--- _id: '5816' 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. article_number: '114701' article_processing_charge: No author: - first_name: Arne full_name: Hollmann, Arne last_name: Hollmann - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Maciej full_name: Kucharski, Maciej last_name: Kucharski - first_name: Dietmar full_name: Kissinger, Dietmar last_name: Kissinger - first_name: Gunter full_name: Fischer, Gunter last_name: Fischer - first_name: Lars R. full_name: Schreiber, Lars R. last_name: Schreiber citation: 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 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 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. 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. 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. 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). date_created: 2019-01-10T14:22:23Z date_published: 2018-11-01T00:00:00Z date_updated: 2024-03-27T23:30:26Z day: '01' department: - _id: GeKa doi: 10.1063/1.5038258 external_id: arxiv: - '1804.09522' isi: - '000451735700054' intvolume: ' 89' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.09522 month: '11' oa: 1 oa_version: Preprint publication: Review of Scientific Instruments publication_identifier: issn: - '00346748' publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: record: - id: '10058' relation: dissertation_contains status: public scopus_import: '1' status: public title: 30 GHz-voltage controlled oscillator operating at 4 K type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 89 year: '2018' ... --- _id: '6263' 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. ' acknowledged_ssus: - _id: M-Shop - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 citation: ama: Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:10.15479/AT:ISTA:th1072 apa: Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072 chicago: Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072. ieee: M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018. ista: Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. mla: Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072. short: M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018. date_created: 2019-04-09T13:57:15Z date_published: 2018-12-28T00:00:00Z date_updated: 2023-09-22T09:20:37Z day: '28' ddc: - '570' - '576' - '579' degree_awarded: PhD department: - _id: ToBo doi: 10.15479/AT:ISTA:th1072 file: - access_level: open_access checksum: fc60585c9eaad868ac007004ef130908 content_type: application/pdf creator: dernst date_created: 2019-04-09T13:49:24Z date_updated: 2021-02-11T11:17:17Z embargo: 2020-01-25 file_id: '6264' file_name: 2018_Thesis_Lukacisinova.pdf file_size: 5656866 relation: main_file - access_level: closed checksum: 264057ec0a92ab348cc83b41f021ba92 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-09T13:49:23Z date_updated: 2020-07-14T12:47:25Z embargo_to: open_access file_id: '6265' file_name: 2018_Thesis_Lukacisinova_source.docx file_size: 5168054 relation: source_file file_date_updated: 2021-02-11T11:17:17Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '91' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1619' relation: part_of_dissertation status: public - id: '696' relation: part_of_dissertation status: public - id: '1027' relation: part_of_dissertation status: public status: public supervisor: - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X title: Genetic determinants of antibiotic resistance evolution type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '544' abstract: - lang: eng 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. acknowledged_ssus: - _id: LifeSc 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, ' article_processing_charge: No author: - first_name: Attila full_name: György, Attila id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87 last_name: György orcid: 0000-0002-1819-198X - first_name: Marko full_name: Roblek, Marko id: 3047D808-F248-11E8-B48F-1D18A9856A87 last_name: Roblek orcid: 0000-0001-9588-1389 - first_name: Aparna full_name: Ratheesh, Aparna id: 2F064CFE-F248-11E8-B48F-1D18A9856A87 last_name: Ratheesh orcid: 0000-0001-7190-0776 - first_name: Katarina full_name: Valosková, Katarina id: 46F146FC-F248-11E8-B48F-1D18A9856A87 last_name: Valosková - first_name: Vera full_name: Belyaeva, Vera id: 47F080FE-F248-11E8-B48F-1D18A9856A87 last_name: Belyaeva - first_name: Stephanie full_name: Wachner, Stephanie id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87 last_name: Wachner - first_name: Yutaka full_name: Matsubayashi, Yutaka last_name: Matsubayashi - first_name: Besaiz full_name: Sanchez Sanchez, Besaiz last_name: Sanchez Sanchez - first_name: Brian full_name: Stramer, Brian last_name: Stramer - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 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' 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' 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.' 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.' 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.' 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.' 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.' date_created: 2018-12-11T11:47:05Z date_published: 2018-03-01T00:00:00Z date_updated: 2024-03-27T23:30:29Z day: '01' ddc: - '570' department: - _id: DaSi doi: 10.1534/g3.117.300452 ec_funded: 1 external_id: isi: - '000426693300011' file: - access_level: open_access checksum: 7d9d28b915159078a4ca7add568010e8 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:48Z date_updated: 2020-07-14T12:46:56Z file_id: '4905' file_name: IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf file_size: 2251222 relation: main_file file_date_updated: 2020-07-14T12:46:56Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 845 - 857 project: - _id: 253B6E48-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29638 name: Drosophila TNFa´s Funktion in Immunzellen - _id: 253B6E48-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29638 name: The role of Drosophila TNF alpha in immune cell invasion - _id: 2637E9C0-B435-11E9-9278-68D0E5697425 grant_number: 'LSC16-021 ' name: Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis - _id: 2536F660-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '334077' name: Investigating the role of transporters in invasive migration through junctions publication: 'G3: Genes, Genomes, Genetics' publication_status: published publisher: Genetics Society of America publist_id: '7271' pubrep_id: '990' quality_controlled: '1' related_material: record: - id: '6530' relation: research_paper - id: '6543' relation: research_paper - id: '11193' relation: dissertation_contains status: public - id: '6546' relation: dissertation_contains status: public scopus_import: '1' status: public title: Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2018' ... --- _id: '612' 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. article_processing_charge: No article_type: original author: - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Carolina full_name: Aguado, Carolina last_name: Aguado - first_name: Francisco full_name: Ciruela, Francisco last_name: Ciruela - first_name: Javier full_name: Cózar, Javier last_name: Cózar - first_name: David full_name: Kleindienst, David id: 42E121A4-F248-11E8-B48F-1D18A9856A87 last_name: Kleindienst - first_name: Luis full_name: De La Ossa, Luis last_name: De La Ossa - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler - first_name: Kevin full_name: Wickman, Kevin last_name: Wickman - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa citation: 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 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 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. 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. 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. 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. 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. date_created: 2018-12-11T11:47:29Z date_published: 2018-04-01T00:00:00Z date_updated: 2024-03-27T23:30:30Z day: '01' ddc: - '571' department: - _id: RySh doi: 10.1007/s00429-017-1568-y ec_funded: 1 external_id: isi: - '000428419500030' file: - access_level: open_access checksum: a55b3103476ecb5f4f983d8801807e8b content_type: application/pdf creator: system date_created: 2018-12-12T10:15:36Z date_updated: 2020-07-14T12:47:20Z file_id: '5157' file_name: IST-2018-1013-v1+1_2018_Kleindienst_Differential.pdf file_size: 5542926 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 223' isi: 1 issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1565 - 1587 project: - _id: 25CBA828-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '720270' name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1) - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Brain Structure and Function publication_status: published publisher: Springer publist_id: '7192' pubrep_id: '1013' quality_controlled: '1' related_material: record: - id: '9562' relation: dissertation_contains status: public scopus_import: '1' status: public title: Differential association of GABAB receptors with their effector ion channels in Purkinje cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 223 year: '2018' ... --- _id: '21' 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 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.. article_number: '4605' article_processing_charge: No article_type: original author: - first_name: 'Claudia ' full_name: 'Espinoza Martinez, Claudia ' id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87 last_name: Espinoza Martinez orcid: 0000-0003-4710-2082 - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán orcid: 0000-0003-2209-5242 - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: 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 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 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. 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. 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. 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). date_created: 2018-12-11T11:44:12Z date_published: 2018-11-02T00:00:00Z date_updated: 2024-03-27T23:30:31Z day: '02' ddc: - '570' department: - _id: PeJo doi: 10.1038/s41467-018-06899-3 ec_funded: 1 external_id: isi: - '000449069700009' file: - access_level: open_access checksum: 9fe2a63bd95a5067d896c087d07998f3 content_type: application/pdf creator: dernst date_created: 2018-12-17T15:41:57Z date_updated: 2020-07-14T12:45:28Z file_id: '5715' file_name: 2018_NatureComm_Espinoza.pdf file_size: 4651930 relation: main_file file_date_updated: 2020-07-14T12:45:28Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '8034' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/ record: - id: '6363' relation: dissertation_contains status: public scopus_import: '1' status: public title: Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 9 year: '2018' ... --- _id: '66' abstract: - lang: eng 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.' alternative_title: - LIPIcs article_number: '11' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: 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' 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' 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. 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.' 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.' 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. conference: end_date: 2018-09-07 location: Beijing, China name: 'CONCUR: Conference on Concurrency Theory' start_date: 2018-09-04 date_created: 2018-12-11T11:44:27Z date_published: 2018-09-01T00:00:00Z date_updated: 2024-03-27T23:30:33Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPIcs.CONCUR.2018.11 ec_funded: 1 external_id: arxiv: - '1806.03108' file: - access_level: open_access checksum: 68a055b1aaa241cc38375083cf832a7d content_type: application/pdf creator: dernst date_created: 2018-12-17T12:08:00Z date_updated: 2020-07-14T12:47:34Z file_id: '5696' file_name: 2018_CONCUR_Chatterjee.pdf file_size: 1078309 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 118' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 266EEEC0-B435-11E9-9278-68D0E5697425 name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts publication_identifier: isbn: - 978-3-95977-087-3 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7988' quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Ergodic mean-payoff games for the analysis of attacks in crypto-currencies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2018' ... --- _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.' 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).' alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: 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' 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' 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. 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.' 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. short: K. Chatterjee, A.K. Goharshady, Y. Velner, in:, Springer, 2018, pp. 739–767. conference: end_date: 2018-04-19 location: Thessaloniki, Greece name: 'ESOP: European Symposium on Programming' start_date: 2018-04-16 date_created: 2018-12-11T11:45:45Z date_published: 2018-04-01T00:00:00Z date_updated: 2024-03-27T23:30:33Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-319-89884-1_26 ec_funded: 1 file: - access_level: open_access checksum: 9c8a8338c571903b599b6ca93abd2cce content_type: application/pdf creator: dernst date_created: 2018-12-17T15:45:49Z date_updated: 2020-07-14T12:46:00Z file_id: '5716' file_name: 2018_ESOP_Chatterjee.pdf file_size: 1394993 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' intvolume: ' 10801' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 739 - 767 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '7554' quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Quantitative analysis of smart contracts tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10801 year: '2018' ... --- _id: '6340' abstract: - lang: eng 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*. article_processing_charge: No author: - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Ali full_name: Behrouz, Ali last_name: Behrouz - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: 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' 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. 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. 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. short: A.K. Goharshady, A. Behrouz, K. Chatterjee, in:, Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–1348. conference: end_date: 2018-08-03 location: Halifax, Canada name: IEEE International Conference on Blockchain start_date: 2018-07-30 date_created: 2019-04-18T10:37:35Z date_published: 2018-09-01T00:00:00Z date_updated: 2024-03-27T23:30:34Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1109/Cybermatics_2018.2018.00231 ec_funded: 1 external_id: arxiv: - '1805.09104' isi: - '000481634500196' file: - access_level: open_access checksum: b25c9bb7cf6e7e6634e692d26d41ead8 content_type: application/pdf creator: akafshda date_created: 2019-04-18T10:36:39Z date_updated: 2020-07-14T12:47:27Z file_id: '6341' file_name: blockchain2018.pdf file_size: 624338 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1343-1348 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 266EEEC0-B435-11E9-9278-68D0E5697425 name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Proceedings of the IEEE International Conference on Blockchain publication_identifier: isbn: - '978-1-5386-7975-3 ' publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Secure Credit Reporting on the Blockchain tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '6009' 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" article_number: '9' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: 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 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 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. 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. 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. 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). date_created: 2019-02-14T14:31:52Z date_published: 2018-08-01T00:00:00Z date_updated: 2024-03-27T23:30:34Z day: '01' department: - _id: KrCh doi: 10.1145/3210257 ec_funded: 1 external_id: arxiv: - '1510.07565' isi: - '000444694800001' intvolume: ' 40' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1510.07565 month: '08' oa: 1 oa_version: Preprint project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: ACM Transactions on Programming Languages and Systems publication_identifier: issn: - 0164-0925 publication_status: published publisher: Association for Computing Machinery (ACM) quality_controlled: '1' related_material: record: - id: '1437' relation: earlier_version status: public - id: '5441' relation: earlier_version status: public - id: '5442' relation: earlier_version status: public - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Algorithms for algebraic path properties in concurrent systems of constant treewidth components type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 40 year: '2018' ... --- _id: '5977' abstract: - lang: eng 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.' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Nastaran full_name: Okati, Nastaran last_name: Okati citation: 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' 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. 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.' 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. 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. conference: end_date: 2018-07-19 location: Stockholm, Sweden name: 'IJCAI: International Joint Conference on Artificial Intelligence' start_date: 2018-07-13 date_created: 2019-02-13T13:26:27Z date_published: 2018-07-17T00:00:00Z date_updated: 2024-03-27T23:30:34Z day: '17' department: - _id: KrCh doi: 10.24963/ijcai.2018/653 ec_funded: 1 external_id: arxiv: - '1804.08984' isi: - '000764175404118' intvolume: ' 2018' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.08984 month: '07' oa: 1 oa_version: Preprint page: 4700-4707 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence publication_identifier: isbn: - 978-099924112-7 issn: - '10450823' publication_status: published publisher: IJCAI quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Computational approaches for stochastic shortest path on succinct MDPs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2018 year: '2018' ... --- _id: '422' 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. article_processing_charge: Yes (via OA deal) author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Markus full_name: Schaner, Markus id: 316CE034-F248-11E8-B48F-1D18A9856A87 last_name: Schaner - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:23Z date_published: 2018-01-01T00:00:00Z date_updated: 2024-03-27T23:30:36Z day: '01' ddc: - '530' department: - _id: BjHo doi: 10.1007/s10494-018-9896-4 ec_funded: 1 external_id: isi: - '000433113900004' file: - access_level: open_access checksum: d7c0bade150faabca150b0a9986e60ca content_type: application/pdf creator: dernst date_created: 2018-12-17T15:52:37Z date_updated: 2020-07-14T12:46:25Z file_id: '5717' file_name: 2018_FlowTurbulenceCombust_Kuehnen.pdf file_size: 2210020 relation: main_file file_date_updated: 2020-07-14T12:46:25Z has_accepted_license: '1' intvolume: ' 100' isi: 1 issue: '4' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 919 - 942 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Flow Turbulence and Combustion publication_status: published publisher: Springer publist_id: '7401' quality_controlled: '1' related_material: record: - id: '7258' relation: dissertation_contains status: public scopus_import: '1' status: public title: Relaminarization by steady modification of the streamwise velocity profile in a pipe tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 100 year: '2018' ... --- _id: '461' abstract: - lang: eng 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. 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. article_processing_charge: No author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 - first_name: Ashley full_name: Willis, Ashley last_name: Willis - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: 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 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 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. 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. 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. short: J. Kühnen, B. Song, D. Scarselli, N.B. Budanur, M. Riedl, A. Willis, M. Avila, B. Hof, Nature Physics 14 (2018) 386–390. date_created: 2018-12-11T11:46:36Z date_published: 2018-01-08T00:00:00Z date_updated: 2024-03-27T23:30:36Z day: '08' department: - _id: BjHo doi: 10.1038/s41567-017-0018-3 ec_funded: 1 external_id: isi: - '000429434100020' intvolume: ' 14' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.06543 month: '01' oa: 1 oa_version: Preprint page: 386-390 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin - _id: 25104D44-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '737549' name: Eliminating turbulence in oil pipelines publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7360' quality_controlled: '1' related_material: record: - id: '12726' relation: dissertation_contains status: public - id: '14530' relation: dissertation_contains status: public - id: '7258' relation: dissertation_contains status: public scopus_import: '1' status: public title: Destabilizing turbulence in pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '449' abstract: - lang: eng 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. article_processing_charge: Yes author: - first_name: Tomas full_name: Prat, Tomas id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87 last_name: Prat - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Mina K full_name: Vasileva, Mina K id: 3407EB18-F248-11E8-B48F-1D18A9856A87 last_name: Vasileva - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Markus full_name: Schmid, Markus last_name: Schmid - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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 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 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. 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). 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. short: T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018). date_created: 2018-12-11T11:46:32Z date_published: 2018-01-29T00:00:00Z date_updated: 2024-03-27T23:30:37Z day: '29' ddc: - '581' department: - _id: JiFr doi: 10.1371/journal.pgen.1007177 ec_funded: 1 external_id: isi: - '000423718600034' file: - access_level: open_access checksum: 0276d66788ec076f4924164a39e6a712 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:52Z date_updated: 2020-07-14T12:46:30Z file_id: '4843' file_name: IST-2018-967-v1+1_journal.pgen.1007177.pdf file_size: 24709062 relation: main_file file_date_updated: 2020-07-14T12:46:30Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '7373' pubrep_id: '967' quality_controlled: '1' related_material: record: - id: '1127' relation: dissertation_contains status: public - id: '7172' relation: dissertation_contains status: public - id: '8822' relation: dissertation_contains status: public scopus_import: '1' status: public title: WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '191' abstract: - lang: eng 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. article_number: '10279' article_processing_charge: No author: - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Melinda F full_name: Abas, Melinda F id: 3CFB3B1C-F248-11E8-B48F-1D18A9856A87 last_name: Abas - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Angharad full_name: Jones, Angharad last_name: Jones - first_name: Sascha full_name: Waidmann, Sascha last_name: Waidmann - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 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 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 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. 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. 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. 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. short: P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018). date_created: 2018-12-11T11:45:06Z date_published: 2018-07-06T00:00:00Z date_updated: 2024-03-27T23:30:37Z day: '06' ddc: - '581' department: - _id: JiFr - _id: EvBe doi: 10.1038/s41598-018-28188-1 ec_funded: 1 external_id: isi: - '000437673200053' file: - access_level: open_access checksum: 266b03f4fb8198e83141617aaa99dcab content_type: application/pdf creator: dernst date_created: 2018-12-17T15:38:56Z date_updated: 2020-07-14T12:45:20Z file_id: '5714' file_name: 2018_ScientificReports_Grones.pdf file_size: 2413876 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Scientific Reports publication_status: published publisher: Springer publist_id: '7729' quality_controlled: '1' related_material: record: - id: '8822' relation: dissertation_contains status: public scopus_import: '1' status: public title: PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2018' ... --- _id: '15' abstract: - lang: eng text: Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux. acknowledged_ssus: - _id: SSU acknowledgement: This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014). article_processing_charge: No author: - first_name: Miroslav full_name: Hons, Miroslav id: 4167FE56-F248-11E8-B48F-1D18A9856A87 last_name: Hons orcid: 0000-0002-6625-3348 - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 - first_name: Jun full_name: Abe, Jun last_name: Abe - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Jens full_name: Stein, Jens last_name: Stein - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 2018;19(6):606-616. doi:10.1038/s41590-018-0109-z apa: Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/s41590-018-0109-z chicago: Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41590-018-0109-z. ieee: M. Hons et al., “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” Nature Immunology, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018. ista: Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616. mla: Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:10.1038/s41590-018-0109-z. short: M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616. date_created: 2018-12-11T11:44:10Z date_published: 2018-05-18T00:00:00Z date_updated: 2024-03-27T23:30:39Z day: '18' department: - _id: MiSi - _id: Bio doi: 10.1038/s41590-018-0109-z ec_funded: 1 external_id: isi: - '000433041500026' pmid: - '29777221' intvolume: ' 19' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/29777221 month: '05' oa: 1 oa_version: Published Version page: 606 - 616 pmid: 1 project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells - _id: 25A48D24-B435-11E9-9278-68D0E5697425 grant_number: ALTF 1396-2014 name: Molecular and system level view of immune cell migration - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Nature Immunology publication_status: published publisher: Nature Publishing Group publist_id: '8040' quality_controlled: '1' related_material: record: - id: '6891' relation: dissertation_contains status: public scopus_import: '1' status: public title: Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '442' abstract: - lang: eng text: The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH. acknowledgement: 'This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ' article_processing_charge: No article_type: original author: - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 2018;8(1). doi:10.21769/BioProtoc.2685 apa: Li, L., Krens, G., Fendrych, M., & Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-Protocol. Bio-protocol. https://doi.org/10.21769/BioProtoc.2685 chicago: Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol. Bio-protocol, 2018. https://doi.org/10.21769/BioProtoc.2685. ieee: L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” Bio-protocol, vol. 8, no. 1. Bio-protocol, 2018. ista: Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1). mla: Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol, vol. 8, no. 1, Bio-protocol, 2018, doi:10.21769/BioProtoc.2685. short: L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018). date_created: 2018-12-11T11:46:30Z date_published: 2018-01-05T00:00:00Z date_updated: 2024-03-27T23:30:42Z day: '05' ddc: - '576' - '581' department: - _id: JiFr - _id: Bio doi: 10.21769/BioProtoc.2685 ec_funded: 1 file: - access_level: open_access checksum: 6644ba698206eda32b0abf09128e63e3 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:43Z date_updated: 2020-07-14T12:46:29Z file_id: '5299' file_name: IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf file_size: 11352389 relation: main_file file_date_updated: 2020-07-14T12:46:29Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Bio-protocol publication_identifier: eissn: - 2331-8325 publication_status: published publisher: Bio-protocol publist_id: '7381' pubrep_id: '970' quality_controlled: '1' related_material: record: - id: '10083' relation: dissertation_contains status: public status: public title: Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2018' ... --- _id: '3' abstract: - lang: eng text: SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder. acknowledged_ssus: - _id: M-Shop - _id: PreCl acknowledgement: This work was supported by the Simons Foundation Autism Research Initiative (grant 401299) to G.N. and the DFG (SPP1738 grant NO 1249) to K.-M.N. article_processing_charge: No article_type: original author: - first_name: Elena full_name: Deliu, Elena id: 37A40D7E-F248-11E8-B48F-1D18A9856A87 last_name: Deliu orcid: 0000-0002-7370-5293 - first_name: Niccoló full_name: Arecco, Niccoló last_name: Arecco - first_name: Jasmin full_name: Morandell, Jasmin id: 4739D480-F248-11E8-B48F-1D18A9856A87 last_name: Morandell - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 - first_name: Ximena full_name: Contreras, Ximena id: 475990FE-F248-11E8-B48F-1D18A9856A87 last_name: Contreras - first_name: Charles full_name: Girardot, Charles last_name: Girardot - first_name: Eva full_name: Käsper, Eva last_name: Käsper - first_name: Alena full_name: Kozlova, Alena id: C50A9596-02D0-11E9-976E-E38CFE5CBC1D last_name: Kozlova - first_name: Kasumi full_name: Kishi, Kasumi id: 3065DFC4-F248-11E8-B48F-1D18A9856A87 last_name: Kishi - first_name: Ilaria full_name: Chiaradia, Ilaria id: B6467F20-02D0-11E9-BDA5-E960C241894A last_name: Chiaradia orcid: 0000-0002-9529-4464 - first_name: Kyung full_name: Noh, Kyung last_name: Noh - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Deliu E, Arecco N, Morandell J, et al. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 2018;21(12):1717-1727. doi:10.1038/s41593-018-0266-2 apa: Deliu, E., Arecco, N., Morandell, J., Dotter, C., Contreras, X., Girardot, C., … Novarino, G. (2018). Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/s41593-018-0266-2 chicago: Deliu, Elena, Niccoló Arecco, Jasmin Morandell, Christoph Dotter, Ximena Contreras, Charles Girardot, Eva Käsper, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience. Nature Publishing Group, 2018. https://doi.org/10.1038/s41593-018-0266-2. ieee: E. Deliu et al., “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition,” Nature Neuroscience, vol. 21, no. 12. Nature Publishing Group, pp. 1717–1727, 2018. ista: Deliu E, Arecco N, Morandell J, Dotter C, Contreras X, Girardot C, Käsper E, Kozlova A, Kishi K, Chiaradia I, Noh K, Novarino G. 2018. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 21(12), 1717–1727. mla: Deliu, Elena, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience, vol. 21, no. 12, Nature Publishing Group, 2018, pp. 1717–27, doi:10.1038/s41593-018-0266-2. short: E. Deliu, N. Arecco, J. Morandell, C. Dotter, X. Contreras, C. Girardot, E. Käsper, A. Kozlova, K. Kishi, I. Chiaradia, K. Noh, G. Novarino, Nature Neuroscience 21 (2018) 1717–1727. date_created: 2018-12-11T11:44:05Z date_published: 2018-11-19T00:00:00Z date_updated: 2024-03-27T23:30:44Z day: '19' ddc: - '570' department: - _id: GaNo - _id: EdHa doi: 10.1038/s41593-018-0266-2 external_id: isi: - '000451324700010' file: - access_level: open_access checksum: 60abd0f05b7cdc08a6b0ec460884084f content_type: application/pdf creator: dernst date_created: 2019-04-09T07:41:57Z date_updated: 2020-07-14T12:45:58Z file_id: '6255' file_name: 2017_NatureNeuroscience_Deliu.pdf file_size: 8167169 relation: main_file file_date_updated: 2020-07-14T12:45:58Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '12' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 1717 - 1727 project: - _id: 254BA948-B435-11E9-9278-68D0E5697425 grant_number: '401299' name: Probing development and reversibility of autism spectrum disorders publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '8054' pubrep_id: '1071' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/ record: - id: '6074' relation: popular_science status: public - id: '12364' relation: dissertation_contains status: public scopus_import: '1' status: public title: Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 21 year: '2018' ... --- _id: '2' abstract: - lang: eng text: Indirect reciprocity explores how humans act when their reputation is at stake, and which social norms they use to assess the actions of others. A crucial question in indirect reciprocity is which social norms can maintain stable cooperation in a society. Past research has highlighted eight such norms, called “leading-eight” strategies. This past research, however, is based on the assumption that all relevant information about other population members is publicly available and that everyone agrees on who is good or bad. Instead, here we explore the reputation dynamics when information is private and noisy. We show that under these conditions, most leading-eight strategies fail to evolve. Those leading-eight strategies that do evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other’s reputation, previous research has highlighted eight crucial moral systems. These “leading-eight” strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems. article_processing_charge: No author: - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 2018;115(48):12241-12246. doi:10.1073/pnas.1810565115 apa: Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Indirect reciprocity with private, noisy, and incomplete information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1810565115 chicago: Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1810565115. ieee: C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity with private, noisy, and incomplete information,” PNAS, vol. 115, no. 48. National Academy of Sciences, pp. 12241–12246, 2018. ista: Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246. mla: Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS, vol. 115, no. 48, National Academy of Sciences, 2018, pp. 12241–46, doi:10.1073/pnas.1810565115. short: C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 12241–12246. date_created: 2018-12-11T11:44:05Z date_published: 2018-11-27T00:00:00Z date_updated: 2024-03-27T23:30:44Z day: '27' department: - _id: KrCh doi: 10.1073/pnas.1810565115 ec_funded: 1 external_id: isi: - '000451351000063' pmid: - '30429320' intvolume: ' 115' isi: 1 issue: '48' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30429320 month: '11' oa: 1 oa_version: Submitted Version page: 12241-12246 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PNAS publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/no-cooperation-without-open-communication/ record: - id: '10293' relation: dissertation_contains status: public scopus_import: '1' status: public title: Indirect reciprocity with private, noisy, and incomplete information type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '67' abstract: - lang: eng text: 'Gene regulatory networks evolve through rewiring of individual components—that is, through changes in regulatory connections. However, the mechanistic basis of regulatory rewiring is poorly understood. Using a canonical gene regulatory system, we quantify the properties of transcription factors that determine the evolutionary potential for rewiring of regulatory connections: robustness, tunability and evolvability. In vivo repression measurements of two repressors at mutated operator sites reveal their contrasting evolutionary potential: while robustness and evolvability were positively correlated, both were in trade-off with tunability. Epistatic interactions between adjacent operators alleviated this trade-off. A thermodynamic model explains how the differences in robustness, tunability and evolvability arise from biophysical characteristics of repressor–DNA binding. The model also uncovers that the energy matrix, which describes how mutations affect repressor–DNA binding, encodes crucial information about the evolutionary potential of a repressor. The biophysical determinants of evolutionary potential for regulatory rewiring constitute a mechanistic framework for understanding network evolution.' article_processing_charge: No article_type: original author: - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y apa: Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. Nature Publishing Group. https://doi.org/10.1038/s41559-018-0651-y chicago: Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution. Nature Publishing Group, 2018. https://doi.org/10.1038/s41559-018-0651-y. ieee: C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018. ista: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643. mla: Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y. short: C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643. date_created: 2018-12-11T11:44:27Z date_published: 2018-09-10T00:00:00Z date_updated: 2024-03-27T23:30:48Z day: '10' ddc: - '570' department: - _id: CaGu - _id: GaTk - _id: JoBo doi: 10.1038/s41559-018-0651-y ec_funded: 1 external_id: isi: - '000447947600021' file: - access_level: open_access checksum: 383a2e2c944a856e2e821ec8e7bf71b6 content_type: application/pdf creator: dernst date_created: 2020-05-14T11:28:52Z date_updated: 2020-07-14T12:47:37Z file_id: '7830' file_name: 2018_NatureEcology_Igler.pdf file_size: 1135973 relation: main_file file_date_updated: 2020-07-14T12:47:37Z has_accepted_license: '1' intvolume: ' 2' isi: 1 issue: '10' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1633 - 1643 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer - _id: 251EE76E-B435-11E9-9278-68D0E5697425 grant_number: '24573' name: Design principles underlying genetic switch architecture (DOC Fellowship) publication: Nature Ecology and Evolution publication_status: published publisher: Nature Publishing Group publist_id: '7987' quality_controlled: '1' related_material: record: - id: '5585' relation: popular_science status: public - id: '6371' relation: dissertation_contains status: public scopus_import: '1' status: public title: Evolutionary potential of transcription factors for gene regulatory rewiring type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2 year: '2018' ... --- _id: '5585' abstract: - lang: eng text: Mean repression values and standard error of the mean are given for all operator mutant libraries. article_processing_charge: No author: - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108 apa: Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108 chicago: Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108. ieee: C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018. ista: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 10.15479/AT:ISTA:108. mla: Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:108. short: C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018). datarep_id: '108' date_created: 2018-12-12T12:31:40Z date_published: 2018-07-20T00:00:00Z date_updated: 2024-03-27T23:30:48Z day: '20' ddc: - '576' department: - _id: CaGu - _id: GaTk doi: 10.15479/AT:ISTA:108 ec_funded: 1 file: - access_level: open_access checksum: 1435781526c77413802adee0d4583cce content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: system date_created: 2018-12-12T13:02:45Z date_updated: 2020-07-14T12:47:07Z file_id: '5611' file_name: IST-2018-108-v1+1_data_figures.xlsx file_size: 16507 relation: main_file file_date_updated: 2020-07-14T12:47:07Z has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ month: '07' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer - _id: 251EE76E-B435-11E9-9278-68D0E5697425 grant_number: '24573' name: Design principles underlying genetic switch architecture (DOC Fellowship) publisher: Institute of Science and Technology Austria related_material: record: - id: '67' relation: research_paper status: public - id: '6371' relation: research_paper status: public status: public title: Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ...