[{"month":"01","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_930","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-12-02T23:30:08Z","publist_id":"7277","date_updated":"2023-09-07T12:41:06Z","date_created":"2018-12-11T11:47:03Z","author":[{"last_name":"Hurny","first_name":"Andrej","orcid":"0000-0003-3638-1426","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Hurny, Andrej"}],"related_material":{"record":[{"id":"1024","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","year":"2018","day":"01","article_processing_charge":"No","has_accepted_license":"1","date_published":"2018-01-01T00:00:00Z","page":"147","citation":{"chicago":"Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_930.","mla":"Hurny, Andrej. Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_930.","short":"A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018.","ista":"Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria.","ieee":"A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018.","apa":"Hurny, A. (2018). Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_930","ama":"Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:10.15479/AT:ISTA:th_930"},"abstract":[{"lang":"eng","text":"The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"file_size":28112114,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst","access_level":"closed","embargo_to":"open_access","file_name":"2018_Hurny_thesis_source.docx","checksum":"0c9d6d1c80d9857e6e545213467bbcb2","date_created":"2019-04-05T09:37:56Z","date_updated":"2020-12-02T23:30:08Z","relation":"source_file","file_id":"6226"},{"checksum":"ecbe481a1413d270bd501b872c7ed54f","date_created":"2019-04-05T09:37:55Z","date_updated":"2020-12-02T09:52:16Z","embargo":"2019-07-10","file_id":"6227","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":12524427,"access_level":"open_access","file_name":"2018_Hurny_thesis.pdf"}],"pubrep_id":"930","title":"Identification and characterization of novel auxin-cytokinin cross-talk components","ddc":["570"],"status":"public","_id":"539","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_identifier":{"issn":["2663-337X"]},"month":"08","doi":"10.15479/AT:ISTA:th_1042","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publist_id":"8006","file_date_updated":"2021-02-11T23:30:22Z","author":[{"full_name":"Gridchyn, Igor","first_name":"Igor","last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929"}],"date_updated":"2023-09-07T12:42:44Z","date_created":"2018-12-11T11:44:21Z","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"27","date_published":"2018-08-27T00:00:00Z","citation":{"ama":"Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:10.15479/AT:ISTA:th_1042","ista":"Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria.","ieee":"I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018.","apa":"Gridchyn, I. (2018). Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1042","mla":"Gridchyn, Igor. Reactivation Content Is Important for Consolidation of Spatial Memory. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1042.","short":"I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018.","chicago":"Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1042."},"page":"104","abstract":[{"lang":"eng","text":"The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1042","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":7666687,"file_name":"2018_Thesis_Gridchyn_source.docx","embargo_to":"open_access","access_level":"closed","date_created":"2019-04-08T13:36:01Z","date_updated":"2021-02-11T23:30:22Z","checksum":"7db4415e435590fa33542c7b0a0321d7","file_id":"6236","relation":"source_file"},{"relation":"main_file","file_id":"6237","embargo":"2019-08-29","date_updated":"2021-02-11T11:17:18Z","date_created":"2019-04-08T13:36:01Z","checksum":"f96f3fe8979f7b1e6db6acaca962b10c","file_name":"2018_Thesis_Gridchyn.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6034153,"creator":"dernst"}],"_id":"48","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Reactivation content is important for consolidation of spatial memory","status":"public","ddc":["573"]},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"96","citation":{"ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","apa":"Belyaeva, V. (2018). Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1064","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:10.15479/AT:ISTA:th1064","chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1064.","mla":"Belyaeva, Vera. Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1064.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018."},"date_published":"2018-07-01T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it."}],"title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","ddc":["570"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9","oa_version":"Published Version","file":[{"file_name":"2018_Thesis_Belyaeva_source.docx","embargo_to":"open_access","access_level":"closed","creator":"dernst","file_size":102737483,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6243","relation":"source_file","date_updated":"2020-07-14T12:48:14Z","date_created":"2019-04-08T14:13:12Z","checksum":"d27b2465cb70d0c9678a0381b9b6ced1"},{"checksum":"a2939b61bde2de7b8ced77bbae0eaaed","date_created":"2019-04-08T14:14:08Z","date_updated":"2021-02-11T11:17:16Z","embargo":"2019-11-19","file_id":"6244","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":88077843,"access_level":"open_access","file_name":"2018_Thesis_Belyaeva.pdf"}],"pubrep_id":"1064","publication_identifier":{"issn":["2663-337X"]},"month":"07","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th1064","publist_id":"8047","file_date_updated":"2021-02-11T11:17:16Z","department":[{"_id":"DaSi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","date_created":"2018-12-11T11:44:08Z","date_updated":"2023-09-07T12:43:10Z","author":[{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","last_name":"Belyaeva","first_name":"Vera","full_name":"Belyaeva, Vera"}]},{"month":"10","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:th_1055","file_date_updated":"2021-02-11T11:17:16Z","publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Institute of Science and Technology Austria","year":"2018","date_updated":"2023-09-07T13:02:37Z","date_created":"2019-04-09T14:13:39Z","author":[{"full_name":"Mckenzie, Catherine","first_name":"Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"new_edition","status":"public","id":"7132"}]},"day":"31","has_accepted_license":"1","article_processing_charge":"No","page":"95","citation":{"ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:10.15479/at:ista:th_1055","ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria.","apa":"Mckenzie, C. (2018). Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th_1055","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission . Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:th_1055.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:th_1055."},"date_published":"2018-10-31T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. ","lang":"eng"}],"ddc":["571","573"],"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6266","file":[{"checksum":"9d2c2dca04b00e485470c28b262af59a","date_created":"2019-04-09T14:12:40Z","date_updated":"2021-02-11T11:17:16Z","embargo":"2019-11-24","file_id":"6267","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4906420,"access_level":"open_access","file_name":"2018_Thesis_McKenzie.pdf"},{"creator":"dernst","file_size":5053545,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2018_Thesis_McKenzie_source.docx","embargo_to":"open_access","access_level":"closed","date_created":"2019-04-09T14:12:40Z","date_updated":"2020-07-14T12:47:25Z","checksum":"50b58c272899601bc6fd9642c4dc97f1","file_id":"6268","relation":"source_file"}],"oa_version":"Published Version","pubrep_id":"1055"},{"ddc":["570","591","596"],"status":"public","title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"50","file":[{"access_level":"open_access","file_name":"2018_Thesis_Capek.pdf","creator":"dernst","content_type":"application/pdf","file_size":31576521,"file_id":"6238","embargo":"2019-06-25","relation":"main_file","checksum":"d3eca3dcacb67bffdde6e6609c31cdd0","date_updated":"2021-02-11T11:17:17Z","date_created":"2019-04-08T13:42:26Z"},{"relation":"source_file","file_id":"6239","checksum":"876deb14067e638aba65d209668bd821","date_updated":"2021-02-11T23:30:21Z","date_created":"2019-04-08T13:42:27Z","access_level":"closed","embargo_to":"open_access","file_name":"2018_Thesis_Capek_source.docx","file_size":38992956,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst"}],"oa_version":"Published Version","pubrep_id":"1031","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation."}],"page":"95","citation":{"short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","mla":"Capek, Daniel. Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1031.","chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1031.","ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:10.15479/AT:ISTA:TH_1031","ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","apa":"Capek, D. (2018). Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1031","ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria."},"date_published":"2018-06-22T00:00:00Z","day":"22","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaHe"}],"year":"2018","date_updated":"2023-09-07T12:48:16Z","date_created":"2018-12-11T11:44:21Z","author":[{"id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","first_name":"Daniel","last_name":"Capek","full_name":"Capek, Daniel"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1100"},{"id":"661","status":"public","relation":"part_of_dissertation"},{"id":"676","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2021-02-11T23:30:21Z","publist_id":"8004","oa":1,"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:TH_1031","month":"06","publication_identifier":{"issn":["2663-337X"]}},{"article_processing_charge":"No","has_accepted_license":"1","day":"30","date_published":"2018-10-30T00:00:00Z","citation":{"ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","apa":"Steinrück, M. (2018). The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1059","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:10.15479/AT:ISTA:th1059","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1059.","mla":"Steinrück, Magdalena. The Influence of Sequence Context on the Evolution of Bacterial Gene Expression. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1059.","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018."},"page":"109","abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1059","oa_version":"Published Version","file":[{"file_id":"5941","relation":"source_file","date_updated":"2020-07-14T12:45:43Z","date_created":"2019-02-08T10:51:22Z","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","file_name":"Thesis_Steinrueck_final.docx","embargo_to":"open_access","access_level":"closed","creator":"dernst","file_size":9190845,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","file_id":"5942","embargo":"2019-11-02","checksum":"3def8b7854c8b42d643597ce0215efac","date_updated":"2021-02-11T11:17:14Z","date_created":"2019-02-08T10:51:22Z","access_level":"open_access","file_name":"Thesis_Steinrueck_final.pdf","content_type":"application/pdf","file_size":7521973,"creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"26","ddc":["576","579"],"title":"The influence of sequence context on the evolution of bacterial gene expression","status":"public","publication_identifier":{"issn":["2663-337X"]},"month":"10","doi":"10.15479/AT:ISTA:th1059","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"oa":1,"publist_id":"8029","file_date_updated":"2021-02-11T11:17:14Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"704"}]},"author":[{"full_name":"Steinrück, Magdalena","orcid":"0000-0003-1229-9719","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","first_name":"Magdalena"}],"date_created":"2018-12-11T11:44:14Z","date_updated":"2023-09-07T12:48:43Z","year":"2018","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published"},{"issue":"11","abstract":[{"lang":"eng","text":"Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field."}],"type":"journal_article","oa_version":"Preprint","_id":"5816","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 89","title":"30 GHz-voltage controlled oscillator operating at 4 K","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-11-01T00:00:00Z","citation":{"ista":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 89(11), 114701.","ieee":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R. Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” Review of Scientific Instruments, vol. 89, no. 11. AIP Publishing, 2018.","apa":"Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., & Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258","ama":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 2018;89(11). doi:10.1063/1.5038258","chicago":"Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments. AIP Publishing, 2018. https://doi.org/10.1063/1.5038258.","mla":"Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments, vol. 89, no. 11, 114701, AIP Publishing, 2018, doi:10.1063/1.5038258.","short":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018)."},"publication":"Review of Scientific Instruments","article_number":"114701","related_material":{"record":[{"id":"10058","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Arne","last_name":"Hollmann","full_name":"Hollmann, Arne"},{"full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","first_name":"Daniel"},{"first_name":"Maciej","last_name":"Kucharski","full_name":"Kucharski, Maciej"},{"full_name":"Kissinger, Dietmar","first_name":"Dietmar","last_name":"Kissinger"},{"first_name":"Gunter","last_name":"Fischer","full_name":"Fischer, Gunter"},{"last_name":"Schreiber","first_name":"Lars R.","full_name":"Schreiber, Lars R."}],"volume":89,"date_created":"2019-01-10T14:22:23Z","date_updated":"2024-03-28T23:30:27Z","year":"2018","publisher":"AIP Publishing","department":[{"_id":"GeKa"}],"publication_status":"published","publication_identifier":{"issn":["00346748"]},"month":"11","doi":"10.1063/1.5038258","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.09522"}],"external_id":{"isi":["000451735700054"],"arxiv":["1804.09522"]},"quality_controlled":"1","isi":1},{"file":[{"relation":"main_file","embargo":"2020-01-25","file_id":"6264","checksum":"fc60585c9eaad868ac007004ef130908","date_updated":"2021-02-11T11:17:17Z","date_created":"2019-04-09T13:49:24Z","access_level":"open_access","file_name":"2018_Thesis_Lukacisinova.pdf","file_size":5656866,"content_type":"application/pdf","creator":"dernst"},{"file_id":"6265","relation":"source_file","date_updated":"2020-07-14T12:47:25Z","date_created":"2019-04-09T13:49:23Z","checksum":"264057ec0a92ab348cc83b41f021ba92","file_name":"2018_Thesis_Lukacisinova_source.docx","embargo_to":"open_access","access_level":"closed","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":5168054}],"oa_version":"Published Version","ddc":["570","576","579"],"status":"public","title":"Genetic determinants of antibiotic resistance evolution","_id":"6263","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Antibiotic resistance can emerge spontaneously through genomic mutation and render treatment ineffective. To counteract this process, in addition to the discovery and description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand its determinantsis needed. To address this challenge, this thesisuncoversnew genetic determinants of resistance evolvability using a customized robotic setup, exploressystematic ways in which resistance evolution is perturbed due to dose-responsecharacteristics of drugs and mutation rate differences,and mathematically investigates the evolutionary fate of one specific type of evolvability modifier -a stress-induced mutagenesis allele.We find severalgenes which strongly inhibit or potentiate resistance evolution. In order to identify them, we first developedan automated high-throughput feedback-controlled protocol whichkeeps the population size and selection pressure approximately constant for hundreds of cultures by dynamically re-diluting the cultures and adjusting the antibiotic concentration. We implementedthis protocol on a customized liquid handling robot and propagated 100 different gene deletion strains of Escherichia coliin triplicate for over 100 generations in tetracycline and in chloramphenicol, and comparedtheir adaptation rates.We find a diminishing returns pattern, where initially sensitive strains adapted more compared to less sensitive ones. Our data uncover that deletions of certain genes which do not affect mutation rate,including efflux pump components, a chaperone and severalstructural and regulatory genes can strongly and reproducibly alterresistance evolution. Sequencing analysis of evolved populations indicates that epistasis with resistance mutations is the most likelyexplanation. This work could inspire treatment strategies in which targeted inhibitors of evolvability mechanisms will be given alongside antibiotics to slow down resistance evolution and extend theefficacy of antibiotics.We implemented astochasticpopulation genetics model, toverifyways in which general properties, namely, dose-response characteristics of drugs and mutation rates, influence evolutionary dynamics. In particular, under the exposure to antibiotics with shallow dose-response curves,bacteria have narrower distributions of fitness effects of new mutations. We show that in silicothis also leads to slower resistance evolution. We see and confirm with experiments that increased mutation rates, apart from speeding up evolution, also leadto high reproducibility of phenotypic adaptation in a context of continually strong selection pressure.Knowledge of these patterns can aid in predicting the dynamics of antibiotic resistance evolutionand adapting treatment schemes accordingly.Focusing on a previously described type of evolvability modifier –a stress-induced mutagenesis allele –we find conditions under which it can persist in a population under periodic selectionakin to clinical treatment. We set up a deterministic infinite populationcontinuous time model tracking the frequencies of a mutator and resistance allele and evaluate various treatment schemes in how well they maintain a stress-induced mutator allele. In particular,a high diversity of stresses is crucial for the persistence of the mutator allele. This leads to a general trade-off where exactly those diversifying treatment schemes which are likely to decrease levels of resistance could lead to stronger selection of highly evolvable genotypes.In the long run, this work will lead to a deeper understanding of the genetic and cellular mechanisms involved in antibiotic resistance evolution and could inspire new strategies for slowing down its rate. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2018-12-28T00:00:00Z","page":"91","citation":{"chicago":"Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072.","short":"M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018.","mla":"Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072.","ieee":"M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018.","apa":"Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072","ista":"Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria.","ama":"Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:10.15479/AT:ISTA:th1072"},"has_accepted_license":"1","article_processing_charge":"No","day":"28","date_updated":"2023-09-22T09:20:37Z","date_created":"2019-04-09T13:57:15Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1619"},{"id":"696","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1027"}]},"author":[{"orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToBo"}],"publication_status":"published","year":"2018","file_date_updated":"2021-02-11T11:17:17Z","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"LifeSc"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th1072","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"12"},{"date_published":"2018-03-01T00:00:00Z","page":"845 - 857","publication":"G3: Genes, Genomes, Genetics","citation":{"ama":"György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 2018;8(3):845-857. doi:10.1534/g3.117.300452","ieee":"A. György et al., “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” G3: Genes, Genomes, Genetics, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.","apa":"György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.117.300452","ista":"György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857.","short":"A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner, Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes, Genetics 8 (2018) 845–857.","mla":"György, Attila, et al. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics, vol. 8, no. 3, Genetics Society of America, 2018, pp. 845–57, doi:10.1534/g3.117.300452.","chicago":"György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/g3.117.300452."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":2251222,"creator":"system","access_level":"open_access","file_name":"IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf","checksum":"7d9d28b915159078a4ca7add568010e8","date_created":"2018-12-12T10:11:48Z","date_updated":"2020-07-14T12:46:56Z","relation":"main_file","file_id":"4905"}],"oa_version":"Published Version","pubrep_id":"990","status":"public","ddc":["570"],"title":"Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues","intvolume":" 8","_id":"544","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult.","lang":"eng"}],"issue":"3","type":"journal_article","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1534/g3.117.300452","quality_controlled":"1","isi":1,"project":[{"grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen"},{"name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF","grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"grant_number":"LSC16-021 ","_id":"2637E9C0-B435-11E9-9278-68D0E5697425","name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis"},{"name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000426693300011"]},"oa":1,"month":"03","date_updated":"2024-03-28T23:30:30Z","date_created":"2018-12-11T11:47:05Z","volume":8,"author":[{"first_name":"Attila","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","full_name":"György, Attila"},{"full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389","id":"3047D808-F248-11E8-B48F-1D18A9856A87","last_name":"Roblek","first_name":"Marko"},{"full_name":"Ratheesh, Aparna","first_name":"Aparna","last_name":"Ratheesh","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7190-0776"},{"full_name":"Valosková, Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","last_name":"Valosková","first_name":"Katarina"},{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","last_name":"Belyaeva","full_name":"Belyaeva, Vera"},{"full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"Wachner"},{"first_name":"Yutaka","last_name":"Matsubayashi","full_name":"Matsubayashi, Yutaka"},{"first_name":"Besaiz","last_name":"Sanchez Sanchez","full_name":"Sanchez Sanchez, Besaiz"},{"full_name":"Stramer, Brian","last_name":"Stramer","first_name":"Brian"},{"last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"}],"related_material":{"record":[{"relation":"research_paper","id":"6530"},{"id":"6543","relation":"research_paper"},{"id":"11193","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"6546"}]},"publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"DaSi"}],"acknowledgement":" A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner by DOC Fellowships from the Austrian Academy of Sciences, ","year":"2018","file_date_updated":"2020-07-14T12:46:56Z","publist_id":"7271","ec_funded":1},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"chicago":"Luján, Rafael, Carolina Aguado, Francisco Ciruela, Javier Cózar, David Kleindienst, Luis De La Ossa, Bernhard Bettler, et al. “Differential Association of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain Structure and Function. Springer, 2018. https://doi.org/10.1007/s00429-017-1568-y.","short":"R. Luján, C. Aguado, F. Ciruela, J. Cózar, D. Kleindienst, L. De La Ossa, B. Bettler, K. Wickman, M. Watanabe, R. Shigemoto, Y. Fukazawa, Brain Structure and Function 223 (2018) 1565–1587.","mla":"Luján, Rafael, et al. “Differential Association of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain Structure and Function, vol. 223, no. 3, Springer, 2018, pp. 1565–87, doi:10.1007/s00429-017-1568-y.","ieee":"R. Luján et al., “Differential association of GABAB receptors with their effector ion channels in Purkinje cells,” Brain Structure and Function, vol. 223, no. 3. Springer, pp. 1565–1587, 2018.","apa":"Luján, R., Aguado, C., Ciruela, F., Cózar, J., Kleindienst, D., De La Ossa, L., … Fukazawa, Y. (2018). Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. Springer. https://doi.org/10.1007/s00429-017-1568-y","ista":"Luján R, Aguado C, Ciruela F, Cózar J, Kleindienst D, De La Ossa L, Bettler B, Wickman K, Watanabe M, Shigemoto R, Fukazawa Y. 2018. Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. 223(3), 1565–1587.","ama":"Luján R, Aguado C, Ciruela F, et al. Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. 2018;223(3):1565-1587. doi:10.1007/s00429-017-1568-y"},"publication":"Brain Structure and Function","page":"1565 - 1587","article_type":"original","date_published":"2018-04-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Metabotropic GABAB receptors mediate slow inhibitory effects presynaptically and postsynaptically through the modulation of different effector signalling pathways. Here, we analysed the distribution of GABAB receptors using highly sensitive SDS-digested freeze-fracture replica labelling in mouse cerebellar Purkinje cells. Immunoreactivity for GABAB1 was observed on presynaptic and, more abundantly, on postsynaptic compartments, showing both scattered and clustered distribution patterns. Quantitative analysis of immunoparticles revealed a somato-dendritic gradient, with the density of immunoparticles increasing 26-fold from somata to dendritic spines. To understand the spatial relationship of GABAB receptors with two key effector ion channels, the G protein-gated inwardly rectifying K+ (GIRK/Kir3) channel and the voltage-dependent Ca2+ channel, biochemical and immunohistochemical approaches were performed. Co-immunoprecipitation analysis demonstrated that GABAB receptors co-assembled with GIRK and CaV2.1 channels in the cerebellum. Using double-labelling immunoelectron microscopic techniques, co-clustering between GABAB1 and GIRK2 was detected in dendritic spines, whereas they were mainly segregated in the dendritic shafts. In contrast, co-clustering of GABAB1 and CaV2.1 was detected in dendritic shafts but not spines. Presynaptically, although no significant co-clustering of GABAB1 and GIRK2 or CaV2.1 channels was detected, inter-cluster distance for GABAB1 and GIRK2 was significantly smaller in the active zone than in the dendritic shafts, and that for GABAB1 and CaV2.1 was significantly smaller in the active zone than in the dendritic shafts and spines. Thus, GABAB receptors are associated with GIRK and CaV2.1 channels in different subcellular compartments. These data provide a better framework for understanding the different roles played by GABAB receptors and their effector ion channels in the cerebellar network."}],"_id":"612","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 223","title":"Differential association of GABAB receptors with their effector ion channels in Purkinje cells","ddc":["571"],"status":"public","pubrep_id":"1013","file":[{"relation":"main_file","file_id":"5157","checksum":"a55b3103476ecb5f4f983d8801807e8b","date_updated":"2020-07-14T12:47:20Z","date_created":"2018-12-12T10:15:36Z","access_level":"open_access","file_name":"IST-2018-1013-v1+1_2018_Kleindienst_Differential.pdf","content_type":"application/pdf","file_size":5542926,"creator":"system"}],"oa_version":"Published Version","month":"04","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000428419500030"]},"project":[{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00429-017-1568-y","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"7192","file_date_updated":"2020-07-14T12:47:20Z","year":"2018","department":[{"_id":"RySh"}],"publisher":"Springer","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]},"author":[{"full_name":"Luján, Rafael","last_name":"Luján","first_name":"Rafael"},{"full_name":"Aguado, 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M"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"status":"public","relation":"dissertation_contains","id":"6363"}]},"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Nature Publishing Group","year":"2018","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J..","month":"11","language":[{"iso":"eng"}],"doi":"10.1038/s41467-018-06899-3","quality_controlled":"1","isi":1,"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}],"external_id":{"isi":["000449069700009"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"lang":"eng","text":"Parvalbumin-positive (PV+) GABAergic interneurons in hippocampal microcircuits are thought to play a key role in several higher network functions, such as feedforward and feedback inhibition, network oscillations, and pattern separation. Fast lateral inhibition mediated by GABAergic interneurons may implement a winner-takes-all mechanism in the hippocampal input layer. However, it is not clear whether the functional connectivity rules of granule cells (GCs) and interneurons in the dentate gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings from up to seven GCs and up to four PV+ interneurons in the dentate gyrus, we find that connectivity is structured in space, synapse-specific, and enriched in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV+ interneuron) is ~ 10-times more abundant than recurrent inhibition (in which a GC inhibits itself). Thus, unique connectivity rules may enable the dentate gyrus to perform specific higher-order computations"}],"issue":"1","type":"journal_article","file":[{"file_id":"5715","relation":"main_file","date_updated":"2020-07-14T12:45:28Z","date_created":"2018-12-17T15:41:57Z","checksum":"9fe2a63bd95a5067d896c087d07998f3","file_name":"2018_NatureComm_Espinoza.pdf","access_level":"open_access","creator":"dernst","file_size":4651930,"content_type":"application/pdf"}],"oa_version":"Published Version","status":"public","title":"Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus","ddc":["570"],"intvolume":" 9","_id":"21","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"02","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-11-02T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"mla":"Espinoza Martinez, Claudia, et al. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” Nature Communications, vol. 9, no. 1, 4605, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06899-3.","short":"C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications 9 (2018).","chicago":"Espinoza Martinez, Claudia , José Guzmán, Xiaomin Zhang, and Peter M Jonas. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06899-3.","ama":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-06899-3","ista":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. 2018. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 9(1), 4605.","ieee":"C. Espinoza Martinez, J. Guzmán, X. Zhang, and P. M. Jonas, “Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","apa":"Espinoza Martinez, C., Guzmán, J., Zhang, X., & Jonas, P. M. (2018). Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06899-3"}},{"article_number":"11","ec_funded":1,"publist_id":"7988","file_date_updated":"2020-07-14T12:47:34Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2018","volume":118,"date_updated":"2024-03-28T23:30:34Z","date_created":"2018-12-11T11:44:27Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"publication_identifier":{"isbn":["978-3-95977-087-3"]},"month":"09","project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1806.03108"]},"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.CONCUR.2018.11","conference":{"name":"CONCUR: Conference on Concurrency Theory","location":"Beijing, China","start_date":"2018-09-04","end_date":"2018-09-07"},"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Crypto-currencies are digital assets designed to work as a medium of exchange, e.g., Bitcoin, but they are susceptible to attacks (dishonest behavior of participants). A framework for the analysis of attacks in crypto-currencies requires (a) modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior; (b) concurrent interactions between participants; and (c) analysis of long-term monetary gains. Traditional game-theoretic approaches for the analysis of security protocols consider either qualitative temporal properties such as safety and termination, or the very special class of one-shot (stateless) games. However, to analyze general attacks on protocols for crypto-currencies, both stateful analysis and quantitative objectives are necessary. In this work our main contributions are as follows: (a) we show how a class of concurrent mean-payo games, namely ergodic games, can model various attacks that arise naturally in crypto-currencies; (b) we present the first practical implementation of algorithms for ergodic games that scales to model realistic problems for crypto-currencies; and (c) we present experimental results showing that our framework can handle games with thousands of states and millions of transitions.","lang":"eng"}],"intvolume":" 118","ddc":["000"],"status":"public","title":"Ergodic mean-payoff games for the analysis of attacks in crypto-currencies","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"66","file":[{"relation":"main_file","file_id":"5696","date_updated":"2020-07-14T12:47:34Z","date_created":"2018-12-17T12:08:00Z","checksum":"68a055b1aaa241cc38375083cf832a7d","file_name":"2018_CONCUR_Chatterjee.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1078309,"creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"mla":"Chatterjee, Krishnendu, et al. Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies. Vol. 118, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.11.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, Y. Velner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Yaron Velner. “Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.11","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. 2018. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 118, 11.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and Y. Velner, “Ergodic mean-payoff games for the analysis of attacks in crypto-currencies,” presented at the CONCUR: Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Velner, Y. (2018). Ergodic mean-payoff games for the analysis of attacks in crypto-currencies (Vol. 118). Presented at the CONCUR: Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11"},"date_published":"2018-09-01T00:00:00Z"},{"volume":10801,"date_updated":"2024-03-28T23:30:33Z","date_created":"2018-12-11T11:45:45Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Goharshady, Amir","first_name":"Amir","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2018","acknowledgement":"The research was partially supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games).","publist_id":"7554","ec_funded":1,"file_date_updated":"2020-07-14T12:46:00Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-89884-1_26","conference":{"end_date":"2018-04-19","location":"Thessaloniki, Greece","start_date":"2018-04-16","name":"ESOP: European Symposium on Programming"},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"04","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1394993,"creator":"dernst","file_name":"2018_ESOP_Chatterjee.pdf","access_level":"open_access","date_created":"2018-12-17T15:45:49Z","date_updated":"2020-07-14T12:46:00Z","checksum":"9c8a8338c571903b599b6ca93abd2cce","relation":"main_file","file_id":"5716"}],"intvolume":" 10801","status":"public","title":"Quantitative analysis of smart contracts","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"311","abstract":[{"lang":"eng","text":"Smart contracts are computer programs that are executed by a network of mutually distrusting agents, without the need of an external trusted authority. Smart contracts handle and transfer assets of considerable value (in the form of crypto-currency like Bitcoin). Hence, it is crucial that their implementation is bug-free. We identify the utility (or expected payoff) of interacting with such smart contracts as the basic and canonical quantitative property for such contracts. We present a framework for such quantitative analysis of smart contracts. Such a formal framework poses new and novel research challenges in programming languages, as it requires modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior and modeling utilities which are not specified as standard temporal properties such as safety and termination. While game-theoretic incentives have been analyzed in the security community, their analysis has been restricted to the very special case of stateless games. However, to analyze smart contracts, stateful analysis is required as it must account for the different program states of the protocol. Our main contributions are as follows: we present (i)~a simplified programming language for smart contracts; (ii)~an automatic translation of the programs to state-based games; (iii)~an abstraction-refinement approach to solve such games; and (iv)~experimental results on real-world-inspired smart contracts."}],"alternative_title":["LNCS"],"type":"conference","date_published":"2018-04-01T00:00:00Z","page":"739 - 767","citation":{"apa":"Chatterjee, K., Goharshady, A. K., & Velner, Y. (2018). Quantitative analysis of smart contracts (Vol. 10801, pp. 739–767). Presented at the ESOP: European Symposium on Programming, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89884-1_26","ieee":"K. Chatterjee, A. K. Goharshady, and Y. Velner, “Quantitative analysis of smart contracts,” presented at the ESOP: European Symposium on Programming, Thessaloniki, Greece, 2018, vol. 10801, pp. 739–767.","ista":"Chatterjee K, Goharshady AK, Velner Y. 2018. Quantitative analysis of smart contracts. ESOP: European Symposium on Programming, LNCS, vol. 10801, 739–767.","ama":"Chatterjee K, Goharshady AK, Velner Y. Quantitative analysis of smart contracts. In: Vol 10801. Springer; 2018:739-767. doi:10.1007/978-3-319-89884-1_26","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Yaron Velner. “Quantitative Analysis of Smart Contracts,” 10801:739–67. Springer, 2018. https://doi.org/10.1007/978-3-319-89884-1_26.","short":"K. Chatterjee, A.K. Goharshady, Y. Velner, in:, Springer, 2018, pp. 739–767.","mla":"Chatterjee, Krishnendu, et al. Quantitative Analysis of Smart Contracts. Vol. 10801, Springer, 2018, pp. 739–67, doi:10.1007/978-3-319-89884-1_26."},"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1"},{"date_updated":"2024-03-28T23:30:34Z","date_created":"2019-04-18T10:37:35Z","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"first_name":"Ali","last_name":"Behrouz","full_name":"Behrouz, Ali"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"department":[{"_id":"KrCh"}],"publisher":"IEEE","publication_status":"published","year":"2018","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:27Z","language":[{"iso":"eng"}],"doi":"10.1109/Cybermatics_2018.2018.00231","conference":{"start_date":"2018-07-30","location":"Halifax, Canada","end_date":"2018-08-03","name":"IEEE International Conference on Blockchain"},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["1805.09104"],"isi":["000481634500196"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"publication_identifier":{"isbn":["978-1-5386-7975-3 "]},"month":"09","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"blockchain2018.pdf","creator":"akafshda","content_type":"application/pdf","file_size":624338,"file_id":"6341","relation":"main_file","checksum":"b25c9bb7cf6e7e6634e692d26d41ead8","date_created":"2019-04-18T10:36:39Z","date_updated":"2020-07-14T12:47:27Z"}],"ddc":["000"],"status":"public","title":"Secure Credit Reporting on the Blockchain","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6340","abstract":[{"text":"We present a secure approach for maintaining andreporting credit history records on the Blockchain. Our ap-proach removes third-parties such as credit reporting agen-cies from the lending process and replaces them with smartcontracts. This allows customers to interact directly with thelenders or banks while ensuring the integrity, unmalleabilityand privacy of their credit data. Additionally, each customerhas full control over complete or selective disclosure of hercredit records, eliminating the risk of privacy violations or databreaches. Moreover, our approach provides strong guaranteesfor the lenders as well. A lender can check both correctness andcompleteness of the credit data disclosed to her. This is the firstapproach that can perform all credit reporting tasks withouta central authority or changing the financial mechanisms*.","lang":"eng"}],"type":"conference","date_published":"2018-09-01T00:00:00Z","page":"1343-1348","citation":{"short":"A.K. Goharshady, A. Behrouz, K. Chatterjee, in:, Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–1348.","mla":"Goharshady, Amir Kafshdar, et al. “Secure Credit Reporting on the Blockchain.” Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–48, doi:10.1109/Cybermatics_2018.2018.00231.","chicago":"Goharshady, Amir Kafshdar, Ali Behrouz, and Krishnendu Chatterjee. “Secure Credit Reporting on the Blockchain.” In Proceedings of the IEEE International Conference on Blockchain, 1343–48. IEEE, 2018. https://doi.org/10.1109/Cybermatics_2018.2018.00231.","ama":"Goharshady AK, Behrouz A, Chatterjee K. Secure Credit Reporting on the Blockchain. In: Proceedings of the IEEE International Conference on Blockchain. IEEE; 2018:1343-1348. doi:10.1109/Cybermatics_2018.2018.00231","apa":"Goharshady, A. K., Behrouz, A., & Chatterjee, K. (2018). Secure Credit Reporting on the Blockchain. In Proceedings of the IEEE International Conference on Blockchain (pp. 1343–1348). Halifax, Canada: IEEE. https://doi.org/10.1109/Cybermatics_2018.2018.00231","ieee":"A. K. Goharshady, A. Behrouz, and K. Chatterjee, “Secure Credit Reporting on the Blockchain,” in Proceedings of the IEEE International Conference on Blockchain, Halifax, Canada, 2018, pp. 1343–1348.","ista":"Goharshady AK, Behrouz A, Chatterjee K. 2018. Secure Credit Reporting on the Blockchain. Proceedings of the IEEE International Conference on Blockchain. IEEE International Conference on Blockchain, 1343–1348."},"publication":"Proceedings of the IEEE International Conference on Blockchain","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"issue":"3","abstract":[{"lang":"eng","text":"We study algorithmic questions wrt algebraic path properties in concurrent systems, where the transitions of the system are labeled from a complete, closed semiring. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.\r\n"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 40","status":"public","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6009","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3210257.","mla":"Chatterjee, Krishnendu, et al. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3, 9, Association for Computing Machinery (ACM), 2018, doi:10.1145/3210257.","short":"K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 40 (2018).","ista":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2018. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 40(3), 9.","apa":"Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A. (2018). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3210257","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3. Association for Computing Machinery (ACM), 2018.","ama":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 2018;40(3). doi:10.1145/3210257"},"publication":"ACM Transactions on Programming Languages and Systems","ec_funded":1,"article_number":"9","volume":40,"date_created":"2019-02-14T14:31:52Z","date_updated":"2024-03-28T23:30:34Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1437"},{"relation":"earlier_version","status":"public","id":"5441"},{"relation":"earlier_version","status":"public","id":"5442"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"}],"publisher":"Association for Computing Machinery (ACM)","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2018","publication_identifier":{"issn":["0164-0925"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1145/3210257","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1510.07565","open_access":"1"}],"external_id":{"arxiv":["1510.07565"],"isi":["000444694800001"]}},{"day":"17","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-17T00:00:00Z","publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","citation":{"short":"K. Chatterjee, H. Fu, A.K. Goharshady, N. Okati, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4700–4707.","mla":"Chatterjee, Krishnendu, et al. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, vol. 2018, IJCAI, 2018, pp. 4700–07, doi:10.24963/ijcai.2018/653.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Nastaran Okati. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018:4700–4707. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/653.","ama":"Chatterjee K, Fu H, Goharshady AK, Okati N. Computational approaches for stochastic shortest path on succinct MDPs. In: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. Vol 2018. IJCAI; 2018:4700-4707. doi:10.24963/ijcai.2018/653","apa":"Chatterjee, K., Fu, H., Goharshady, A. K., & Okati, N. (2018). Computational approaches for stochastic shortest path on succinct MDPs. In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence (Vol. 2018, pp. 4700–4707). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/653","ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and N. Okati, “Computational approaches for stochastic shortest path on succinct MDPs,” in Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4700–4707.","ista":"Chatterjee K, Fu H, Goharshady AK, Okati N. 2018. Computational approaches for stochastic shortest path on succinct MDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4700–4707."},"page":"4700-4707","abstract":[{"text":"We consider the stochastic shortest path (SSP)problem for succinct Markov decision processes(MDPs), where the MDP consists of a set of vari-ables, and a set of nondeterministic rules that up-date the variables. First, we show that several ex-amples from the AI literature can be modeled assuccinct MDPs. Then we present computationalapproaches for upper and lower bounds for theSSP problem: (a) for computing upper bounds, ourmethod is polynomial-time in the implicit descrip-tion of the MDP; (b) for lower bounds, we present apolynomial-time (in the size of the implicit descrip-tion) reduction to quadratic programming. Our ap-proach is applicable even to infinite-state MDPs.Finally, we present experimental results to demon-strate the effectiveness of our approach on severalclassical examples from the AI literature.","lang":"eng"}],"type":"conference","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5977","title":"Computational approaches for stochastic shortest path on succinct MDPs","status":"public","intvolume":" 2018","month":"07","publication_identifier":{"isbn":["978-099924112-7"],"issn":["10450823"]},"conference":{"location":"Stockholm, Sweden","start_date":"2018-07-13","end_date":"2018-07-19","name":"IJCAI: International Joint Conference on Artificial Intelligence"},"doi":"10.24963/ijcai.2018/653","language":[{"iso":"eng"}],"external_id":{"isi":["000764175404118"],"arxiv":["1804.08984"]},"main_file_link":[{"url":"https://arxiv.org/abs/1804.08984","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"ec_funded":1,"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Goharshady","first_name":"Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir"},{"last_name":"Okati","first_name":"Nastaran","full_name":"Okati, Nastaran"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"date_created":"2019-02-13T13:26:27Z","date_updated":"2024-03-28T23:30:34Z","volume":2018,"year":"2018","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IJCAI"},{"month":"01","language":[{"iso":"eng"}],"doi":"10.1007/s10494-018-9896-4","project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000433113900004"]},"publist_id":"7401","ec_funded":1,"file_date_updated":"2020-07-14T12:46:25Z","volume":100,"date_created":"2018-12-11T11:46:23Z","date_updated":"2024-03-28T23:30:36Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7258"}]},"author":[{"orcid":"0000-0003-4312-0179","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","first_name":"Jakob","full_name":"Kühnen, Jakob"},{"full_name":"Scarselli, Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","first_name":"Davide","last_name":"Scarselli"},{"full_name":"Schaner, Markus","id":"316CE034-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","last_name":"Schaner"},{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BjHo"}],"publisher":"Springer","publication_status":"published","year":"2018","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2018-01-01T00:00:00Z","page":"919 - 942","citation":{"ista":"Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942.","apa":"Kühnen, J., Scarselli, D., Schaner, M., & Hof, B. (2018). Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. Springer. https://doi.org/10.1007/s10494-018-9896-4","ieee":"J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady modification of the streamwise velocity profile in a pipe,” Flow Turbulence and Combustion, vol. 100, no. 4. Springer, pp. 919–942, 2018.","ama":"Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 2018;100(4):919-942. doi:10.1007/s10494-018-9896-4","chicago":"Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion. Springer, 2018. https://doi.org/10.1007/s10494-018-9896-4.","mla":"Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion, vol. 100, no. 4, Springer, 2018, pp. 919–42, doi:10.1007/s10494-018-9896-4.","short":"J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942."},"publication":"Flow Turbulence and Combustion","issue":"4","abstract":[{"lang":"eng","text":"We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device which injects fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the skin friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant local skin friction drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle."}],"type":"journal_article","file":[{"file_id":"5717","relation":"main_file","checksum":"d7c0bade150faabca150b0a9986e60ca","date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-17T15:52:37Z","access_level":"open_access","file_name":"2018_FlowTurbulenceCombust_Kuehnen.pdf","creator":"dernst","content_type":"application/pdf","file_size":2210020}],"oa_version":"Published Version","intvolume":" 100","status":"public","title":"Relaminarization by steady modification of the streamwise velocity profile in a pipe","ddc":["530"],"_id":"422","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"type":"journal_article","abstract":[{"text":"Turbulence is the major cause of friction losses in transport processes and it is responsible for a drastic drag increase in flows over bounding surfaces. While much effort is invested into developing ways to control and reduce turbulence intensities, so far no methods exist to altogether eliminate turbulence if velocities are sufficiently large. We demonstrate for pipe flow that appropriate distortions to the velocity profile lead to a complete collapse of turbulence and subsequently friction losses are reduced by as much as 90%. Counterintuitively, the return to laminar motion is accomplished by initially increasing turbulence intensities or by transiently amplifying wall shear. Since neither the Reynolds number nor the shear stresses decrease (the latter often increase), these measures are not indicative of turbulence collapse. Instead, an amplification mechanism measuring the interaction between eddies and the mean shear is found to set a threshold below which turbulence is suppressed beyond recovery.","lang":"eng"}],"title":"Destabilizing turbulence in pipe flow","status":"public","intvolume":" 14","_id":"461","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","scopus_import":"1","day":"08","article_processing_charge":"No","page":"386-390","publication":"Nature Physics","citation":{"chicago":"Kühnen, Jakob, Baofang Song, Davide Scarselli, Nazmi B Budanur, Michael Riedl, Ashley Willis, Marc Avila, and Björn Hof. “Destabilizing Turbulence in Pipe Flow.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-017-0018-3.","short":"J. Kühnen, B. Song, D. Scarselli, N.B. Budanur, M. Riedl, A. Willis, M. Avila, B. Hof, Nature Physics 14 (2018) 386–390.","mla":"Kühnen, Jakob, et al. “Destabilizing Turbulence in Pipe Flow.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 386–90, doi:10.1038/s41567-017-0018-3.","apa":"Kühnen, J., Song, B., Scarselli, D., Budanur, N. B., Riedl, M., Willis, A., … Hof, B. (2018). Destabilizing turbulence in pipe flow. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-017-0018-3","ieee":"J. Kühnen et al., “Destabilizing turbulence in pipe flow,” Nature Physics, vol. 14. Nature Publishing Group, pp. 386–390, 2018.","ista":"Kühnen J, Song B, Scarselli D, Budanur NB, Riedl M, Willis A, Avila M, Hof B. 2018. Destabilizing turbulence in pipe flow. Nature Physics. 14, 386–390.","ama":"Kühnen J, Song B, Scarselli D, et al. Destabilizing turbulence in pipe flow. Nature Physics. 2018;14:386-390. doi:10.1038/s41567-017-0018-3"},"date_published":"2018-01-08T00:00:00Z","ec_funded":1,"publist_id":"7360","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"BjHo"}],"acknowledgement":"We acknowledge the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 737549) and the Deutsche Forschungsgemeinschaft (Project No. FOR 1182) for financial support. We thank our technician P. Maier for providing highly valuable ideas and greatly supporting us in all technical aspects. We thank M. Schaner for technical drawings, construction and design. We thank M. Schwegel for a Matlab code to post-process experimental data.","year":"2018","date_created":"2018-12-11T11:46:36Z","date_updated":"2024-03-28T23:30:36Z","volume":14,"author":[{"full_name":"Kühnen, Jakob","first_name":"Jakob","last_name":"Kühnen","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179"},{"first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang"},{"orcid":"0000-0001-5227-4271","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","first_name":"Davide","full_name":"Scarselli, Davide"},{"full_name":"Budanur, Nazmi B","first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010"},{"orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl","first_name":"Michael","full_name":"Riedl, Michael"},{"first_name":"Ashley","last_name":"Willis","full_name":"Willis, Ashley"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"related_material":{"record":[{"id":"12726","status":"public","relation":"dissertation_contains"},{"id":"14530","status":"public","relation":"dissertation_contains"},{"id":"7258","status":"public","relation":"dissertation_contains"}]},"month":"01","quality_controlled":"1","isi":1,"project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7"},{"grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425","name":"Eliminating turbulence in oil pipelines","call_identifier":"H2020"}],"external_id":{"isi":["000429434100020"]},"main_file_link":[{"url":"https://arxiv.org/abs/1711.06543","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41567-017-0018-3"},{"file_date_updated":"2020-07-14T12:46:30Z","publist_id":"7373","ec_funded":1,"date_created":"2018-12-11T11:46:32Z","date_updated":"2024-03-28T23:30:38Z","volume":14,"author":[{"full_name":"Prat, Tomas","last_name":"Prat","first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","first_name":"Jakub","last_name":"Hajny","full_name":"Hajny, Jakub"},{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","first_name":"Mina K","full_name":"Vasileva, Mina K"},{"full_name":"Molnar, Gergely","first_name":"Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"full_name":"Schmid, Markus","first_name":"Markus","last_name":"Schmid"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"related_material":{"record":[{"id":"1127","relation":"dissertation_contains","status":"public"},{"id":"7172","status":"public","relation":"dissertation_contains"},{"id":"8822","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Public Library of Science","year":"2018","month":"01","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1007177","quality_controlled":"1","isi":1,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000423718600034"]},"abstract":[{"text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"4843","relation":"main_file","checksum":"0276d66788ec076f4924164a39e6a712","date_created":"2018-12-12T10:10:52Z","date_updated":"2020-07-14T12:46:30Z","access_level":"open_access","file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","creator":"system","content_type":"application/pdf","file_size":24709062}],"pubrep_id":"967","title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","ddc":["581"],"status":"public","intvolume":" 14","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"449","day":"29","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2018-01-29T00:00:00Z","publication":"PLoS Genetics","citation":{"chicago":"Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007177.","short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","mla":"Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics, vol. 14, no. 1, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007177.","apa":"Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007177","ieee":"T. Prat et al., “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” PLoS Genetics, vol. 14, no. 1. Public Library of Science, 2018.","ista":"Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1).","ama":"Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 2018;14(1). doi:10.1371/journal.pgen.1007177"}},{"date_published":"2018-07-06T00:00:00Z","citation":{"ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-28188-1","ieee":"P. Grones et al., “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” Scientific Reports, vol. 8, no. 1. Springer, 2018.","apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., & Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. Springer. https://doi.org/10.1038/s41598-018-28188-1","ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279.","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports, vol. 8, no. 1, 10279, Springer, 2018, doi:10.1038/s41598-018-28188-1.","chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports. Springer, 2018. https://doi.org/10.1038/s41598-018-28188-1."},"publication":"Scientific Reports","article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","file":[{"relation":"main_file","file_id":"5714","date_updated":"2020-07-14T12:45:20Z","date_created":"2018-12-17T15:38:56Z","checksum":"266b03f4fb8198e83141617aaa99dcab","file_name":"2018_ScientificReports_Grones.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2413876,"creator":"dernst"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"191","intvolume":" 8","status":"public","title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","ddc":["581"],"issue":"1","abstract":[{"text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals.","lang":"eng"}],"type":"journal_article","doi":"10.1038/s41598-018-28188-1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000437673200053"]},"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"isi":1,"quality_controlled":"1","month":"07","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8822"}]},"author":[{"last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"full_name":"Abas, Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda F","last_name":"Abas"},{"full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub"},{"full_name":"Jones, Angharad","first_name":"Angharad","last_name":"Jones"},{"first_name":"Sascha","last_name":"Waidmann","full_name":"Waidmann, Sascha"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"volume":8,"date_updated":"2024-03-28T23:30:38Z","date_created":"2018-12-11T11:45:06Z","year":"2018","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Springer","publication_status":"published","ec_funded":1,"publist_id":"7729","file_date_updated":"2020-07-14T12:45:20Z","article_number":"10279"}]