.2019.8851954."},"department":[{"_id":"ToHe"}],"title":"Response characterization for auditing cell dynamics in long short-term memory networks","external_id":{"arxiv":["1809.03864"]},"author":[{"first_name":"Ramin","full_name":"Hasani, Ramin","last_name":"Hasani"},{"last_name":"Amini","full_name":"Amini, Alexander","first_name":"Alexander"},{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Felix","last_name":"Naser","full_name":"Naser, Felix"},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"}],"article_number":"8851954","_id":"6985","status":"public","conference":{"name":"IJCNN: International Joint Conference on Neural Networks","location":"Budapest, Hungary","end_date":"2019-07-19","start_date":"2019-07-14"},"type":"conference","publication":"Proceedings of the International Joint Conference on Neural Networks","language":[{"iso":"eng"}],"day":"30","publication_status":"published","year":"2019","publication_identifier":{"isbn":["9781728119854"]},"date_created":"2019-11-04T15:59:58Z","date_published":"2019-09-30T00:00:00Z","doi":"10.1109/ijcnn.2019.8851954","oa_version":"Preprint","abstract":[{"lang":"eng","text":"In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets."}],"month":"09","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1809.03864","open_access":"1"}],"quality_controlled":"1","publisher":"IEEE","scopus_import":1},{"abstract":[{"lang":"eng","text":"We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds."}],"oa_version":"Published Version","scopus_import":1,"month":"10","intvolume":" 12","publication_identifier":{"issn":["1999-4893"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"267756d8f9db572f496cd1663c89d59a","file_id":"7008","date_updated":"2020-07-14T12:47:47Z","file_size":696791,"creator":"dernst","date_created":"2019-11-12T14:48:45Z","file_name":"2019_Algorithms_Mondelli.pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6675"}]},"issue":"10","volume":12,"_id":"7007","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-02-23T12:49:28Z","ddc":["510"],"department":[{"_id":"MaMo"}],"file_date_updated":"2020-07-14T12:47:47Z","quality_controlled":"1","publisher":"MDPI","oa":1,"has_accepted_license":"1","year":"2019","day":"18","publication":"Algorithms","date_published":"2019-10-18T00:00:00Z","doi":"10.3390/a12100218","date_created":"2019-11-12T14:46:19Z","article_number":"218","citation":{"ieee":"M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019.","short":"M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019).","ama":"Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218","apa":"Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218","mla":"Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218.","ista":"Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive relay channel. Algorithms. 12(10), 218.","chicago":"Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"first_name":"S. Hamed","last_name":"Hassani","full_name":"Hassani, S. Hamed"},{"full_name":"Urbanke, Rüdiger","last_name":"Urbanke","first_name":"Rüdiger"}],"external_id":{"arxiv":["1801.03153"]},"title":"A new coding paradigm for the primitive relay channel"},{"status":"public","conference":{"name":"Research on isometries as preserver problems and related topics","end_date":"2019-01-30","location":"Kyoto, Japan","start_date":"2019-01-28"},"type":"conference","_id":"7035","department":[{"_id":"LaEr"}],"title":"Dirac masses and isometric rigidity","article_processing_charge":"No","author":[{"last_name":"Geher","full_name":"Geher, Gyorgy Pal","first_name":"Gyorgy Pal"},{"first_name":"Tamas","full_name":"Titkos, Tamas","last_name":"Titkos"},{"orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel","last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:33Z","citation":{"mla":"Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","short":"G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,” in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41.","apa":"Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan: Research Institute for Mathematical Sciences, Kyoto University.","ama":"Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In: Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences, Kyoto University; 2019:34-41.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute for Mathematical Sciences, Kyoto University, 2019.","ista":"Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity. Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related topics vol. 2125, 34–41."},"intvolume":" 2125","month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html"}],"publisher":"Research Institute for Mathematical Sciences, Kyoto University","quality_controlled":"1","oa_version":"Submitted Version","abstract":[{"text":"The aim of this short note is to expound one particular issue that was discussed during the talk [10] given at the symposium ”Researches on isometries as preserver problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new results.From an isometric point of view, in some cases, metric spaces of measures are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations of the underlying space. Of course, it depends on the particular choice of the metric how nice these transformations should be. Sometimes, as we will see, being a homeomorphism is enough to generate an isometry. But sometimes we need more: the transformation must preserve the underlying distance as well. Statements claiming that isometries in questions are necessarily induced by homeomorphisms are called Banach-Stone-type results, while results asserting that the underlying transformation is necessarily an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural question arises:Is it enough to understand how an isometry acts on the set of Dirac masses? Does this action extend uniquely to all measures?In what follows, we will thoroughly investigate this question.","lang":"eng"}],"date_created":"2019-11-18T15:39:53Z","date_published":"2019-01-30T00:00:00Z","volume":2125,"page":"34-41","language":[{"iso":"eng"}],"publication":"Kyoto RIMS Kôkyûroku","day":"30","year":"2019","publication_status":"published"},{"_id":"7171","status":"public","type":"book_editor","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-22T14:40:58Z","citation":{"chicago":"Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature, 2019. https://doi.org/10.1007/978-3-658-26763-6.","ista":"Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.","mla":"Kersting, Kristian, et al., editors. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed., Springer Nature, 2019, doi:10.1007/978-3-658-26763-6.","ieee":"K. Kersting, C. Lampert, and C. Rothkopf, Eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed. Wiesbaden: Springer Nature, 2019.","short":"K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.","ama":"Kersting K, Lampert C, Rothkopf C, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature; 2019. doi:10.1007/978-3-658-26763-6","apa":"Kersting, K., Lampert, C., & Rothkopf, C. (Eds.). (2019). Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt (1st ed.). Wiesbaden: Springer Nature. https://doi.org/10.1007/978-3-658-26763-6"},"editor":[{"first_name":"Kristian","full_name":"Kersting, Kristian","last_name":"Kersting"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"},{"last_name":"Rothkopf","full_name":"Rothkopf, Constantin","first_name":"Constantin"}],"title":"Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt","department":[{"_id":"ChLa"}],"article_processing_charge":"No","oa_version":"None","abstract":[{"text":"Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens. Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten möchten. Auch für Schülerinnen und Schüler geeignet!","lang":"ger"}],"month":"10","place":"Wiesbaden","publisher":"Springer Nature","quality_controlled":"1","edition":"1","day":"30","language":[{"iso":"ger"}],"publication_identifier":{"eisbn":["978-3-658-26763-6"],"isbn":["978-3-658-26762-9"]},"publication_status":"published","year":"2019","related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/book-release-how-machines-learn/"}]},"doi":"10.1007/978-3-658-26763-6","date_published":"2019-10-30T00:00:00Z","date_created":"2019-12-11T14:15:56Z","page":"XIV, 245"},{"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","date_created":"2020-01-29T16:17:05Z","doi":"10.4230/LIPICS.SOCG.2019.39","date_published":"2019-06-01T00:00:00Z","publication":"35th International Symposium on Computational Geometry (SoCG 2019)","day":"01","year":"2019","has_accepted_license":"1","project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"article_number":"39","title":"Z_2-Genus of graphs and minimum rank of partial symmetric matrices","article_processing_charge":"No","external_id":{"arxiv":["1903.08637"]},"author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"Jan","last_name":"Kyncl","full_name":"Kyncl, Jan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fulek R, Kyncl J. 2019. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. 35th International Symposium on Computational Geometry (SoCG 2019). SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 39.","chicago":"Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” In 35th International Symposium on Computational Geometry (SoCG 2019), Vol. 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.39.","apa":"Fulek, R., & Kyncl, J. (2019). Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In 35th International Symposium on Computational Geometry (SoCG 2019) (Vol. 129). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.39","ama":"Fulek R, Kyncl J. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In: 35th International Symposium on Computational Geometry (SoCG 2019). Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.SOCG.2019.39","ieee":"R. Fulek and J. Kyncl, “Z_2-Genus of graphs and minimum rank of partial symmetric matrices,” in 35th International Symposium on Computational Geometry (SoCG 2019), Portland, OR, United States, 2019, vol. 129.","short":"R. Fulek, J. Kyncl, in:, 35th International Symposium on Computational Geometry (SoCG 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","mla":"Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” 35th International Symposium on Computational Geometry (SoCG 2019), vol. 129, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.SOCG.2019.39."},"intvolume":" 129","month":"06","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The genus g(G) of a graph G is the minimum g such that G has an embedding on the orientable surface M_g of genus g. A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum g such that G has an independently even drawing on M_g. By a result of Battle, Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph is additive over 2-connected blocks as well, and asked whether this result can be extended to so-called 2-amalgamations, as an analogue of results by Decker, Glover, Huneke, and Stahl for the genus. We give the following partial answer. If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1. For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest. "}],"volume":129,"language":[{"iso":"eng"}],"file":[{"date_created":"2020-02-04T09:14:31Z","file_name":"2019_LIPIcs_Fulek.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:57Z","file_size":628347,"file_id":"7445","checksum":"aac37b09118cc0ab58cf77129e691f8c","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-95977-104-7"],"issn":["1868-8969"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2019-06-21","location":"Portland, OR, United States","start_date":"2019-06-18"},"type":"conference","_id":"7401","file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"UlWa"}],"ddc":["000"],"date_updated":"2021-01-12T08:13:24Z"},{"project":[{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"},{"first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","last_name":"Giacobbe"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kim G.","last_name":"Larsen","full_name":"Larsen, Kim G."},{"last_name":"Mikučionis","full_name":"Mikučionis, Marius","first_name":"Marius"}],"article_processing_charge":"No","title":"Continuous-time models for system design and analysis","editor":[{"full_name":"Steffen, Bernhard","last_name":"Steffen","first_name":"Bernhard"},{"first_name":"Gerhard","last_name":"Woeginger","full_name":"Woeginger, Gerhard"}],"citation":{"chicago":"Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius Mikučionis. “Continuous-Time Models for System Design and Analysis.” In Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77. LNCS. Springer Nature, 2019. https://doi.org/10.1007/978-3-319-91908-9_22.","ista":"Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time models for system design and analysis. In: Computing and Software Science. Lecture Notes in Computer Science, vol. 10000, 452–477.","mla":"Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.” Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:10.1007/978-3-319-91908-9_22.","ama":"Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time models for system design and analysis. In: Steffen B, Woeginger G, eds. Computing and Software Science. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:10.1007/978-3-319-91908-9_22","apa":"Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., & Mikučionis, M. (2019). Continuous-time models for system design and analysis. In B. Steffen & G. Woeginger (Eds.), Computing and Software Science (Vol. 10000, pp. 452–477). Springer Nature. https://doi.org/10.1007/978-3-319-91908-9_22","short":"R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B. Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature, 2019, pp. 452–477.","ieee":"R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time models for system design and analysis,” in Computing and Software Science, vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS, funded by the Danish National Research Foundation and the National Science Foundation, China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant LASSO.","page":"452-477","doi":"10.1007/978-3-319-91908-9_22","date_published":"2019-10-05T00:00:00Z","date_created":"2020-02-05T10:51:44Z","year":"2019","day":"05","publication":"Computing and Software Science","type":"book_chapter","status":"public","series_title":"LNCS","_id":"7453","department":[{"_id":"ToHe"}],"date_updated":"2022-09-06T08:25:52Z","alternative_title":["Lecture Notes in Computer Science"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-319-91908-9_22"}],"month":"10","intvolume":" 10000","abstract":[{"lang":"eng","text":"We illustrate the ingredients of the state-of-the-art of model-based approach for the formal design and verification of cyber-physical systems. To capture the interaction between a discrete controller and its continuously evolving environment, we use the formal models of timed and hybrid automata. We explain the steps of modeling and verification in the tools Uppaal and SpaceEx using a case study based on a dual-chamber implantable pacemaker monitoring a human heart. We show how to design a model as a composition of components, how to construct models at varying levels of detail, how to establish that one model is an abstraction of another, how to specify correctness requirements using temporal logic, and how to verify that a model satisfies a logical requirement."}],"oa_version":"Published Version","volume":10000,"publication_identifier":{"eisbn":["9783319919089"],"eissn":["0302-9743"],"isbn":["9783319919072"],"issn":["1611-3349"]},"publication_status":"published","language":[{"iso":"eng"}]},{"project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications. Gakko Tosho, 2019.","ista":"Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 28(2), 425–447.","mla":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.","short":"L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications 28 (2019) 425–447.","ieee":"L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control problems for dissipative evolution,” Advances in Mathematical Sciences and Applications, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.","apa":"Portinale, L., & Stefanelli, U. (2019). Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. Gakko Tosho.","ama":"Portinale L, Stefanelli U. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 2019;28(2):425-447."},"title":"Penalization via global functionals of optimal-control problems for dissipative evolution","author":[{"last_name":"Portinale","full_name":"Portinale, Lorenzo","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stefanelli, Ulisse","last_name":"Stefanelli","first_name":"Ulisse"}],"article_processing_charge":"No","external_id":{"arxiv":["1910.10050"]},"acknowledgement":"This work is supported by Vienna Science and Technology Fund (WWTF) through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and I 2375.","quality_controlled":"1","publisher":"Gakko Tosho","oa":1,"day":"22","publication":"Advances in Mathematical Sciences and Applications","year":"2019","date_published":"2019-10-22T00:00:00Z","date_created":"2020-02-28T10:54:41Z","page":"425-447","_id":"7550","status":"public","type":"journal_article","article_type":"original","date_updated":"2022-06-17T07:52:41Z","department":[{"_id":"JaMa"}],"oa_version":"Preprint","abstract":[{"text":"We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. ","lang":"eng"}],"month":"10","intvolume":" 28","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1910.10050","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1343-4373"]},"publication_status":"published","volume":28,"issue":"2"},{"day":"18","language":[{"iso":"eng"}],"publication":"arXiv:1912.08579","publication_status":"submitted","year":"2019","date_published":"2019-12-18T00:00:00Z","date_created":"2020-02-28T10:57:08Z","page":"5","oa_version":"Preprint","abstract":[{"lang":"eng","text":"There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. "}],"month":"12","publisher":"ArXiv","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1912.08579","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. arXiv:1912.08579. ArXiv.","ama":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579.","ieee":"W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” arXiv:1912.08579. ArXiv.","short":"W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).","mla":"Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579, ArXiv.","ista":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:1912.08579, .","chicago":"Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d."},"date_updated":"2021-01-12T08:14:09Z","department":[{"_id":"GaTk"}],"title":"Action at a distance in transcriptional regulation","author":[{"last_name":"Bialek","full_name":"Bialek, William","first_name":"William"},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"article_processing_charge":"No","external_id":{"arxiv":["1912.08579"]},"_id":"7552","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"status":"public","type":"preprint"},{"oa_version":"Published Version","abstract":[{"text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.","lang":"eng"}],"intvolume":" 61","month":"05","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2020-03-24T07:36:36Z","file_name":"2019_ARCH19_Immler.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:00Z","file_size":1934830,"checksum":"9138977a06fcd6a95976eb4bca875f0c","file_id":"7617","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["23987340"]},"volume":61,"_id":"7576","status":"public","conference":{"start_date":"2019-04-15","location":"Montreal, Canada","end_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"type":"conference","ddc":["000"],"date_updated":"2021-01-12T08:14:17Z","file_date_updated":"2020-07-14T12:48:00Z","department":[{"_id":"ToHe"}],"oa":1,"quality_controlled":"1","publisher":"EasyChair Publications","publication":"EPiC Series in Computing","day":"25","year":"2019","has_accepted_license":"1","date_created":"2020-03-08T23:00:49Z","date_published":"2019-05-25T00:00:00Z","doi":"10.29007/m75b","page":"41-61","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair Publications, 2019, pp. 41–61, doi:10.29007/m75b.","apa":"Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair Publications. https://doi.org/10.29007/m75b","ama":"Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing. Vol 61. EasyChair Publications; 2019:41-61. doi:10.29007/m75b","ieee":"F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 41–61.","short":"F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair Publications, 2019, pp. 41–61.","chicago":"Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair Publications, 2019. https://doi.org/10.29007/m75b.","ista":"Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61."},"title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics","article_processing_charge":"No","author":[{"first_name":"Fabian","last_name":"Immler","full_name":"Immler, Fabian"},{"first_name":"Matthias","full_name":"Althoff, Matthias","last_name":"Althoff"},{"last_name":"Benet","full_name":"Benet, Luis","first_name":"Luis"},{"full_name":"Chapoutot, Alexandre","last_name":"Chapoutot","first_name":"Alexandre"},{"first_name":"Xin","last_name":"Chen","full_name":"Chen, Xin"},{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"full_name":"Geretti, Luca","last_name":"Geretti","first_name":"Luca"},{"first_name":"Niklas","full_name":"Kochdumper, Niklas","last_name":"Kochdumper"},{"last_name":"Sanders","full_name":"Sanders, David P.","first_name":"David P."},{"last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"}]},{"date_updated":"2021-01-12T08:17:18Z","department":[{"_id":"LaEr"}],"_id":"8175","type":"conference","conference":{"name":"FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics","end_date":"2019-07-05","location":"Ljubljana, Slovenia","start_date":"2019-07-01"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.08750"}],"month":"07","citation":{"apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.","ama":"Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics; 2019.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana, Slovenia, 2019.","mla":"Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics, 2019.","ista":"Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34.","chicago":"Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics, 2019."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Dan","last_name":"Betea","full_name":"Betea, Dan"},{"first_name":"Jérémie","last_name":"Bouttier","full_name":"Bouttier, Jérémie"},{"last_name":"Nejjar","full_name":"Nejjar, Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"last_name":"Vuletíc","full_name":"Vuletíc, Mirjana","first_name":"Mirjana"}],"external_id":{"arxiv":["1902.08750"]},"article_processing_charge":"No","title":"New edge asymptotics of skew Young diagrams via free boundaries","article_number":"34","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"year":"2019","day":"01","publication":"Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics","date_published":"2019-07-01T00:00:00Z","date_created":"2020-07-26T22:01:04Z","acknowledgement":"D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n","publisher":"Formal Power Series and Algebraic Combinatorics","quality_controlled":"1","oa":1},{"year":"2019","publication_status":"published","publication_identifier":{"eissn":["23987340"]},"publication":"EPiC Series in Computing","language":[{"iso":"eng"}],"day":"25","page":"14-40","date_created":"2020-09-26T14:23:54Z","date_published":"2019-05-25T00:00:00Z","doi":"10.29007/bj1w","volume":61,"abstract":[{"text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://easychair.org/publications/open/1gbP","open_access":"1"}],"oa":1,"publisher":"EasyChair","quality_controlled":"1","intvolume":" 61","month":"05","date_updated":"2021-01-12T08:20:05Z","citation":{"ista":"Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.","chicago":"Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper, Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.","short":"M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling, S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.","ieee":"M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 14–40.","apa":"Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp, S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40). Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w","ama":"Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing. Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w","mla":"Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol. 61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Matthias","full_name":"Althoff, Matthias","last_name":"Althoff"},{"first_name":"Stanley","last_name":"Bak","full_name":"Bak, Stanley"},{"first_name":"Marcelo","full_name":"Forets, Marcelo","last_name":"Forets"},{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"first_name":"Niklas","last_name":"Kochdumper","full_name":"Kochdumper, Niklas"},{"full_name":"Ray, Rajarshi","last_name":"Ray","first_name":"Rajarshi"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065"},{"first_name":"Stefan","last_name":"Schupp","full_name":"Schupp, Stefan"}],"department":[{"_id":"ToHe"}],"title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics","_id":"8570","conference":{"start_date":"2019-04-15","end_date":"2019-04-15","location":"Montreal, Canada","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"type":"conference","status":"public"},{"article_processing_charge":"No","external_id":{"pmid":["31000601"]},"author":[{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"first_name":"Akemi","last_name":"Ono","full_name":"Ono, Akemi"},{"first_name":"Stefan","full_name":"Scholten, Stefan","last_name":"Scholten"},{"first_name":"Tetsu","last_name":"Kinoshita","full_name":"Kinoshita, Tetsu"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Takashi","last_name":"Okamoto","full_name":"Okamoto, Takashi"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."}],"title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","citation":{"chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.","ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116","ieee":"M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","page":"9652-9657","date_created":"2021-06-04T12:38:20Z","date_published":"2019-05-07T00:00:00Z","doi":"10.1073/pnas.1821435116","year":"2019","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences","day":"07","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","keyword":["Multidisciplinary"],"status":"public","_id":"9460","file_date_updated":"2021-06-04T12:50:47Z","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T07:52:30Z","ddc":["580"],"extern":"1","scopus_import":"1","intvolume":" 116","month":"05","abstract":[{"text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","issue":"19","volume":116,"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_PNAS_Kim.pdf","date_created":"2021-06-04T12:50:47Z","file_size":1142540,"date_updated":"2021-06-04T12:50:47Z","creator":"asandaue","success":1,"file_id":"9461","checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}]},{"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.","lang":"eng"}],"month":"08","intvolume":" 12","scopus_import":1,"file":[{"file_size":1177482,"date_updated":"2020-07-14T12:47:40Z","creator":"dernst","file_name":"2019_BMC_Antoniou.pdf","date_created":"2019-08-23T11:10:35Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6829","checksum":"4a2bb7994b7f2c432bf44f5127ea3102"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1756-0500"]},"publication_status":"published","volume":12,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9784"}]},"_id":"6819","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-02-23T14:08:14Z","department":[{"_id":"LifeSc"}],"file_date_updated":"2020-07-14T12:47:40Z","quality_controlled":"1","publisher":"BioMed Central","oa":1,"day":"08","publication":"BMC Research Notes","has_accepted_license":"1","year":"2019","doi":"10.1186/s13104-019-4534-3","date_published":"2019-08-08T00:00:00Z","date_created":"2019-08-18T22:00:39Z","article_number":"494","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494.","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019).","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.","mla":"Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3."},"title":"Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","author":[{"first_name":"Michael N.","last_name":"Antoniou","full_name":"Antoniou, Michael N."},{"full_name":"Nicolas, Armel","last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mesnage","full_name":"Mesnage, Robin","first_name":"Robin"},{"last_name":"Biserni","full_name":"Biserni, Martina","first_name":"Martina"},{"full_name":"Rao, Francesco V.","last_name":"Rao","first_name":"Francesco V."},{"first_name":"Cristina Vazquez","last_name":"Martin","full_name":"Martin, Cristina Vazquez"}],"article_processing_charge":"No","external_id":{"pmid":["31395095"]}},{"_id":"9784","type":"research_data_reference","status":"public","date_updated":"2023-02-23T12:52:29Z","citation":{"mla":"Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019).","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019.","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1.","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"last_name":"Antoniou","full_name":"Antoniou, Michael N.","first_name":"Michael N."},{"last_name":"Nicolas","full_name":"Nicolas, Armel","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mesnage, Robin","last_name":"Mesnage","first_name":"Robin"},{"full_name":"Biserni, Martina","last_name":"Biserni","first_name":"Martina"},{"first_name":"Francesco V.","full_name":"Rao, Francesco V.","last_name":"Rao"},{"last_name":"Martin","full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez"}],"department":[{"_id":"LifeSc"}],"title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","abstract":[{"lang":"eng","text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures."}],"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9411761.v1"}],"publisher":"Springer Nature","month":"08","year":"2019","day":"09","date_created":"2021-08-06T08:14:05Z","doi":"10.6084/m9.figshare.9411761.v1","date_published":"2019-08-09T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6819"}]}},{"article_processing_charge":"No","author":[{"orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"title":"Data from: Is the sky the limit? On the expansion threshold of a species' range","citation":{"ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.","chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37","ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.","short":"J. Polechova, (2019).","mla":"Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37."},"date_updated":"2023-02-23T11:14:30Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9839","date_created":"2021-08-09T13:07:28Z","date_published":"2019-06-22T00:00:00Z","doi":"10.5061/dryad.5vv37","related_material":{"record":[{"status":"public","id":"315","relation":"used_in_publication"}]},"year":"2019","day":"22","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.5vv37"}],"publisher":"Dryad","month":"06","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"oa_version":"Published Version"},{"article_number":"62","citation":{"ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.","ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4","apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019.","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"pmid":["31601251"]},"author":[{"full_name":"Harris, Keith D.","last_name":"Harris","first_name":"Keith D."},{"first_name":"James P. B.","full_name":"Lloyd, James P. B.","last_name":"Lloyd"},{"first_name":"Katherine","last_name":"Domb","full_name":"Domb, Katherine"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"}],"title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2019","has_accepted_license":"1","publication":"Epigenetics and Chromatin","day":"10","date_created":"2021-06-08T09:21:51Z","doi":"10.1186/s13072-019-0307-4","date_published":"2019-10-10T00:00:00Z","_id":"9530","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2021-12-14T07:53:00Z","ddc":["570"],"extern":"1","department":[{"_id":"DaZi"}],"file_date_updated":"2021-06-08T09:29:19Z","abstract":[{"text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"10","publication_status":"published","publication_identifier":{"eissn":["1756-8935"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-06-08T09:29:19Z","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","creator":"asandaue","date_updated":"2021-06-08T09:29:19Z","file_size":3221067,"checksum":"86ff50a7517891511af2733c76c81b67","file_id":"9531","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"volume":12},{"_id":"12192","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["580"],"extern":"1","date_updated":"2023-05-08T10:54:12Z","file_date_updated":"2023-02-07T09:42:46Z","department":[{"_id":"XiFe"}],"oa_version":"Published Version","abstract":[{"text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.","lang":"eng"}],"intvolume":" 8","month":"05","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2023-02-07T09:42:46Z","file_name":"2019_elife_He.pdf","date_updated":"2023-02-07T09:42:46Z","file_size":2493837,"creator":"alisjak","checksum":"ea6b89c20d59e5eb3646916fe5d568ad","file_id":"12525","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"volume":8,"article_number":"42530","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019. https://doi.org/10.7554/elife.42530.","ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530.","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019.","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).","ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530","apa":"He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530"},"title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","article_processing_charge":"No","external_id":{"unknown":["31135340"]},"author":[{"first_name":"Shengbo","full_name":"He, Shengbo","last_name":"He"},{"last_name":"Vickers","full_name":"Vickers, Martin","first_name":"Martin"},{"first_name":"Jingyi","full_name":"Zhang, Jingyi","last_name":"Zhang"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"}],"acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications, Ltd","publication":"eLife","day":"28","year":"2019","has_accepted_license":"1","date_created":"2023-01-16T09:17:21Z","date_published":"2019-05-28T00:00:00Z","doi":"10.7554/elife.42530"},{"date_updated":"2023-05-08T10:54:54Z","extern":"1","department":[{"_id":"XiFe"}],"_id":"12190","type":"journal_article","article_type":"original","status":"public","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"publication_identifier":{"issn":["0960-9822"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"16","volume":29,"abstract":[{"text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","month":"08","intvolume":" 29","citation":{"chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084.","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.","mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.","ieee":"E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019.","short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3.","apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084","ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Lawrence","full_name":"Lawrence, Emma J.","first_name":"Emma J."},{"first_name":"Hongbo","full_name":"Gao, Hongbo","last_name":"Gao"},{"full_name":"Tock, Andrew J.","last_name":"Tock","first_name":"Andrew J."},{"last_name":"Lambing","full_name":"Lambing, Christophe","first_name":"Christophe"},{"first_name":"Alexander R.","last_name":"Blackwell","full_name":"Blackwell, Alexander R."},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"full_name":"Henderson, Ian R.","last_name":"Henderson","first_name":"Ian R."}],"article_processing_charge":"No","external_id":{"pmid":["31378616"]},"title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","year":"2019","day":"19","publication":"Current Biology","page":"2676-2686.e3","date_published":"2019-08-19T00:00:00Z","doi":"10.1016/j.cub.2019.06.084","date_created":"2023-01-16T09:16:33Z","acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","quality_controlled":"1","publisher":"Elsevier BV"},{"oa_version":"Published Version","month":"02","publisher":"Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz","main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf"}],"oa":1,"file":[{"creator":"dernst","date_updated":"2023-05-16T07:27:09Z","file_size":1097603,"date_created":"2023-05-16T07:27:09Z","file_name":"2019_AHPC_Schloegl.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"12970","checksum":"acc8272027faaf30709c51ac5c58ffa4","success":1}],"day":"27","publication":"AHPC19 - Austrian HPC Meeting 2019 ","language":[{"iso":"eng"}],"has_accepted_license":"1","year":"2019","publication_status":"published","date_published":"2019-02-27T00:00:00Z","date_created":"2023-05-05T12:48:48Z","page":"25","_id":"12901","status":"public","type":"conference_abstract","conference":{"location":"Grundlsee, Austria","end_date":"2019-02-27","start_date":"2019-02-25","name":"AHPC: Austrian HPC Meeting"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"citation":{"ista":"Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25.","short":"A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","ama":"Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.","apa":"Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.","mla":"Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25."},"date_updated":"2023-05-16T07:29:32Z","department":[{"_id":"ScienComp"}],"title":"Is Debian suitable for running an HPC Cluster?","file_date_updated":"2023-05-16T07:27:09Z","author":[{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100"},{"full_name":"Kiss, Janos","last_name":"Kiss","first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","full_name":"Elefante, Stefano","last_name":"Elefante"}],"article_processing_charge":"No"},{"status":"public","conference":{"name":"CCCG: Canadian Conference in Computational Geometry","start_date":"2019-08-08","end_date":"2019-08-10","location":"Edmonton, Canada"},"type":"conference","_id":"6989","department":[{"_id":"HeEd"}],"title":"Folding polyominoes with holes into a cube","article_processing_charge":"No","external_id":{"arxiv":["1910.09917"]},"author":[{"last_name":"Aichholzer","full_name":"Aichholzer, Oswin","first_name":"Oswin"},{"first_name":"Hugo A","last_name":"Akitaya","full_name":"Akitaya, Hugo A"},{"last_name":"Cheung","full_name":"Cheung, Kenneth C","first_name":"Kenneth C"},{"full_name":"Demaine, Erik D","last_name":"Demaine","first_name":"Erik D"},{"first_name":"Martin L","full_name":"Demaine, Martin L","last_name":"Demaine"},{"first_name":"Sandor P","full_name":"Fekete, Sandor P","last_name":"Fekete"},{"last_name":"Kleist","full_name":"Kleist, Linda","first_name":"Linda"},{"last_name":"Kostitsyna","full_name":"Kostitsyna, Irina","first_name":"Irina"},{"full_name":"Löffler, Maarten","last_name":"Löffler","first_name":"Maarten"},{"first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322"},{"first_name":"Klara","last_name":"Mundilova","full_name":"Mundilova, Klara"},{"first_name":"Christiane","last_name":"Schmidt","full_name":"Schmidt, Christiane"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–70.","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–170.","ieee":"O. Aichholzer et al., “Folding polyominoes with holes into a cube,” in Proceedings of the 31st Canadian Conference on Computational Geometry, Edmonton, Canada, 2019, pp. 164–170.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a cube. In Proceedings of the 31st Canadian Conference on Computational Geometry (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.","ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: Proceedings of the 31st Canadian Conference on Computational Geometry. Canadian Conference on Computational Geometry; 2019:164-170.","chicago":"Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” In Proceedings of the 31st Canadian Conference on Computational Geometry, 164–70. Canadian Conference on Computational Geometry, 2019.","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference on Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 164–170."},"date_updated":"2023-08-04T10:57:42Z","month":"08","main_file_link":[{"url":"https://cccg.ca/proceedings/2019/proceedings.pdf","open_access":"1"}],"oa":1,"scopus_import":"1","quality_controlled":"1","publisher":"Canadian Conference on Computational Geometry","acknowledgement":"This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank all other participants for a fruitful atmosphere.","oa_version":"Published Version","abstract":[{"lang":"eng","text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. "}],"date_created":"2019-11-04T16:46:11Z","date_published":"2019-08-01T00:00:00Z","related_material":{"record":[{"id":"8317","status":"public","relation":"extended_version"}]},"page":"164-170","publication":"Proceedings of the 31st Canadian Conference on Computational Geometry","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2019"},{"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","date_created":"2019-09-18T08:04:26Z","doi":"10.4230/LIPICS.MFCS.2019.11","date_published":"2019-08-01T00:00:00Z","day":"01","year":"2019","has_accepted_license":"1","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"}],"article_number":"11","title":"Bidding mechanisms in graph games","external_id":{"arxiv":["1905.03835"]},"author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic","full_name":"Zikelic, Dorde"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Avni, G., Henzinger, T. A., & Zikelic, D. (2019). Bidding mechanisms in graph games (Vol. 138). Presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2019.11","ama":"Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.MFCS.2019.11","short":"G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","ieee":"G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,” presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany, 2019, vol. 138.","mla":"Avni, Guy, et al. Bidding Mechanisms in Graph Games. Vol. 138, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.MFCS.2019.11.","ista":"Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games. MFCS: nternational Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 138, 11.","chicago":"Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.MFCS.2019.11."},"intvolume":" 138","month":"08","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the \"bank\" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. ","lang":"eng"}],"ec_funded":1,"volume":138,"related_material":{"record":[{"relation":"later_version","status":"public","id":"9239"}]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_LIPIcs_Avni.pdf","date_created":"2019-09-27T11:45:15Z","file_size":554457,"date_updated":"2020-07-14T12:47:42Z","creator":"kschuh","file_id":"6913","checksum":"6346e116a4f4ed1414174d96d2c4fbd7","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","status":"public","conference":{"start_date":"2019-08-26","location":"Aachen, Germany","end_date":"2019-08-30","name":"MFCS: nternational Symposium on Mathematical Foundations of Computer Science"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"6884","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:42Z","ddc":["004"],"date_updated":"2023-08-07T14:08:34Z"},{"_id":"9726","type":"research_data_reference","status":"public","citation":{"chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001.","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001.","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001","apa":"Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001","short":"M.C. Ucar, R. Lipowsky, (2019).","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019."},"date_updated":"2023-08-17T14:07:52Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"last_name":"Ucar","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"last_name":"Lipowsky","full_name":"Lipowsky, Reinhard","first_name":"Reinhard"}],"department":[{"_id":"EdHa"}],"title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","abstract":[{"lang":"eng","text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)"}],"oa_version":"Published Version","publisher":"American Chemical Society ","month":"12","year":"2019","day":"19","date_created":"2021-07-27T09:51:46Z","date_published":"2019-12-19T00:00:00Z","doi":"10.1021/acs.nanolett.9b04445.s001","related_material":{"record":[{"relation":"used_in_publication","id":"7166","status":"public"}]}},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8.","ista":"Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 3(1–2), 29–58.","mla":"Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8.","ieee":"J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion, geodesic convexity and the variation of tangent spaces,” Journal of Applied and Computational Topology, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019.","short":"J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational Topology 3 (2019) 29–58.","ama":"Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8","apa":"Boissonnat, J.-D., Lieutier, A., & Wintraecken, M. (2019). The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8"},"title":"The reach, metric distortion, geodesic convexity and the variation of tangent spaces","author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Journal of Applied and Computational Topology","has_accepted_license":"1","year":"2019","date_published":"2019-06-01T00:00:00Z","doi":"10.1007/s41468-019-00029-8","date_created":"2019-07-24T08:37:29Z","page":"29–58","_id":"6671","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2023-08-22T12:37:47Z","file_date_updated":"2020-07-14T12:47:36Z","department":[{"_id":"HeEd"}],"oa_version":"Published Version","abstract":[{"text":"In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.","lang":"eng"}],"month":"06","intvolume":" 3","file":[{"checksum":"a5b244db9f751221409cf09c97ee0935","file_id":"6741","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_JournAppliedComputTopol_Boissonnat.pdf","date_created":"2019-07-31T08:09:56Z","creator":"dernst","file_size":2215157,"date_updated":"2020-07-14T12:47:36Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"publication_status":"published","issue":"1-2","volume":3,"ec_funded":1},{"department":[{"_id":"JaMa"}],"date_updated":"2023-08-24T14:20:49Z","article_type":"original","type":"journal_article","status":"public","_id":"301","volume":129,"issue":"3","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1611.04177","open_access":"1"}],"month":"03","intvolume":" 129","abstract":[{"lang":"eng","text":"A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense."}],"oa_version":"Preprint","author":[{"first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate","last_name":"Gerencser"},{"first_name":"István","last_name":"Gyöngy","full_name":"Gyöngy, István"}],"external_id":{"isi":["000458945300012"],"arxiv":["1611.04177"]},"article_processing_charge":"No","title":"A Feynman–Kac formula for stochastic Dirichlet problems","citation":{"chicago":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier, 2019. https://doi.org/10.1016/j.spa.2018.04.003.","ista":"Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012.","mla":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003.","apa":"Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2018.04.003","ama":"Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003","short":"M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012.","ieee":"M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” Stochastic Processes and their Applications, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"995-1012","doi":"10.1016/j.spa.2018.04.003","date_published":"2019-03-01T00:00:00Z","date_created":"2018-12-11T11:45:42Z","isi":1,"year":"2019","day":"01","publication":"Stochastic Processes and their Applications","quality_controlled":"1","publisher":"Elsevier","oa":1},{"quality_controlled":"1","publisher":"Springer","oa":1,"day":"01","publication":"Communications in Mathematical Physics","has_accepted_license":"1","isi":1,"year":"2019","date_published":"2019-06-01T00:00:00Z","doi":"10.1007/s00220-018-3239-0","date_created":"2018-12-11T11:44:31Z","page":"723-776","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:10.1007/s00220-018-3239-0.","short":"A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776.","ieee":"A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” Communications in Mathematical Physics, vol. 368, no. 2. Springer, pp. 723–776, 2019.","ama":"Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 2019;368(2):723-776. doi:10.1007/s00220-018-3239-0","apa":"Deuchert, A., Seiringer, R., & Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-018-3239-0","chicago":"Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics. Springer, 2019. https://doi.org/10.1007/s00220-018-3239-0.","ista":"Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776."},"title":"Bose–Einstein condensation in a dilute, trapped gas at positive temperature","author":[{"last_name":"Deuchert","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"},{"full_name":"Yngvason, Jakob","last_name":"Yngvason","first_name":"Jakob"}],"publist_id":"7974","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000467796800007"]},"oa_version":"Published Version","abstract":[{"text":"We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer.","lang":"eng"}],"month":"06","intvolume":" 368","scopus_import":"1","file":[{"file_name":"2018_CommunMathPhys_Deuchert.pdf","date_created":"2018-12-17T10:34:06Z","file_size":893902,"date_updated":"2020-07-14T12:48:07Z","creator":"dernst","file_id":"5688","checksum":"c7e9880b43ac726712c1365e9f2f73a6","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"2","volume":368,"ec_funded":1,"_id":"80","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_updated":"2023-08-24T14:27:51Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:48:07Z"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved."}],"month":"03","intvolume":" 34","scopus_import":"1","file":[{"file_id":"7245","checksum":"ef24572d6ebcc1452c067e05410cc4a2","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-01-09T10:55:58Z","file_name":"2019_Trends_Evolution_Faria.pdf","creator":"cziletti","date_updated":"2020-07-14T12:47:13Z","file_size":1946795}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["01695347"]},"publication_status":"published","volume":34,"issue":"3","ec_funded":1,"_id":"5911","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"ddc":["570"],"date_updated":"2023-08-24T14:29:48Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:13Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"01","publication":"Trends in Ecology and Evolution","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1016/j.tree.2018.12.005","date_published":"2019-03-01T00:00:00Z","date_created":"2019-02-03T22:59:15Z","page":"239-248","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005","apa":"Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005","mla":"Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005.","ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005."},"title":"Evolving inversions","author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"}],"article_processing_charge":"No","external_id":{"isi":["000459899000013"]}},{"abstract":[{"text":"We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P = W conjecture for a suitable wild Hitchin system.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.03382"}],"month":"10","intvolume":" 21","publication_identifier":{"eissn":["1435-9855"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"10","volume":21,"ec_funded":1,"_id":"439","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-24T14:24:49Z","department":[{"_id":"TaHa"}],"quality_controlled":"1","publisher":"European Mathematical Society","oa":1,"isi":1,"year":"2019","day":"01","publication":"Journal of the European Mathematical Society","page":"2995-3052","doi":"10.4171/JEMS/896","date_published":"2019-10-01T00:00:00Z","date_created":"2018-12-11T11:46:29Z","project":[{"call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593"}],"citation":{"chicago":"Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society. European Mathematical Society, 2019. https://doi.org/10.4171/JEMS/896.","ista":"Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052.","mla":"Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society, vol. 21, no. 10, European Mathematical Society, 2019, pp. 2995–3052, doi:10.4171/JEMS/896.","apa":"Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/896","ama":"Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 2019;21(10):2995-3052. doi:10.4171/JEMS/896","short":"T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052.","ieee":"T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of wild character varieties,” Journal of the European Mathematical Society, vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Hausel","full_name":"Hausel, Tamas","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"id":"43D735EE-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Mereb","full_name":"Mereb, Martin"},{"first_name":"Michael","full_name":"Wong, Michael","last_name":"Wong"}],"publist_id":"7384","article_processing_charge":"No","external_id":{"arxiv":["1604.03382"],"isi":["000480413600002"]},"title":"Arithmetic and representation theory of wild character varieties"},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41431-018-0231-2"}],"month":"01","intvolume":" 27","abstract":[{"lang":"eng","text":"Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771."}],"pmid":1,"oa_version":"Published Version","volume":27,"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"105","department":[{"_id":"GaNo"}],"date_updated":"2023-08-24T14:28:24Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.","page":"161-166","doi":"10.1038/s41431-018-0231-2","date_published":"2019-01-01T00:00:00Z","date_created":"2018-12-11T11:44:39Z","isi":1,"year":"2019","day":"01","publication":"European Journal of Human Genetics","publist_id":"7949","author":[{"full_name":"Marsh, Ashley","last_name":"Marsh","first_name":"Ashley"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lockhart, Paul","last_name":"Lockhart","first_name":"Paul"},{"first_name":"Richard","last_name":"Leventer","full_name":"Leventer, Richard"}],"external_id":{"pmid":["30089829"],"isi":["000454111500019"]},"article_processing_charge":"No","title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","citation":{"ista":"Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166.","chicago":"Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2.","ama":"Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166. doi:10.1038/s41431-018-0231-2","apa":"Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","ieee":"A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics, vol. 27. Springer Nature, pp. 161–166, 2019.","mla":"Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature, 2019, pp. 161–66, doi:10.1038/s41431-018-0231-2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"isi":1,"year":"2019","day":"5","publication":"Journal of Differential Equations","page":"3732-3763","doi":"10.1016/j.jde.2018.09.012","date_published":"2019-03-05T00:00:00Z","date_created":"2018-12-11T11:44:26Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"citation":{"ista":"Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763.","chicago":"Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.09.012.","ama":"Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012","apa":"Dareiotis, K., Gerencser, M., & Gess, B. (2019). Entropy solutions for stochastic porous media equations. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.09.012","ieee":"K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic porous media equations,” Journal of Differential Equations, vol. 266, no. 6. Elsevier, pp. 3732–3763, 2019.","short":"K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763.","mla":"Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations, vol. 266, no. 6, Elsevier, 2019, pp. 3732–63, doi:10.1016/j.jde.2018.09.012."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Dareiotis","full_name":"Dareiotis, Konstantinos","first_name":"Konstantinos"},{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","full_name":"Gerencser, Mate","last_name":"Gerencser"},{"first_name":"Benjamin","last_name":"Gess","full_name":"Gess, Benjamin"}],"publist_id":"7989","external_id":{"arxiv":["1803.06953"],"isi":["000456332500026"]},"article_processing_charge":"No","title":"Entropy solutions for stochastic porous media equations","publication_status":"published","language":[{"iso":"eng"}],"volume":266,"issue":"6","abstract":[{"lang":"eng","text":"We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1803.06953","open_access":"1"}],"month":"03","intvolume":" 266","date_updated":"2023-08-24T14:30:16Z","department":[{"_id":"JaMa"}],"_id":"65","article_type":"original","type":"journal_article","status":"public"},{"article_number":"331","external_id":{"isi":["000456392400012"]},"article_processing_charge":"No","author":[{"first_name":"Réka","full_name":"Mócsai, Réka","last_name":"Mócsai"},{"first_name":"Rudolf","last_name":"Figl","full_name":"Figl, Rudolf"},{"full_name":"Troschl, Clemens","last_name":"Troschl","first_name":"Clemens"},{"first_name":"Richard","full_name":"Strasser, Richard","last_name":"Strasser"},{"last_name":"Svehla","full_name":"Svehla, Elisabeth","first_name":"Elisabeth"},{"last_name":"Windwarder","full_name":"Windwarder, Markus","first_name":"Markus"},{"full_name":"Thader, Andreas","last_name":"Thader","first_name":"Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Friedrich","full_name":"Altmann, Friedrich","last_name":"Altmann"}],"title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","citation":{"chicago":"Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-018-36884-1.","ista":"Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331.","mla":"Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:10.1038/s41598-018-36884-1.","short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019).","ieee":"R. Mócsai et al., “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019.","apa":"Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-36884-1","ama":"Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-36884-1"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","date_created":"2019-02-03T22:59:13Z","doi":"10.1038/s41598-018-36884-1","date_published":"2019-01-23T00:00:00Z","year":"2019","has_accepted_license":"1","isi":1,"publication":"Scientific Reports","day":"23","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"5907","department":[{"_id":"FlSc"}],"file_date_updated":"2020-07-14T12:47:13Z","date_updated":"2023-08-24T14:33:16Z","ddc":["580"],"scopus_import":"1","intvolume":" 9","month":"01","abstract":[{"text":"Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins.","lang":"eng"}],"oa_version":"Published Version","volume":9,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":2124292,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_name":"2019_ScientificReports_Mocsai.pdf","date_created":"2019-02-05T13:10:02Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5923","checksum":"4129c7d7663d1f8a1edf8c4232372f66"}]},{"volume":116,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1818099116","open_access":"1"}],"month":"01","intvolume":" 116","abstract":[{"lang":"eng","text":"The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants."}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"JiFr"}],"date_updated":"2023-08-24T14:31:09Z","article_type":"original","type":"journal_article","status":"public","_id":"5908","page":"1420-1429","date_published":"2019-01-22T00:00:00Z","doi":"10.1073/pnas.1818099116","date_created":"2019-02-03T22:59:14Z","isi":1,"year":"2019","day":"22","publication":"Proceedings of the National Academy of Sciences of the United States of America","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"author":[{"first_name":"Eunkyoung","full_name":"Lee, Eunkyoung","last_name":"Lee"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Pérez-Sancho, Jessica","last_name":"Pérez-Sancho","first_name":"Jessica"},{"last_name":"Benitez-Fuente","full_name":"Benitez-Fuente, Francisco","first_name":"Francisco"},{"last_name":"Strelau","full_name":"Strelau, Matthew","first_name":"Matthew"},{"full_name":"Macho, Alberto P.","last_name":"Macho","first_name":"Alberto P."},{"first_name":"Miguel A.","full_name":"Botella, Miguel A.","last_name":"Botella"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Rosado, Abel","last_name":"Rosado","first_name":"Abel"}],"article_processing_charge":"No","external_id":{"pmid":["30610176"],"isi":["000456336100050"]},"title":"Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis","citation":{"short":"E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P. Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 1420–1429.","ieee":"E. Lee et al., “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4. National Academy of Sciences, pp. 1420–1429, 2019.","ama":"Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(4):1420-1429. doi:10.1073/pnas.1818099116","apa":"Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho, A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1818099116","mla":"Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1420–29, doi:10.1073/pnas.1818099116.","ista":"Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 116(4), 1420–1429.","chicago":"Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1818099116."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"_id":"5680","status":"public","type":"journal_article","date_updated":"2023-08-24T14:34:12Z","department":[{"_id":"NiBa"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones."}],"intvolume":" 166","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["23818115"],"issn":["23818107"]},"issue":"1","volume":166,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142.","short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92.","ieee":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019.","apa":"Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis. https://doi.org/10.1080/23818107.2018.1545142","ama":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142","chicago":"Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142.","ista":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92."},"title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","external_id":{"isi":["000463802800009"]},"article_processing_charge":"No","author":[{"first_name":"Christophe","last_name":"Andalo","full_name":"Andalo, Christophe"},{"last_name":"Burrus","full_name":"Burrus, Monique","first_name":"Monique"},{"first_name":"Sandrine","full_name":"Paute, Sandrine","last_name":"Paute"},{"last_name":"Lauzeral","full_name":"Lauzeral, Christine","first_name":"Christine"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David"}],"publisher":"Taylor and Francis","quality_controlled":"1","publication":"Botany Letters","day":"01","year":"2019","isi":1,"date_created":"2018-12-16T22:59:20Z","date_published":"2019-01-01T00:00:00Z","doi":"10.1080/23818107.2018.1545142","page":"80-92"},{"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019. https://doi.org/10.1002/jgt.22436.","ista":"Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394.","mla":"Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436.","apa":"Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436","ama":"Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436","short":"S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394.","ieee":"S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394, 2019."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1309.2399"],"isi":["000485392800004"]},"article_processing_charge":"No","author":[{"full_name":"Chaplick, Steven","last_name":"Chaplick","first_name":"Steven"},{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"last_name":"Klavík","full_name":"Klavík, Pavel","first_name":"Pavel"}],"title":"Extending partial representations of circle graphs","oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2019","isi":1,"publication":"Journal of Graph Theory","day":"01","page":"365-394","date_created":"2018-12-30T22:59:15Z","doi":"10.1002/jgt.22436","date_published":"2019-08-01T00:00:00Z","_id":"5790","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-24T14:30:43Z","department":[{"_id":"UlWa"}],"abstract":[{"lang":"eng","text":"The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2399"}],"scopus_import":"1","intvolume":" 91","month":"08","publication_status":"published","publication_identifier":{"issn":["03649024"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":91,"issue":"4"},{"intvolume":" 576","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.05324"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently.","lang":"eng"}],"ec_funded":1,"volume":576,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"405","department":[{"_id":"LaEr"}],"date_updated":"2023-08-24T14:31:47Z","oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office – NKFIH (grant no. K124152)","date_created":"2018-12-11T11:46:17Z","date_published":"2019-09-01T00:00:00Z","doi":"10.1016/j.laa.2018.03.002","page":"67-78","publication":"Linear Algebra and Its Applications","day":"01","year":"2019","isi":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"title":"Jointly convex quantum Jensen divergences","article_processing_charge":"No","external_id":{"arxiv":["1712.05324"],"isi":["000470955300005"]},"publist_id":"7424","author":[{"last_name":"Virosztek","full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019.","short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","ama":"Virosztek D. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 2019;576:67-78. doi:10.1016/j.laa.2018.03.002","apa":"Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002","mla":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002.","ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78.","chicago":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications. Elsevier, 2019. https://doi.org/10.1016/j.laa.2018.03.002."}},{"year":"2019","isi":1,"publication":"Transactions of the American Mathematical Society","day":"15","page":"5757-5785","date_created":"2018-12-11T11:45:01Z","doi":"10.1090/tran/7514","date_published":"2019-04-15T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"American Mathematical Society","citation":{"chicago":"Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7514.","ista":"Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785.","mla":"Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514.","ama":"Browning TD, Loughran D. Sieving rational points on varieties. Transactions of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514","apa":"Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7514","short":"T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785.","ieee":"T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions of the American Mathematical Society, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000464034200019"],"arxiv":["1705.01999"]},"publist_id":"7746","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning"},{"full_name":"Loughran, Daniel","last_name":"Loughran","first_name":"Daniel"}],"title":"Sieving rational points on varieties","publication_status":"published","publication_identifier":{"eissn":["10886850"],"issn":["00029947"]},"language":[{"iso":"eng"}],"issue":"8","volume":371,"abstract":[{"text":"An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1705.01999","open_access":"1"}],"scopus_import":"1","intvolume":" 371","month":"04","date_updated":"2023-08-24T14:34:56Z","department":[{"_id":"TiBr"}],"_id":"175","type":"journal_article","status":"public"},{"date_created":"2018-12-11T11:45:48Z","doi":"10.1007/s00440-018-0841-1","date_published":"2019-04-01T00:00:00Z","page":"697–758","publication":"Probability Theory and Related Fields","day":"01","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n","title":"Singular SPDEs in domains with boundaries","external_id":{"isi":["000463613800001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Gerencser","full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate"},{"first_name":"Martin","full_name":"Hairer, Martin","last_name":"Hairer"}],"publist_id":"7546","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0841-1.","ista":"Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758.","mla":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields, vol. 173, no. 3–4, Springer, 2019, pp. 697–758, doi:10.1007/s00440-018-0841-1.","ama":"Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 2019;173(3-4):697–758. doi:10.1007/s00440-018-0841-1","apa":"Gerencser, M., & Hairer, M. (2019). Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0841-1","ieee":"M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” Probability Theory and Related Fields, vol. 173, no. 3–4. Springer, pp. 697–758, 2019.","short":"M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758."},"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"volume":173,"issue":"3-4","language":[{"iso":"eng"}],"file":[{"file_name":"2018_ProbTheory_Gerencser.pdf","date_created":"2018-12-17T16:25:24Z","creator":"dernst","file_size":893182,"date_updated":"2020-07-14T12:46:03Z","checksum":"288d16ef7291242f485a9660979486e3","file_id":"5722","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"intvolume":" 173","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition.","lang":"eng"}],"department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:46:03Z","ddc":["510"],"date_updated":"2023-08-24T14:38:32Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"319"}]