[{"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. ","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"new_edition","id":"7132","status":"public"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"9d2c2dca04b00e485470c28b262af59a","file_id":"6267","embargo":"2019-11-24","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-04-09T14:12:40Z","file_name":"2018_Thesis_McKenzie.pdf","creator":"dernst","date_updated":"2021-02-11T11:17:16Z","file_size":4906420},{"file_id":"6268","checksum":"50b58c272899601bc6fd9642c4dc97f1","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2019-04-09T14:12:40Z","file_name":"2018_Thesis_McKenzie_source.docx","creator":"dernst","date_updated":"2020-07-14T12:47:25Z","file_size":5053545}],"type":"dissertation","pubrep_id":"1055","status":"public","_id":"6266","department":[{"_id":"HaJa"}],"file_date_updated":"2021-02-11T11:17:16Z","date_updated":"2023-09-07T13:02:37Z","supervisor":[{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"ddc":["571","573"],"oa":1,"publisher":"Institute of Science and Technology Austria","page":"95","date_created":"2019-04-09T14:13:39Z","doi":"10.15479/at:ista:th_1055","date_published":"2018-10-31T00:00:00Z","year":"2018","has_accepted_license":"1","day":"31","article_processing_charge":"No","author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine"}],"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","citation":{"ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:th_1055.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:10.15479/at:ista:th_1055","apa":"Mckenzie, C. (2018). Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th_1055","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018.","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission . Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:th_1055."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"_id":"50","type":"dissertation","status":"public","pubrep_id":"1031","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:48:16Z","ddc":["570","591","596"],"file_date_updated":"2021-02-11T23:30:21Z","department":[{"_id":"CaHe"}],"abstract":[{"text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"2018_Thesis_Capek.pdf","date_created":"2019-04-08T13:42:26Z","creator":"dernst","file_size":31576521,"date_updated":"2021-02-11T11:17:17Z","embargo":"2019-06-25","checksum":"d3eca3dcacb67bffdde6e6609c31cdd0","file_id":"6238","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"876deb14067e638aba65d209668bd821","file_id":"6239","file_size":38992956,"date_updated":"2021-02-11T23:30:21Z","creator":"dernst","file_name":"2018_Thesis_Capek_source.docx","date_created":"2019-04-08T13:42:27Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1100","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"661"},{"relation":"part_of_dissertation","id":"676","status":"public"}]},"citation":{"chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1031.","ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria.","mla":"Capek, Daniel. Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1031.","ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:10.15479/AT:ISTA:TH_1031","apa":"Capek, D. (2018). Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1031"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8004","author":[{"id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Capek","full_name":"Capek, Daniel","orcid":"0000-0001-5199-9940"}],"article_processing_charge":"No","title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2018","day":"22","page":"95","date_published":"2018-06-22T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1031","date_created":"2018-12-11T11:44:21Z"},{"status":"public","pubrep_id":"1059","type":"dissertation","_id":"26","department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:14Z","ddc":["576","579"],"supervisor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"date_updated":"2023-09-07T12:48:43Z","month":"10","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"704","status":"public"}]},"file":[{"checksum":"413cbce1cd1debeae3abe2a25dbc70d1","file_id":"5941","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Steinrueck_final.docx","date_created":"2019-02-08T10:51:22Z","creator":"dernst","file_size":9190845,"date_updated":"2020-07-14T12:45:43Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"3def8b7854c8b42d643597ce0215efac","file_id":"5942","embargo":"2019-11-02","creator":"dernst","date_updated":"2021-02-11T11:17:14Z","file_size":7521973,"date_created":"2019-02-08T10:51:22Z","file_name":"Thesis_Steinrueck_final.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","title":"The influence of sequence context on the evolution of bacterial gene expression","author":[{"orcid":"0000-0003-1229-9719","full_name":"Steinrück, Magdalena","last_name":"Steinrück","first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8029","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Steinrück, Magdalena. The Influence of Sequence Context on the Evolution of Bacterial Gene Expression. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1059.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","apa":"Steinrück, M. (2018). The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1059","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:10.15479/AT:ISTA:th1059","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1059.","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/AT:ISTA:th1059","date_published":"2018-10-30T00:00:00Z","date_created":"2018-12-11T11:44:14Z","page":"109","day":"30","has_accepted_license":"1","year":"2018"},{"date_published":"2018-11-01T00:00:00Z","doi":"10.1063/1.5038258","date_created":"2019-01-10T14:22:23Z","day":"01","publication":"Review of Scientific Instruments","isi":1,"year":"2018","publisher":"AIP Publishing","quality_controlled":"1","oa":1,"title":"30 GHz-voltage controlled oscillator operating at 4 K","author":[{"first_name":"Arne","last_name":"Hollmann","full_name":"Hollmann, Arne"},{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kucharski","full_name":"Kucharski, Maciej","first_name":"Maciej"},{"full_name":"Kissinger, Dietmar","last_name":"Kissinger","first_name":"Dietmar"},{"first_name":"Gunter","last_name":"Fischer","full_name":"Fischer, Gunter"},{"full_name":"Schreiber, Lars R.","last_name":"Schreiber","first_name":"Lars R."}],"article_processing_charge":"No","external_id":{"arxiv":["1804.09522"],"isi":["000451735700054"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","apa":"Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., & Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258","ama":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 2018;89(11). doi:10.1063/1.5038258","short":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018).","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."},"article_number":"114701","volume":89,"related_material":{"record":[{"relation":"dissertation_contains","id":"10058","status":"public"}]},"issue":"11","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00346748"]},"publication_status":"published","month":"11","intvolume":" 89","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.09522"}],"oa_version":"Preprint","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."}],"department":[{"_id":"GeKa"}],"date_updated":"2024-03-27T23:30:26Z","status":"public","type":"journal_article","_id":"5816"},{"citation":{"short":"M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018.","ieee":"M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018.","apa":"Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072","ama":"Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:10.15479/AT:ISTA:th1072","mla":"Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072.","ista":"Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria.","chicago":"Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta"}],"title":"Genetic determinants of antibiotic resistance evolution","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2018","has_accepted_license":"1","day":"28","page":"91","date_created":"2019-04-09T13:57:15Z","date_published":"2018-12-28T00:00:00Z","doi":"10.15479/AT:ISTA:th1072","_id":"6263","type":"dissertation","status":"public","date_updated":"2023-09-22T09:20:37Z","supervisor":[{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","last_name":"Bollenbach","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570","576","579"],"file_date_updated":"2021-02-11T11:17:17Z","department":[{"_id":"ToBo"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"LifeSc"}],"abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"12","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2020-01-25","file_id":"6264","checksum":"fc60585c9eaad868ac007004ef130908","creator":"dernst","file_size":5656866,"date_updated":"2021-02-11T11:17:17Z","file_name":"2018_Thesis_Lukacisinova.pdf","date_created":"2019-04-09T13:49:24Z"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"6265","checksum":"264057ec0a92ab348cc83b41f021ba92","file_size":5168054,"date_updated":"2020-07-14T12:47:25Z","creator":"dernst","file_name":"2018_Thesis_Lukacisinova_source.docx","date_created":"2019-04-09T13:49:23Z"}],"related_material":{"record":[{"status":"public","id":"1619","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"696"},{"id":"1027","status":"public","relation":"part_of_dissertation"}]}},{"_id":"544","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"990","status":"public","date_updated":"2024-03-27T23:30:29Z","ddc":["570"],"department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:46:56Z","abstract":[{"text":"Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 8","month":"03","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"4905","checksum":"7d9d28b915159078a4ca7add568010e8","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf","date_created":"2018-12-12T10:11:48Z","file_size":2251222,"date_updated":"2020-07-14T12:46:56Z","creator":"system"}],"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"volume":8,"related_material":{"record":[{"id":"6530","relation":"research_paper"},{"relation":"research_paper","id":"6543"},{"relation":"dissertation_contains","status":"public","id":"11193"},{"id":"6546","status":"public","relation":"dissertation_contains"}]},"issue":"3","project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The role of Drosophila TNF alpha in immune cell invasion","grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_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"},{"call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077"}],"citation":{"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.","ieee":"A. György et al., “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” G3: Genes, Genomes, Genetics, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.","apa":"György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.117.300452","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000426693300011"]},"article_processing_charge":"No","publist_id":"7271","author":[{"last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roblek","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko","first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7190-0776","full_name":"Ratheesh, Aparna","last_name":"Ratheesh","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","first_name":"Aparna"},{"first_name":"Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","full_name":"Valosková, Katarina","last_name":"Valosková"},{"last_name":"Belyaeva","full_name":"Belyaeva, Vera","first_name":"Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wachner","full_name":"Wachner, Stephanie","first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Matsubayashi, Yutaka","last_name":"Matsubayashi","first_name":"Yutaka"},{"first_name":"Besaiz","last_name":"Sanchez Sanchez","full_name":"Sanchez Sanchez, Besaiz"},{"last_name":"Stramer","full_name":"Stramer, Brian","first_name":"Brian"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"title":"Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues","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, ","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","year":"2018","has_accepted_license":"1","isi":1,"publication":"G3: Genes, Genomes, Genetics","day":"01","page":"845 - 857","date_created":"2018-12-11T11:47:05Z","date_published":"2018-03-01T00:00:00Z","doi":"10.1534/g3.117.300452"},{"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."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 223","publication_status":"published","file":[{"date_created":"2018-12-12T10:15:36Z","file_name":"IST-2018-1013-v1+1_2018_Kleindienst_Differential.pdf","date_updated":"2020-07-14T12:47:20Z","file_size":5542926,"creator":"system","checksum":"a55b3103476ecb5f4f983d8801807e8b","file_id":"5157","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"3","volume":223,"related_material":{"record":[{"status":"public","id":"9562","relation":"dissertation_contains"}]},"ec_funded":1,"_id":"612","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"1013","date_updated":"2024-03-27T23:30:30Z","ddc":["571"],"file_date_updated":"2020-07-14T12:47:20Z","department":[{"_id":"RySh"}],"quality_controlled":"1","publisher":"Springer","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Brain Structure and Function","page":"1565 - 1587","doi":"10.1007/s00429-017-1568-y","date_published":"2018-04-01T00:00:00Z","date_created":"2018-12-11T11:47:29Z","project":[{"call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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.","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","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.","short":"R. Luján, C. Aguado, F. Ciruela, J. Cózar, D. Kleindienst, L. De La Ossa, B. Bettler, K. Wickman, M. Watanabe, R. Shigemoto, Y. Fukazawa, Brain Structure and Function 223 (2018) 1565–1587.","mla":"Luján, Rafael, et al. “Differential Association of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain Structure and Function, vol. 223, no. 3, Springer, 2018, pp. 1565–87, doi:10.1007/s00429-017-1568-y."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7192","author":[{"first_name":"Rafael","full_name":"Luján, Rafael","last_name":"Luján"},{"last_name":"Aguado","full_name":"Aguado, Carolina","first_name":"Carolina"},{"full_name":"Ciruela, Francisco","last_name":"Ciruela","first_name":"Francisco"},{"first_name":"Javier","last_name":"Cózar","full_name":"Cózar, Javier"},{"first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","full_name":"Kleindienst, David"},{"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"},{"full_name":"Watanabe, Masahiko","last_name":"Watanabe","first_name":"Masahiko"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"}],"external_id":{"isi":["000428419500030"]},"article_processing_charge":"No","title":"Differential association of GABAB receptors with their effector ion channels in Purkinje cells"},{"_id":"21","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2024-03-27T23:30:31Z","file_date_updated":"2020-07-14T12:45:28Z","department":[{"_id":"PeJo"}],"oa_version":"Published Version","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"}],"intvolume":" 9","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-17T15:41:57Z","file_name":"2018_NatureComm_Espinoza.pdf","date_updated":"2020-07-14T12:45:28Z","file_size":4651930,"creator":"dernst","checksum":"9fe2a63bd95a5067d896c087d07998f3","file_id":"5715","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"id":"6363","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/","relation":"press_release","description":"News on IST Homepage"}]},"volume":9,"issue":"1","article_number":"4605","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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","short":"C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications 9 (2018).","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.","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.","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.","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."},"title":"Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus","article_processing_charge":"No","external_id":{"isi":["000449069700009"]},"author":[{"last_name":"Espinoza Martinez","orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"},{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","last_name":"Guzmán","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242"},{"last_name":"Zhang","full_name":"Zhang, Xiaomin","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8034","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..","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Communications","day":"02","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:12Z","doi":"10.1038/s41467-018-06899-3","date_published":"2018-11-02T00:00:00Z"},{"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"68a055b1aaa241cc38375083cf832a7d","file_id":"5696","date_updated":"2020-07-14T12:47:34Z","file_size":1078309,"creator":"dernst","date_created":"2018-12-17T12:08:00Z","file_name":"2018_CONCUR_Chatterjee.pdf"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-95977-087-3"]},"ec_funded":1,"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"volume":118,"oa_version":"Published Version","abstract":[{"text":"Crypto-currencies are digital assets designed to work as a medium of exchange, e.g., Bitcoin, but they are susceptible to attacks (dishonest behavior of participants). A framework for the analysis of attacks in crypto-currencies requires (a) modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior; (b) concurrent interactions between participants; and (c) analysis of long-term monetary gains. Traditional game-theoretic approaches for the analysis of security protocols consider either qualitative temporal properties such as safety and termination, or the very special class of one-shot (stateless) games. However, to analyze general attacks on protocols for crypto-currencies, both stateful analysis and quantitative objectives are necessary. In this work our main contributions are as follows: (a) we show how a class of concurrent mean-payo games, namely ergodic games, can model various attacks that arise naturally in crypto-currencies; (b) we present the first practical implementation of algorithms for ergodic games that scales to model realistic problems for crypto-currencies; and (c) we present experimental results showing that our framework can handle games with thousands of states and millions of transitions.","lang":"eng"}],"intvolume":" 118","month":"09","alternative_title":["LIPIcs"],"scopus_import":"1","ddc":["000"],"date_updated":"2024-03-27T23:30:33Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:34Z","_id":"66","status":"public","conference":{"name":"CONCUR: Conference on Concurrency Theory","location":"Beijing, China","end_date":"2018-09-07","start_date":"2018-09-04"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","day":"01","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:27Z","doi":"10.4230/LIPIcs.CONCUR.2018.11","date_published":"2018-09-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","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.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, Y. Velner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","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.","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.","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."},"title":"Ergodic mean-payoff games for the analysis of attacks in crypto-currencies","external_id":{"arxiv":["1806.03108"]},"article_processing_charge":"No","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"publist_id":"7988","article_number":"11","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}]},{"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:46:00Z","file_size":1394993,"date_created":"2018-12-17T15:45:49Z","file_name":"2018_ESOP_Chatterjee.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9c8a8338c571903b599b6ca93abd2cce","file_id":"5716"}],"ec_funded":1,"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"volume":10801,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 10801","month":"04","date_updated":"2024-03-27T23:30:33Z","ddc":["000"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:00Z","_id":"311","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"end_date":"2018-04-19","location":"Thessaloniki, Greece","start_date":"2018-04-16","name":"ESOP: European Symposium on Programming"},"type":"conference","status":"public","year":"2018","has_accepted_license":"1","day":"01","page":"739 - 767","date_created":"2018-12-11T11:45:45Z","doi":"10.1007/978-3-319-89884-1_26","date_published":"2018-04-01T00:00:00Z","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).","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"short":"K. Chatterjee, A.K. Goharshady, Y. Velner, in:, Springer, 2018, pp. 739–767.","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.","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","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.","ista":"Chatterjee K, Goharshady AK, Velner Y. 2018. Quantitative analysis of smart contracts. ESOP: European Symposium on Programming, LNCS, vol. 10801, 739–767.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"publist_id":"7554","title":"Quantitative analysis of smart contracts","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}]},{"ddc":["000"],"date_updated":"2024-03-27T23:30:34Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:27Z","_id":"6340","status":"public","type":"conference","conference":{"name":"IEEE International Conference on Blockchain","start_date":"2018-07-30","end_date":"2018-08-03","location":"Halifax, Canada"},"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"file":[{"creator":"akafshda","date_updated":"2020-07-14T12:47:27Z","file_size":624338,"date_created":"2019-04-18T10:36:39Z","file_name":"blockchain2018.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"b25c9bb7cf6e7e6634e692d26d41ead8","file_id":"6341"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-5386-7975-3 "]},"publication_status":"published","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"oa_version":"Submitted Version","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*."}],"month":"09","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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"},"title":"Secure Credit Reporting on the Blockchain","author":[{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"first_name":"Ali","last_name":"Behrouz","full_name":"Behrouz, Ali"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"article_processing_charge":"No","external_id":{"isi":["000481634500196"],"arxiv":["1805.09104"]},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"day":"01","publication":"Proceedings of the IEEE International Conference on Blockchain","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1109/Cybermatics_2018.2018.00231","date_published":"2018-09-01T00:00:00Z","date_created":"2019-04-18T10:37:35Z","page":"1343-1348","quality_controlled":"1","publisher":"IEEE","oa":1},{"issue":"3","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1437"},{"status":"public","id":"5441","relation":"earlier_version"},{"relation":"earlier_version","id":"5442","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8934"}]},"volume":40,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0164-0925"]},"publication_status":"published","month":"08","intvolume":" 40","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1510.07565","open_access":"1"}],"oa_version":"Preprint","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"}],"department":[{"_id":"KrCh"}],"date_updated":"2024-03-27T23:30:34Z","status":"public","type":"journal_article","_id":"6009","date_published":"2018-08-01T00:00:00Z","doi":"10.1145/3210257","date_created":"2019-02-14T14:31:52Z","day":"01","publication":"ACM Transactions on Programming Languages and Systems","isi":1,"year":"2018","quality_controlled":"1","publisher":"Association for Computing Machinery (ACM)","oa":1,"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389"},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"}],"article_processing_charge":"No","external_id":{"isi":["000444694800001"],"arxiv":["1510.07565"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","short":"K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 40 (2018).","ama":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 2018;40(3). doi:10.1145/3210257","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.","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."},"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"article_number":"9"},{"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"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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.","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."},"title":"Computational approaches for stochastic shortest path on succinct MDPs","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir"},{"full_name":"Okati, Nastaran","last_name":"Okati","first_name":"Nastaran"}],"external_id":{"arxiv":["1804.08984"],"isi":["000764175404118"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"IJCAI","oa":1,"day":"17","publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","isi":1,"year":"2018","doi":"10.24963/ijcai.2018/653","date_published":"2018-07-17T00:00:00Z","date_created":"2019-02-13T13:26:27Z","page":"4700-4707","_id":"5977","status":"public","type":"conference","conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","location":"Stockholm, Sweden","end_date":"2018-07-19","start_date":"2018-07-13"},"date_updated":"2024-03-27T23:30:34Z","department":[{"_id":"KrCh"}],"oa_version":"Preprint","abstract":[{"text":"We consider the stochastic shortest path (SSP)problem for succinct Markov decision processes(MDPs), where the MDP consists of a set of vari-ables, and a set of nondeterministic rules that up-date the variables. First, we show that several ex-amples from the AI literature can be modeled assuccinct MDPs. Then we present computationalapproaches for upper and lower bounds for theSSP problem: (a) for computing upper bounds, ourmethod is polynomial-time in the implicit descrip-tion of the MDP; (b) for lower bounds, we present apolynomial-time (in the size of the implicit descrip-tion) reduction to quadratic programming. Our ap-proach is applicable even to infinite-state MDPs.Finally, we present experimental results to demon-strate the effectiveness of our approach on severalclassical examples from the AI literature.","lang":"eng"}],"month":"07","intvolume":" 2018","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.08984"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-099924112-7"],"issn":["10450823"]},"publication_status":"published","volume":2018,"related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"ec_funded":1},{"citation":{"ista":"Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942.","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.","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","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","short":"J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7401","author":[{"first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179"},{"first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide"},{"last_name":"Schaner","full_name":"Schaner, Markus","first_name":"Markus","id":"316CE034-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000433113900004"]},"title":"Relaminarization by steady modification of the streamwise velocity profile in a pipe","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Flow Turbulence and Combustion","page":"919 - 942","doi":"10.1007/s10494-018-9896-4","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:46:23Z","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2024-03-27T23:30:36Z","ddc":["530"],"file_date_updated":"2020-07-14T12:46:25Z","department":[{"_id":"BjHo"}],"_id":"422","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"file_id":"5717","checksum":"d7c0bade150faabca150b0a9986e60ca","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_FlowTurbulenceCombust_Kuehnen.pdf","date_created":"2018-12-17T15:52:37Z","file_size":2210020,"date_updated":"2020-07-14T12:46:25Z","creator":"dernst"}],"language":[{"iso":"eng"}],"volume":100,"related_material":{"record":[{"id":"7258","status":"public","relation":"dissertation_contains"}]},"issue":"4","ec_funded":1,"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."}],"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 100"},{"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"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.","date_published":"2018-01-08T00:00:00Z","doi":"10.1038/s41567-017-0018-3","date_created":"2018-12-11T11:46:36Z","page":"386-390","day":"08","publication":"Nature Physics","isi":1,"year":"2018","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"737549","name":"Eliminating turbulence in oil pipelines"}],"title":"Destabilizing turbulence in pipe flow","publist_id":"7360","author":[{"last_name":"Kühnen","full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179","first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide","last_name":"Scarselli","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271"},{"orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl"},{"last_name":"Willis","full_name":"Willis, Ashley","first_name":"Ashley"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"article_processing_charge":"No","external_id":{"isi":["000429434100020"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kühnen, Jakob, Baofang Song, Davide Scarselli, Nazmi B Budanur, Michael Riedl, Ashley Willis, Marc Avila, and Björn Hof. “Destabilizing Turbulence in Pipe Flow.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-017-0018-3.","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.","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","short":"J. Kühnen, B. Song, D. Scarselli, N.B. Budanur, M. Riedl, A. Willis, M. Avila, B. Hof, Nature Physics 14 (2018) 386–390.","ieee":"J. Kühnen et al., “Destabilizing turbulence in pipe flow,” Nature Physics, vol. 14. Nature Publishing Group, pp. 386–390, 2018."},"month":"01","intvolume":" 14","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.06543"}],"oa_version":"Preprint","abstract":[{"text":"Turbulence is the major cause of friction losses in transport processes and it is responsible for a drastic drag increase in flows over bounding surfaces. While much effort is invested into developing ways to control and reduce turbulence intensities, so far no methods exist to altogether eliminate turbulence if velocities are sufficiently large. We demonstrate for pipe flow that appropriate distortions to the velocity profile lead to a complete collapse of turbulence and subsequently friction losses are reduced by as much as 90%. Counterintuitively, the return to laminar motion is accomplished by initially increasing turbulence intensities or by transiently amplifying wall shear. Since neither the Reynolds number nor the shear stresses decrease (the latter often increase), these measures are not indicative of turbulence collapse. Instead, an amplification mechanism measuring the interaction between eddies and the mean shear is found to set a threshold below which turbulence is suppressed beyond recovery.","lang":"eng"}],"volume":14,"related_material":{"record":[{"relation":"dissertation_contains","id":"12726","status":"public"},{"id":"14530","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"7258","status":"public"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"461","department":[{"_id":"BjHo"}],"date_updated":"2024-03-27T23:30:36Z"},{"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"citation":{"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.","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","short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","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.","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.","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)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000423718600034"]},"article_processing_charge":"Yes","author":[{"full_name":"Prat, Tomas","last_name":"Prat","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas"},{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny"},{"first_name":"Wim","full_name":"Grunewald, Wim","last_name":"Grunewald"},{"last_name":"Vasileva","full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K"},{"last_name":"Molnar","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"first_name":"Markus","last_name":"Schmid","full_name":"Schmid, Markus"},{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"publist_id":"7373","title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","year":"2018","isi":1,"has_accepted_license":"1","publication":"PLoS Genetics","day":"29","date_created":"2018-12-11T11:46:32Z","date_published":"2018-01-29T00:00:00Z","doi":"10.1371/journal.pgen.1007177","_id":"449","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"967","status":"public","date_updated":"2024-03-27T23:30:37Z","ddc":["581"],"file_date_updated":"2020-07-14T12:46:30Z","department":[{"_id":"JiFr"}],"abstract":[{"text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 14","month":"01","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":24709062,"date_updated":"2020-07-14T12:46:30Z","creator":"system","file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","date_created":"2018-12-12T10:10:52Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4843","checksum":"0276d66788ec076f4924164a39e6a712"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"1127","relation":"dissertation_contains"},{"status":"public","id":"7172","relation":"dissertation_contains"},{"status":"public","id":"8822","relation":"dissertation_contains"}]},"volume":14,"issue":"1"},{"date_updated":"2024-03-27T23:30:37Z","ddc":["581"],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:45:20Z","_id":"191","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"file_name":"2018_ScientificReports_Grones.pdf","date_created":"2018-12-17T15:38:56Z","creator":"dernst","file_size":2413876,"date_updated":"2020-07-14T12:45:20Z","file_id":"5714","checksum":"266b03f4fb8198e83141617aaa99dcab","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"1","related_material":{"record":[{"status":"public","id":"8822","relation":"dissertation_contains"}]},"volume":8,"ec_funded":1,"abstract":[{"text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 8","citation":{"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.","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.","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","ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-28188-1","ieee":"P. Grones et al., “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” Scientific Reports, vol. 8, no. 1. Springer, 2018.","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports, vol. 8, no. 1, 10279, Springer, 2018, doi:10.1038/s41598-018-28188-1."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7729","author":[{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"full_name":"Abas, Melinda F","last_name":"Abas","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda F"},{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub"},{"full_name":"Jones, Angharad","last_name":"Jones","first_name":"Angharad"},{"first_name":"Sascha","full_name":"Waidmann, Sascha","last_name":"Waidmann"},{"full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"article_processing_charge":"No","external_id":{"isi":["000437673200053"]},"title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","article_number":"10279","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"isi":1,"has_accepted_license":"1","year":"2018","day":"06","publication":"Scientific Reports","date_published":"2018-07-06T00:00:00Z","doi":"10.1038/s41598-018-28188-1","date_created":"2018-12-11T11:45:06Z","publisher":"Springer","quality_controlled":"1","oa":1},{"_id":"15","type":"journal_article","status":"public","date_updated":"2024-03-27T23:30:39Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221"}],"month":"05","intvolume":" 19","publication_status":"published","language":[{"iso":"eng"}],"volume":19,"issue":"6","related_material":{"record":[{"relation":"dissertation_contains","id":"6891","status":"public"}]},"ec_funded":1,"project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014"},{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"citation":{"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.","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.","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","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8040","author":[{"first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav"},{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","last_name":"Kopf","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F"},{"last_name":"Gärtner","full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R"},{"first_name":"Jun","last_name":"Abe","full_name":"Abe, Jun"},{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stein","full_name":"Stein, Jens","first_name":"Jens"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"article_processing_charge":"No","external_id":{"pmid":["29777221"],"isi":["000433041500026"]},"title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","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).","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"isi":1,"year":"2018","day":"18","publication":"Nature Immunology","page":"606 - 616","doi":"10.1038/s41590-018-0109-z","date_published":"2018-05-18T00:00:00Z","date_created":"2018-12-11T11:44:10Z"},{"file":[{"file_id":"5299","checksum":"6644ba698206eda32b0abf09128e63e3","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:43Z","file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","date_updated":"2020-07-14T12:46:29Z","file_size":11352389,"creator":"system"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2331-8325"]},"publication_status":"published","related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"volume":8,"issue":"1","ec_funded":1,"oa_version":"Published Version","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."}],"month":"01","intvolume":" 8","ddc":["576","581"],"date_updated":"2024-03-27T23:30:42Z","file_date_updated":"2020-07-14T12:46:29Z","department":[{"_id":"JiFr"},{"_id":"Bio"}],"_id":"442","status":"public","pubrep_id":"970","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"05","publication":"Bio-protocol","has_accepted_license":"1","year":"2018","date_published":"2018-01-05T00:00:00Z","doi":"10.21769/BioProtoc.2685","date_created":"2018-12-11T11:46:30Z","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]. ","publisher":"Bio-protocol","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018)."},"title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","publist_id":"7381","author":[{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}]},{"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","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.","page":"1717 - 1727","date_created":"2018-12-11T11:44:05Z","date_published":"2018-11-19T00:00:00Z","doi":"10.1038/s41593-018-0266-2","year":"2018","has_accepted_license":"1","isi":1,"publication":"Nature Neuroscience","day":"19","project":[{"_id":"254BA948-B435-11E9-9278-68D0E5697425","name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299"}],"external_id":{"isi":["000451324700010"]},"article_processing_charge":"No","author":[{"full_name":"Deliu, Elena","orcid":"0000-0002-7370-5293","last_name":"Deliu","first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arecco","full_name":"Arecco, Niccoló","first_name":"Niccoló"},{"full_name":"Morandell, Jasmin","last_name":"Morandell","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","last_name":"Dotter","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena"},{"last_name":"Girardot","full_name":"Girardot, Charles","first_name":"Charles"},{"first_name":"Eva","full_name":"Käsper, Eva","last_name":"Käsper"},{"id":"C50A9596-02D0-11E9-976E-E38CFE5CBC1D","first_name":"Alena","last_name":"Kozlova","full_name":"Kozlova, Alena"},{"last_name":"Kishi","full_name":"Kishi, Kasumi","first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"id":"B6467F20-02D0-11E9-BDA5-E960C241894A","first_name":"Ilaria","orcid":"0000-0002-9529-4464","full_name":"Chiaradia, Ilaria","last_name":"Chiaradia"},{"first_name":"Kyung","last_name":"Noh","full_name":"Noh, Kyung"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8054","title":"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition","citation":{"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.","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.","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":" 21","month":"11","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"}],"oa_version":"Submitted Version","issue":"12","volume":21,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"6074","status":"public","relation":"popular_science"},{"status":"public","id":"12364","relation":"dissertation_contains"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:45:58Z","file_size":8167169,"date_created":"2019-04-09T07:41:57Z","file_name":"2017_NatureNeuroscience_Deliu.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6255","checksum":"60abd0f05b7cdc08a6b0ec460884084f"}],"article_type":"original","type":"journal_article","pubrep_id":"1071","status":"public","_id":"3","department":[{"_id":"GaNo"},{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:45:58Z","date_updated":"2024-03-27T23:30:44Z","ddc":["570"]},{"scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30429320","open_access":"1"}],"month":"11","intvolume":" 115","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","issue":"48","volume":115,"related_material":{"record":[{"status":"public","id":"10293","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/no-cooperation-without-open-communication/"}]},"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"2","department":[{"_id":"KrCh"}],"date_updated":"2024-03-27T23:30:44Z","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"page":"12241-12246","doi":"10.1073/pnas.1810565115","date_published":"2018-11-27T00:00:00Z","date_created":"2018-12-11T11:44:05Z","isi":1,"year":"2018","day":"27","publication":"PNAS","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"author":[{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"external_id":{"isi":["000451351000063"],"pmid":["30429320"]},"article_processing_charge":"No","title":"Indirect reciprocity with private, noisy, and incomplete information","citation":{"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.","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.","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","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","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.","short":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"title":"Evolutionary potential of transcription factors for gene regulatory rewiring","external_id":{"isi":["000447947600021"]},"article_processing_charge":"No","author":[{"full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"publist_id":"7987","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.","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","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","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.","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.","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."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"date_created":"2018-12-11T11:44:27Z","doi":"10.1038/s41559-018-0651-y","date_published":"2018-09-10T00:00:00Z","page":"1633 - 1643","publication":"Nature Ecology and Evolution","day":"10","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:47:37Z","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"JoBo"}],"ddc":["570"],"date_updated":"2024-03-27T23:30:48Z","status":"public","article_type":"original","type":"journal_article","_id":"67","ec_funded":1,"related_material":{"record":[{"relation":"popular_science","id":"5585","status":"public"},{"status":"public","id":"6371","relation":"dissertation_contains"}]},"issue":"10","volume":2,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"383a2e2c944a856e2e821ec8e7bf71b6","file_id":"7830","creator":"dernst","file_size":1135973,"date_updated":"2020-07-14T12:47:37Z","file_name":"2018_NatureEcology_Igler.pdf","date_created":"2020-05-14T11:28:52Z"}],"publication_status":"published","intvolume":" 2","month":"09","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}]},{"date_updated":"2024-03-27T23:30:48Z","citation":{"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.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","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","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","mla":"Igler, Claudia, et al. 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Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"author":[{"last_name":"Igler","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"},{"last_name":"Lagator","full_name":"Lagator, Mato","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"article_processing_charge":"No","title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:07Z","_id":"5585","type":"research_data","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)"},"status":"public","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"},{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","datarep_id":"108","year":"2018","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","checksum":"1435781526c77413802adee0d4583cce","file_id":"5611","creator":"system","file_size":16507,"date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-108-v1+1_data_figures.xlsx","date_created":"2018-12-12T13:02:45Z"}],"day":"20","date_published":"2018-07-20T00:00:00Z","related_material":{"record":[{"relation":"research_paper","id":"67","status":"public"},{"relation":"research_paper","id":"6371","status":"public"}]},"doi":"10.15479/AT:ISTA:108","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2018-12-12T12:31:40Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Mean repression values and standard error of the mean are given for all operator mutant libraries."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"07"},{"article_processing_charge":"No","publist_id":"6382","author":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"title":"Viewpoint: Microwave quantum states beat the heat","citation":{"chicago":"Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics. American Physical Society, 2017. https://doi.org/10.1103/Physics.10.32.","ista":"Fink JM. 2017. Viewpoint: Microwave quantum states beat the heat. Physics. 10(32).","mla":"Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics, vol. 10, no. 32, American Physical Society, 2017, doi:10.1103/Physics.10.32.","apa":"Fink, J. M. (2017). Viewpoint: Microwave quantum states beat the heat. Physics. American Physical Society. https://doi.org/10.1103/Physics.10.32","ama":"Fink JM. Viewpoint: Microwave quantum states beat the heat. Physics. 2017;10(32). doi:10.1103/Physics.10.32","short":"J.M. Fink, Physics 10 (2017).","ieee":"J. M. Fink, “Viewpoint: Microwave quantum states beat the heat,” Physics, vol. 10, no. 32. American Physical Society, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2018-12-11T11:49:41Z","date_published":"2017-03-27T00:00:00Z","doi":"10.1103/Physics.10.32","year":"2017","has_accepted_license":"1","publication":"Physics","day":"27","article_type":"review","type":"journal_article","status":"public","_id":"1013","department":[{"_id":"JoFi"}],"file_date_updated":"2019-10-24T11:38:14Z","date_updated":"2022-06-07T10:58:31Z","ddc":["530"],"intvolume":" 10","month":"03","abstract":[{"lang":"eng","text":"From microwave ovens to satellite television to the GPS and data services on our mobile phones, microwave technology is everywhere today. But one technology that has so far failed to prove its worth in this wavelength regime is quantum communication that uses the states of single photons as information carriers. This is because single microwave photons, as opposed to classical microwave signals, are extremely vulnerable to noise from thermal excitations in the channels through which they travel. Two new independent studies, one by Ze-Liang Xiang at Technische Universität Wien (Vienna), Austria, and colleagues [1] and another by Benoît Vermersch at the University of Innsbruck, also in Austria, and colleagues [2] now describe a theoretical protocol for microwave quantum communication that is resilient to thermal and other types of noise. Their approach could become a powerful technique to establish fast links between superconducting data processors in a future all-microwave quantum network."}],"oa_version":"Published Version","issue":"32","volume":10,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6968","success":1,"creator":"dernst","date_updated":"2019-10-24T11:38:14Z","file_size":193622,"date_created":"2019-10-24T11:38:14Z","file_name":"2017_Physics_Fink.pdf"}]},{"article_type":"letter_note","type":"journal_article","status":"public","keyword":["biophysics"],"_id":"10126","date_updated":"2021-11-03T10:02:45Z","extern":"1","main_file_link":[{"url":"https://www.cell.com/biophysj/fulltext/S0006-3495(16)33153-8","open_access":"1"}],"month":"02","intvolume":" 112","oa_version":"Published Version","volume":112,"issue":"3","publication_identifier":{"issn":["0006-3495"]},"publication_status":"published","language":[{"iso":"eng"}],"article_number":"391a","author":[{"full_name":"Vahid Belarghou, Afshin","last_name":"Vahid Belarghou","first_name":"Afshin"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Timon","full_name":"Idema, Timon","last_name":"Idema"}],"article_processing_charge":"No","title":"Curvature mediated interactions in highly curved membranes","citation":{"chicago":"Vahid Belarghou, Afshin, Anđela Šarić, and Timon Idema. “Curvature Mediated Interactions in Highly Curved Membranes.” Biophysical Journal. Elsevier , 2017. https://doi.org/10.1016/j.bpj.2016.11.2123.","ista":"Vahid Belarghou A, Šarić A, Idema T. 2017. Curvature mediated interactions in highly curved membranes. Biophysical Journal. 112(3), 391a.","mla":"Vahid Belarghou, Afshin, et al. “Curvature Mediated Interactions in Highly Curved Membranes.” Biophysical Journal, vol. 112, no. 3, 391a, Elsevier , 2017, doi:10.1016/j.bpj.2016.11.2123.","ama":"Vahid Belarghou A, Šarić A, Idema T. Curvature mediated interactions in highly curved membranes. Biophysical Journal. 2017;112(3). doi:10.1016/j.bpj.2016.11.2123","apa":"Vahid Belarghou, A., Šarić, A., & Idema, T. (2017). Curvature mediated interactions in highly curved membranes. Biophysical Journal. Elsevier . https://doi.org/10.1016/j.bpj.2016.11.2123","short":"A. Vahid Belarghou, A. Šarić, T. Idema, Biophysical Journal 112 (2017).","ieee":"A. Vahid Belarghou, A. Šarić, and T. Idema, “Curvature mediated interactions in highly curved membranes,” Biophysical Journal, vol. 112, no. 3. Elsevier , 2017."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Elsevier ","quality_controlled":"1","oa":1,"date_published":"2017-02-03T00:00:00Z","doi":"10.1016/j.bpj.2016.11.2123","date_created":"2021-10-12T07:47:55Z","year":"2017","day":"03","publication":"Biophysical Journal"},{"status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/3.0/legalcode","image":"/images/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0)","short":"CC BY-ND (3.0)"},"_id":"10175","file_date_updated":"2021-10-28T15:02:56Z","extern":"1","ddc":["510"],"date_updated":"2021-10-28T15:16:25Z","month":"11","intvolume":" 24","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study periodic homogenization by Γ-convergence of integral functionals with integrands W(x,ξ) having no polynomial growth and which are both not necessarily continuous with respect to the space variable and not necessarily convex with respect to the matrix variable. This allows to deal with homogenization of composite hyperelastic materials consisting of two or more periodic components whose the energy densities tend to infinity as the volume of matter tends to zero, i.e., W(x,ξ)=∑j∈J1Vj(x)Hj(ξ) where {Vj}j∈J is a finite family of open disjoint subsets of RN, with |∂Vj|=0 for all j∈J and ∣∣RN∖⋃j∈JVj|=0, and, for each j∈J, Hj(ξ)→∞ as detξ→0. In fact, our results apply to integrands of type W(x,ξ)=a(x)H(ξ) when H(ξ)→∞ as detξ→0 and a∈L∞(RN;[0,∞[) is 1-periodic and is either continuous almost everywhere or not continuous. When a is not continuous, we obtain a density homogenization formula which is a priori different from the classical one by Braides–Müller. Although applications to hyperelasticity are limited due to the fact that our framework is not consistent with the constraint of noninterpenetration of the matter, our results can be of technical interest to analysis of homogenization of integral functionals."}],"volume":24,"issue":"2","license":"https://creativecommons.org/licenses/by-nd/3.0/","file":[{"file_size":850726,"date_updated":"2021-10-28T15:02:56Z","creator":"cziletti","file_name":"2017_AMBP_AnzaHafsa.pdf","date_created":"2021-10-28T15:02:56Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"18f40d13dc5d1e24438260b1875b886f","file_id":"10194"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2118-7436"],"issn":["1259-1734"]},"publication_status":"published","title":"Homogenization of nonconvex unbounded singular integrals","author":[{"full_name":"Anza Hafsa, Omar","last_name":"Anza Hafsa","first_name":"Omar"},{"full_name":"Clozeau, Nicolas","last_name":"Clozeau","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","first_name":"Nicolas"},{"full_name":"Mandallena, Jean-Philippe","last_name":"Mandallena","first_name":"Jean-Philippe"}],"article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"chicago":"Anza Hafsa, Omar, Nicolas Clozeau, and Jean-Philippe Mandallena. “Homogenization of Nonconvex Unbounded Singular Integrals.” Annales Mathématiques Blaise Pascal. Université Clermont Auvergne, 2017. https://doi.org/10.5802/ambp.367.","ista":"Anza Hafsa O, Clozeau N, Mandallena J-P. 2017. Homogenization of nonconvex unbounded singular integrals. Annales mathématiques Blaise Pascal. 24(2), 135–193.","mla":"Anza Hafsa, Omar, et al. “Homogenization of Nonconvex Unbounded Singular Integrals.” Annales Mathématiques Blaise Pascal, vol. 24, no. 2, Université Clermont Auvergne, 2017, pp. 135–93, doi:10.5802/ambp.367.","ama":"Anza Hafsa O, Clozeau N, Mandallena J-P. Homogenization of nonconvex unbounded singular integrals. Annales mathématiques Blaise Pascal. 2017;24(2):135-193. doi:10.5802/ambp.367","apa":"Anza Hafsa, O., Clozeau, N., & Mandallena, J.-P. (2017). Homogenization of nonconvex unbounded singular integrals. Annales Mathématiques Blaise Pascal. Université Clermont Auvergne. https://doi.org/10.5802/ambp.367","short":"O. Anza Hafsa, N. Clozeau, J.-P. Mandallena, Annales Mathématiques Blaise Pascal 24 (2017) 135–193.","ieee":"O. Anza Hafsa, N. Clozeau, and J.-P. Mandallena, “Homogenization of nonconvex unbounded singular integrals,” Annales mathématiques Blaise Pascal, vol. 24, no. 2. Université Clermont Auvergne, pp. 135–193, 2017."},"publisher":"Université Clermont Auvergne","quality_controlled":"1","oa":1,"date_published":"2017-11-20T00:00:00Z","doi":"10.5802/ambp.367","date_created":"2021-10-23T10:54:23Z","page":"135-193","day":"20","publication":"Annales mathématiques Blaise Pascal","has_accepted_license":"1","year":"2017"},{"acknowledgement":"Research supported by Microsoft, the Danish National Research Foundation, the Lundbeck Foundation, Carlsberg Foundation, Villum Foundation, and the European Commission.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"year":"2017","day":"31","publication":"APS Physics, Physical Review Letters","doi":"10.1103/PhysRevLett.118.137701","date_published":"2017-03-31T00:00:00Z","date_created":"2018-12-11T11:44:39Z","article_number":"137701","citation":{"chicago":"Albrecht, S M, Esben Hansen, Andrew P Higginbotham, Ferdinand Kuemmeth, Thomas Jespersen, Jesper Nygård, Peter Krogstrup, Jeroen Danon, Karsten Flensberg, and Charles Marcus. “Transport Signatures of Quasiparticle Poisoning in a Majorana Island.” APS Physics, Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.137701.","ista":"Albrecht SM, Hansen E, Higginbotham AP, Kuemmeth F, Jespersen T, Nygård J, Krogstrup P, Danon J, Flensberg K, Marcus C. 2017. Transport signatures of quasiparticle poisoning in a majorana island. APS Physics, Physical Review Letters. 118(13), 137701.","mla":"Albrecht, S. M., et al. “Transport Signatures of Quasiparticle Poisoning in a Majorana Island.” APS Physics, Physical Review Letters, vol. 118, no. 13, 137701, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.137701.","ama":"Albrecht SM, Hansen E, Higginbotham AP, et al. Transport signatures of quasiparticle poisoning in a majorana island. APS Physics, Physical Review Letters. 2017;118(13). doi:10.1103/PhysRevLett.118.137701","apa":"Albrecht, S. M., Hansen, E., Higginbotham, A. P., Kuemmeth, F., Jespersen, T., Nygård, J., … Marcus, C. (2017). Transport signatures of quasiparticle poisoning in a majorana island. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.137701","short":"S.M. Albrecht, E. Hansen, A.P. Higginbotham, F. Kuemmeth, T. Jespersen, J. Nygård, P. Krogstrup, J. Danon, K. Flensberg, C. Marcus, APS Physics, Physical Review Letters 118 (2017).","ieee":"S. M. Albrecht et al., “Transport signatures of quasiparticle poisoning in a majorana island,” APS Physics, Physical Review Letters, vol. 118, no. 13. American Physical Society, 2017."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7951","author":[{"full_name":"Albrecht, S M","last_name":"Albrecht","first_name":"S M"},{"full_name":"Hansen, Esben","last_name":"Hansen","first_name":"Esben"},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand"},{"first_name":"Thomas","full_name":"Jespersen, Thomas","last_name":"Jespersen"},{"last_name":"Nygård","full_name":"Nygård, Jesper","first_name":"Jesper"},{"first_name":"Peter","last_name":"Krogstrup","full_name":"Krogstrup, Peter"},{"first_name":"Jeroen","full_name":"Danon, Jeroen","last_name":"Danon"},{"first_name":"Karsten","last_name":"Flensberg","full_name":"Flensberg, Karsten"},{"full_name":"Marcus, Charles","last_name":"Marcus","first_name":"Charles"}],"external_id":{"arxiv":["1612.05748"]},"title":"Transport signatures of quasiparticle poisoning in a majorana island","abstract":[{"lang":"eng","text":"We investigate effects of quasiparticle poisoning in a Majorana island with strong tunnel coupling to normal-metal leads. In addition to the main Coulomb blockade diamonds, "shadow" diamonds appear, shifted by 1e in gate voltage, consistent with transport through an excited (poisoned) state of the island. Comparison to a simple model yields an estimate of parity lifetime for the strongly coupled island (∼1 μs) and sets a bound for a weakly coupled island (>10 μs). Fluctuations in the gate-voltage spacing of Coulomb peaks at high field, reflecting Majorana hybridization, are enhanced by the reduced lever arm at strong coupling. When converted from gate voltage to energy units, fluctuations are consistent with previous measurements."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1612.05748","open_access":"1"}],"month":"03","intvolume":" 118","publication_status":"published","language":[{"iso":"eng"}],"volume":118,"issue":"13","_id":"103","type":"journal_article","status":"public","date_updated":"2021-01-12T06:47:47Z","extern":"1"},{"date_created":"2021-11-29T08:51:38Z","doi":"10.7554/elife.30292","date_published":"2017-11-09T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"eLife","day":"09","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","external_id":{"pmid":["29119945"]},"article_processing_charge":"No","author":[{"first_name":"Sebastian Carsten Johannes","last_name":"Helle","full_name":"Helle, Sebastian Carsten Johannes"},{"first_name":"Qian","full_name":"Feng, Qian","last_name":"Feng"},{"full_name":"Aebersold, Mathias J","last_name":"Aebersold","first_name":"Mathias J"},{"last_name":"Hirt","full_name":"Hirt, Luca","first_name":"Luca"},{"first_name":"Raphael R","full_name":"Grüter, Raphael R","last_name":"Grüter"},{"last_name":"Vahid","full_name":"Vahid, Afshin","first_name":"Afshin"},{"last_name":"Sirianni","full_name":"Sirianni, Andrea","first_name":"Andrea"},{"last_name":"Mostowy","full_name":"Mostowy, Serge","first_name":"Serge"},{"first_name":"Jess G","last_name":"Snedeker","full_name":"Snedeker, Jess G"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"Timon","full_name":"Idema, Timon","last_name":"Idema"},{"first_name":"Tomaso","full_name":"Zambelli, Tomaso","last_name":"Zambelli"},{"last_name":"Kornmann","full_name":"Kornmann, Benoît","first_name":"Benoît"}],"title":"Mechanical force induces mitochondrial fission","citation":{"chicago":"Helle, Sebastian Carsten Johannes, Qian Feng, Mathias J Aebersold, Luca Hirt, Raphael R Grüter, Afshin Vahid, Andrea Sirianni, et al. “Mechanical Force Induces Mitochondrial Fission.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30292.","ista":"Helle SCJ, Feng Q, Aebersold MJ, Hirt L, Grüter RR, Vahid A, Sirianni A, Mostowy S, Snedeker JG, Šarić A, Idema T, Zambelli T, Kornmann B. 2017. Mechanical force induces mitochondrial fission. eLife. 6, e30292.","mla":"Helle, Sebastian Carsten Johannes, et al. “Mechanical Force Induces Mitochondrial Fission.” ELife, vol. 6, e30292, eLife Sciences Publications, 2017, doi:10.7554/elife.30292.","short":"S.C.J. Helle, Q. Feng, M.J. Aebersold, L. Hirt, R.R. Grüter, A. Vahid, A. Sirianni, S. Mostowy, J.G. Snedeker, A. Šarić, T. Idema, T. Zambelli, B. Kornmann, ELife 6 (2017).","ieee":"S. C. J. Helle et al., “Mechanical force induces mitochondrial fission,” eLife, vol. 6. eLife Sciences Publications, 2017.","ama":"Helle SCJ, Feng Q, Aebersold MJ, et al. Mechanical force induces mitochondrial fission. eLife. 2017;6. doi:10.7554/elife.30292","apa":"Helle, S. C. J., Feng, Q., Aebersold, M. J., Hirt, L., Grüter, R. R., Vahid, A., … Kornmann, B. (2017). Mechanical force induces mitochondrial fission. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30292"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"e30292","volume":6,"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2017_eLife_Helle.pdf","date_created":"2021-11-29T09:07:41Z","creator":"cchlebak","file_size":6120157,"date_updated":"2021-11-29T09:07:41Z","success":1,"file_id":"10372","checksum":"c35f42dcfb007f6d6c761a27e24c26d3","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"main_file_link":[{"url":"https://elifesciences.org/articles/30292","open_access":"1"}],"scopus_import":"1","intvolume":" 6","month":"11","abstract":[{"text":"Eukaryotic cells are densely packed with macromolecular complexes and intertwining organelles, continually transported and reshaped. Intriguingly, organelles avoid clashing and entangling with each other in such limited space. Mitochondria form extensive networks constantly remodeled by fission and fusion. Here, we show that mitochondrial fission is triggered by mechanical forces. Mechano-stimulation of mitochondria – via encounter with motile intracellular pathogens, via external pressure applied by an atomic force microscope, or via cell migration across uneven microsurfaces – results in the recruitment of the mitochondrial fission machinery, and subsequent division. We propose that MFF, owing to affinity for narrow mitochondria, acts as a membrane-bound force sensor to recruit the fission machinery to mechanically strained sites. Thus, mitochondria adapt to the environment by sensing and responding to biomechanical cues. Our findings that mechanical triggers can be coupled to biochemical responses in membrane dynamics may explain how organelles orderly cohabit in the crowded cytoplasm.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"file_date_updated":"2021-11-29T09:07:41Z","date_updated":"2021-11-29T09:28:14Z","ddc":["572"],"extern":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"status":"public","_id":"10370"},{"intvolume":" 3","month":"11","main_file_link":[{"url":"https://pubs.acs.org/doi/10.1021/acscentsci.7b00392","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Biological membranes have a central role in mediating the organization of membrane-curving proteins, a dynamic process that has proven to be challenging to probe experimentally. Using atomic force microscopy, we capture the hierarchically organized assemblies of Bin/amphiphysin/Rvs (BAR) proteins on supported lipid membranes. Their structure reveals distinct long linear aggregates of proteins, regularly spaced by up to 300 nm. Employing accurate free-energy calculations from large-scale coarse-grained computer simulations, we found that the membrane mediates the interaction among protein filaments as a combination of short- and long-ranged interactions. The long-ranged component acts at strikingly long distances, giving rise to a variety of micron-sized ordered patterns. This mechanism may contribute to the long-ranged spatiotemporal control of membrane remodeling by proteins in the cell."}],"issue":"12","volume":3,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10371","checksum":"1cf3e5e5342f2d728f47560acc3ec560","success":1,"date_updated":"2021-11-29T09:00:40Z","file_size":2635263,"creator":"cchlebak","date_created":"2021-11-29T09:00:40Z","file_name":"2017_ACSCentSci_Simunovic.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2374-7943"],"eissn":["2374-7951"]},"keyword":["general chemical engineering","general chemistry"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"10369","file_date_updated":"2021-11-29T09:00:40Z","ddc":["540"],"extern":"1","date_updated":"2021-11-29T09:28:06Z","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","acknowledgement":"M.S. and G.A.V. acknowledge their research reported in this publication as being supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01-GM063796. Computational resources were provided to M.S. and G.A.V. by the National Science Foundation through XSEDE (Grant TG-MCA94P017, supercomputers Stampede and Gordon), and also by the Blue Waters computing project at the National Center for Supercomputing Applications (University of Illinois at Urbana–Champaign, NSF Awards OCI-0725070 and ACI-1238993). A.Š. acknowledges support from the Human Frontier Science Program and Royal Society. J.M.H. and K.Y.C.L. acknowledge the support from the National Science Foundation (Grant MCB-1413613) and the NSF-supported MRSEC program at the University of Chicago (Grant DMR-1420709). We are grateful to Carsten Mim and Vinzenz Unger of Northwestern University for generously providing us with the protein. We thank all the members of the Voth group for fruitful discussions, especially John M. A. Grime.","date_created":"2021-11-29T08:49:50Z","date_published":"2017-11-21T00:00:00Z","doi":"10.1021/acscentsci.7b00392","page":"1246-1253","publication":"ACS Central Science","day":"21","year":"2017","has_accepted_license":"1","title":"Long-range organization of membrane-curving proteins","external_id":{"pmid":["29296664"]},"article_processing_charge":"No","author":[{"first_name":"Mijo","last_name":"Simunovic","full_name":"Simunovic, Mijo"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"},{"first_name":"J. Michael","last_name":"Henderson","full_name":"Henderson, J. Michael"},{"full_name":"Lee, Ka Yee C.","last_name":"Lee","first_name":"Ka Yee C."},{"first_name":"Gregory A.","last_name":"Voth","full_name":"Voth, Gregory A."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Simunovic, Mijo, et al. “Long-Range Organization of Membrane-Curving Proteins.” ACS Central Science, vol. 3, no. 12, American Chemical Society, 2017, pp. 1246–53, doi:10.1021/acscentsci.7b00392.","apa":"Simunovic, M., Šarić, A., Henderson, J. M., Lee, K. Y. C., & Voth, G. A. (2017). Long-range organization of membrane-curving proteins. ACS Central Science. American Chemical Society. https://doi.org/10.1021/acscentsci.7b00392","ama":"Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. Long-range organization of membrane-curving proteins. ACS Central Science. 2017;3(12):1246-1253. doi:10.1021/acscentsci.7b00392","ieee":"M. Simunovic, A. Šarić, J. M. Henderson, K. Y. C. Lee, and G. A. Voth, “Long-range organization of membrane-curving proteins,” ACS Central Science, vol. 3, no. 12. American Chemical Society, pp. 1246–1253, 2017.","short":"M. Simunovic, A. Šarić, J.M. Henderson, K.Y.C. Lee, G.A. Voth, ACS Central Science 3 (2017) 1246–1253.","chicago":"Simunovic, Mijo, Anđela Šarić, J. Michael Henderson, Ka Yee C. Lee, and Gregory A. Voth. “Long-Range Organization of Membrane-Curving Proteins.” ACS Central Science. American Chemical Society, 2017. https://doi.org/10.1021/acscentsci.7b00392.","ista":"Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. 2017. Long-range organization of membrane-curving proteins. ACS Central Science. 3(12), 1246–1253."}},{"abstract":[{"lang":"eng","text":"Electric charges are conserved. The same would be expected to hold for magnetic charges, yet magnetic monopoles have never been observed. It is therefore surprising that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations, suggest that colloidal particles heated or cooled in certain polar or paramagnetic solvents may behave as if they carry an electric/magnetic charge. Here, we present numerical simulations that show that the field distribution around a pair of such heated/cooled colloidal particles agrees quantitatively with the theoretical predictions for a pair of oppositely charged electric or magnetic monopoles. However, in other respects, the nonequilibrium colloidal particles do not behave as monopoles: They cannot be moved by a homogeneous applied field. The numerical evidence for the monopole-like fields around heated/cooled colloidal particles is crucial because the experimental and numerical determination of forces between such colloidal particles would be complicated by the presence of other effects, such as thermophoresis."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/114/19/4911"}],"month":"04","intvolume":" 114","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":114,"issue":"19","_id":"10373","type":"journal_article","article_type":"original","status":"public","keyword":["multidisciplinary"],"date_updated":"2021-11-29T09:59:12Z","extern":"1","acknowledgement":"P.W. acknowledges many invaluable discussions with Martin Neumann, Chao Zhang, Michiel Sprik, Aleks Reinhardt, Carl Pölking, and Tine Curk. We acknowledge financial support from the Austrian Academy of Sciences through a doctoral (DOC) fellowship (to P.W.), the Austrian Science Fund (FWF) within the Spezialforschungsbereich Vienna Computational Materials Laboratory (Project F41) (C.D.), and the European Union Early Training Network NANOTRANS (Grant 674979 to D. Frenkel). The results presented here have been achieved in part using the Vienna Scientific Cluster.","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"year":"2017","day":"24","publication":"Proceedings of the National Academy of Sciences","page":"4911-4914","date_published":"2017-04-24T00:00:00Z","doi":"10.1073/pnas.1621494114","date_created":"2021-11-29T09:28:24Z","citation":{"chicago":"Wirnsberger, Peter, Domagoj Fijan, Roger A. Lightwood, Anđela Šarić, Christoph Dellago, and Daan Frenkel. “Numerical Evidence for Thermally Induced Monopoles.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621494114.","ista":"Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. 2017. Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. 114(19), 4911–4914.","mla":"Wirnsberger, Peter, et al. “Numerical Evidence for Thermally Induced Monopoles.” Proceedings of the National Academy of Sciences, vol. 114, no. 19, National Academy of Sciences, 2017, pp. 4911–14, doi:10.1073/pnas.1621494114.","apa":"Wirnsberger, P., Fijan, D., Lightwood, R. A., Šarić, A., Dellago, C., & Frenkel, D. (2017). Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1621494114","ama":"Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. 2017;114(19):4911-4914. doi:10.1073/pnas.1621494114","short":"P. Wirnsberger, D. Fijan, R.A. Lightwood, A. Šarić, C. Dellago, D. Frenkel, Proceedings of the National Academy of Sciences 114 (2017) 4911–4914.","ieee":"P. Wirnsberger, D. Fijan, R. A. Lightwood, A. Šarić, C. Dellago, and D. Frenkel, “Numerical evidence for thermally induced monopoles,” Proceedings of the National Academy of Sciences, vol. 114, no. 19. National Academy of Sciences, pp. 4911–4914, 2017."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Wirnsberger","full_name":"Wirnsberger, Peter","first_name":"Peter"},{"last_name":"Fijan","full_name":"Fijan, Domagoj","first_name":"Domagoj"},{"last_name":"Lightwood","full_name":"Lightwood, Roger A.","first_name":"Roger A."},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"Christoph","full_name":"Dellago, Christoph","last_name":"Dellago"},{"last_name":"Frenkel","full_name":"Frenkel, Daan","first_name":"Daan"}],"article_processing_charge":"No","external_id":{"pmid":["28439003"],"arxiv":["1610.06840"]},"title":"Numerical evidence for thermally induced monopoles"},{"_id":"10374","tmp":{"short":"CC BY-NC (3.0)","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","image":"/images/cc_by_nc.png"},"type":"journal_article","article_type":"original","keyword":["general chemistry"],"status":"public","date_updated":"2021-11-29T10:00:00Z","ddc":["540"],"extern":"1","abstract":[{"text":"The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's disease. The macroscopic behaviour associated with such processes is remarkably diverse, ranging from simple nucleated growth to highly cooperative processes with a well-defined lagtime. Thus, conventionally, different molecular mechanisms have been used to explain the self-assembly of different proteins. Here we show that this range of behaviour can be quantitatively captured by a single unifying Petri net that describes filamentous growth in terms of aggregate number and aggregate mass concentrations. By considering general features associated with a particular network connectivity, we are able to establish directly the rate-determining steps of the overall aggregation reaction from the system's scaling behaviour. We illustrate the power of this framework on a range of different experimental and simulated aggregating systems. The approach is general and will be applicable to any future extensions of the reaction network of filamentous self-assembly.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlelanding/2017/SC/C7SC01965C","open_access":"1"}],"scopus_import":"1","intvolume":" 8","month":"08","publication_status":"published","publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/3.0/","volume":8,"issue":"10","citation":{"chicago":"Meisl, Georg, Luke Rajah, Samuel A. I. Cohen, Manuela Pfammatter, Anđela Šarić, Erik Hellstrand, Alexander K. Buell, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous Self-Assembly.” Chemical Science. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c7sc01965c.","ista":"Meisl G, Rajah L, Cohen SAI, Pfammatter M, Šarić A, Hellstrand E, Buell AK, Aguzzi A, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ. 2017. Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. 8(10), 7087–7097.","mla":"Meisl, Georg, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous Self-Assembly.” Chemical Science, vol. 8, no. 10, Royal Society of Chemistry, 2017, pp. 7087–97, doi:10.1039/c7sc01965c.","apa":"Meisl, G., Rajah, L., Cohen, S. A. I., Pfammatter, M., Šarić, A., Hellstrand, E., … Knowles, T. P. J. (2017). Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/c7sc01965c","ama":"Meisl G, Rajah L, Cohen SAI, et al. Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. 2017;8(10):7087-7097. doi:10.1039/c7sc01965c","ieee":"G. Meisl et al., “Scaling behaviour and rate-determining steps in filamentous self-assembly,” Chemical Science, vol. 8, no. 10. Royal Society of Chemistry, pp. 7087–7097, 2017.","short":"G. Meisl, L. Rajah, S.A.I. Cohen, M. Pfammatter, A. Šarić, E. Hellstrand, A.K. Buell, A. Aguzzi, S. Linse, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Chemical Science 8 (2017) 7087–7097."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"pmid":["29147538"]},"author":[{"last_name":"Meisl","full_name":"Meisl, Georg","first_name":"Georg"},{"first_name":"Luke","last_name":"Rajah","full_name":"Rajah, Luke"},{"full_name":"Cohen, Samuel A. I.","last_name":"Cohen","first_name":"Samuel A. I."},{"first_name":"Manuela","full_name":"Pfammatter, Manuela","last_name":"Pfammatter"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"full_name":"Hellstrand, Erik","last_name":"Hellstrand","first_name":"Erik"},{"first_name":"Alexander K.","full_name":"Buell, Alexander K.","last_name":"Buell"},{"first_name":"Adriano","full_name":"Aguzzi, Adriano","last_name":"Aguzzi"},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"first_name":"Christopher M.","last_name":"Dobson","full_name":"Dobson, Christopher M."},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."}],"title":"Scaling behaviour and rate-determining steps in filamentous self-assembly","acknowledgement":"The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (SL, TPJK), Sidney Sussex College Cambridge (GM), the Frances and Augusta Newman Foundation (TPJK), the Biotechnology and Biological Science Research Council (TPJK), the Swedish Research Council (SL), the Academy of Medical Sciences (AŠ), Wellcome Trust (AŠ), and the Cambridge Centre for Misfolding Diseases (CMD, TPJK, MV).","oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1","year":"2017","publication":"Chemical Science","day":"31","page":"7087-7097","date_created":"2021-11-29T09:29:31Z","date_published":"2017-08-31T00:00:00Z","doi":"10.1039/c7sc01965c"},{"quality_controlled":"1","publisher":"Royal Society of Chemistry","oa":1,"acknowledgement":"This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program.","date_published":"2017-06-15T00:00:00Z","doi":"10.1039/c7sm00433h","date_created":"2021-11-29T10:00:39Z","page":"4924-4930","day":"15","publication":"Soft Matter","year":"2017","title":"Curvature variation controls particle aggregation on fluid vesicles","author":[{"last_name":"Vahid","full_name":"Vahid, Afshin","first_name":"Afshin"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"last_name":"Idema","full_name":"Idema, Timon","first_name":"Timon"}],"article_processing_charge":"No","external_id":{"pmid":["28677712"],"arxiv":["1703.00776"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Vahid, Afshin, Anđela Šarić, and Timon Idema. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” Soft Matter. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c7sm00433h.","ista":"Vahid A, Šarić A, Idema T. 2017. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 13(28), 4924–4930.","mla":"Vahid, Afshin, et al. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” Soft Matter, vol. 13, no. 28, Royal Society of Chemistry, 2017, pp. 4924–30, doi:10.1039/c7sm00433h.","ama":"Vahid A, Šarić A, Idema T. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 2017;13(28):4924-4930. doi:10.1039/c7sm00433h","apa":"Vahid, A., Šarić, A., & Idema, T. (2017). Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c7sm00433h","short":"A. Vahid, A. Šarić, T. Idema, Soft Matter 13 (2017) 4924–4930.","ieee":"A. Vahid, A. Šarić, and T. Idema, “Curvature variation controls particle aggregation on fluid vesicles,” Soft Matter, vol. 13, no. 28. Royal Society of Chemistry, pp. 4924–4930, 2017."},"month":"06","intvolume":" 13","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://pubs.rsc.org/en/content/articlelanding/2017/SM/C7SM00433H"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins influence the membrane shape, the membrane shape affects the interactions between the proteins. To study these membrane-mediated interactions on closed and anisotropically curved membranes, we use colloids adhered to ellipsoidal membrane vesicles as a model system. We find that two particles on a closed system always attract each other, and tend to align with the direction of largest curvature. Multiple particles form arcs, or, at large enough numbers, a complete ring surrounding the vesicle in its equatorial plane. The resulting vesicle shape resembles a snowman. Our results indicate that these physical interactions on membranes with anisotropic shapes can be exploited by cells to drive macromolecules to preferred regions of cellular or intracellular membranes, and utilized to initiate dynamic processes such as cell division. The same principle could be used to find the midplane of an artificial vesicle, as a first step towards dividing it into two equal parts."}],"volume":13,"issue":"28","license":"https://creativecommons.org/licenses/by/3.0/","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"publication_status":"published","status":"public","keyword":["condensed matter physics","general chemistry"],"type":"journal_article","article_type":"original","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"_id":"10375","extern":"1","date_updated":"2021-11-29T10:33:36Z"},{"oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4.","date_created":"2021-12-05T23:01:49Z","doi":"10.1145/3158121","date_published":"2017-12-07T00:00:00Z","publication":"Proceedings of the ACM on Programming Languages","day":"07","year":"2017","article_number":"33","title":"A new proof rule for almost-sure termination","external_id":{"arxiv":["1711.03588"]},"article_processing_charge":"No","author":[{"last_name":"Mciver","full_name":"Mciver, Annabelle","first_name":"Annabelle"},{"full_name":"Morgan, Carroll","last_name":"Morgan","first_name":"Carroll"},{"first_name":"Benjamin Lucien","last_name":"Kaminski","full_name":"Kaminski, Benjamin Lucien"},{"last_name":"Katoen","full_name":"Katoen, Joost P","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.","chicago":"Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121.","short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","ieee":"A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ama":"Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158121","apa":"Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158121","mla":"Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:10.1145/3158121."},"intvolume":" 2","month":"12","main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158121","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains.","lang":"eng"}],"issue":"POPL","volume":2,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2475-1421"]},"status":"public","conference":{"start_date":"2018-01-07","location":"Los Angeles, CA, United States","end_date":"2018-01-13","name":"POPL: Programming Languages"},"type":"journal_article","article_type":"original","_id":"10418","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-12-07T08:04:14Z"},{"type":"dissertation","status":"public","keyword":["physics","superconductivity","magnetic force microscopy","phase slips"],"_id":"10663","author":[{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn","first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"}],"article_processing_charge":"No","title":"Magnetic force microscopy studies of mesoscopic superconducting structures","supervisor":[{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"date_updated":"2022-01-25T15:00:26Z","citation":{"mla":"Polshyn, Hryhoriy. Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures. University of Illinois at Urbana-Champaign, 2017.","short":"H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures, University of Illinois at Urbana-Champaign, 2017.","ieee":"H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting structures,” University of Illinois at Urbana-Champaign, 2017.","apa":"Polshyn, H. (2017). Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","ama":"Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting structures. 2017.","chicago":"Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures.” University of Illinois at Urbana-Champaign, 2017.","ista":"Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign."},"extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["Graduate Dissertations and Theses at Illinois"],"publisher":"University of Illinois at Urbana-Champaign","main_file_link":[{"url":"http://hdl.handle.net/2142/99178","open_access":"1"}],"oa":1,"month":"09","abstract":[{"text":"The superconducting state of matter enables one to observe quantum effects on the macroscopic scale and hosts many fascinating phenomena. Topological defects of the superconducting order parameter, such as vortices and fluxoid states in multiply connected structures, are often the key ingredients of these phenomena. This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures. The technique relies on the magneto-mechanical coupling of a MFM cantilever to the motion of fluxons. The novelty of the technique is that a magnetic particle attached to the cantilever is used not only to sense the state of a SC structure, but also as a primary source of the inhomogeneous magnetic field which induces that state. Φ0-MFM enables us to map the transitions between tip-induced states during a scan: at the positions of the tip, where the two lowest energy states become degenerate, small oscillations of the tip drive the transitions between these states, which causes a significant shift in the resonant frequency and dissipation of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions form concentric contours on a scan. We show that the changes in the cantilever resonant frequency and dissipation are well-described by a stochastic resonance (SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR model to qualitatively study the effects of a locally applied magnetic field on the phase slip rate in rings containing constrictions. The states with multiple vortices or winding numbers could be useful for the development of novel superconducting devices, or the study of vortex interactions and interference effects. Using Φ0-MFM allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions allow us to identify the underlying states and to investigate their energetics and dynamics even in complicated structures.","lang":"eng"}],"oa_version":"Published Version","page":"103","date_published":"2017-09-18T00:00:00Z","date_created":"2022-01-25T14:54:14Z","publication_status":"published","year":"2017","degree_awarded":"PhD","day":"18","language":[{"iso":"eng"}]},{"oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2022-02-08T09:49:17Z","date_published":"2017-03-01T00:00:00Z","year":"2017","publication":"APS March Meeting 2017","day":"01","article_number":"P39.00011","article_processing_charge":"No","author":[{"last_name":"Polshyn","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy"},{"first_name":"Tyler","last_name":"Naibert","full_name":"Naibert, Tyler"},{"first_name":"Raffi","full_name":"Budakian, Raffi","last_name":"Budakian"}],"title":" Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures","citation":{"mla":"Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” APS March Meeting 2017, vol. 62, no. 4, P39.00011, American Physical Society, 2017.","apa":"Polshyn, H., Naibert, T., & Budakian, R. (2017). Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In APS March Meeting 2017 (Vol. 62). New Orleans, LA, United States: American Physical Society.","ama":"Polshyn H, Naibert T, Budakian R. Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In: APS March Meeting 2017. Vol 62. American Physical Society; 2017.","short":"H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American Physical Society, 2017.","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures,” in APS March Meeting 2017, New Orleans, LA, United States, 2017, vol. 62, no. 4.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In APS March Meeting 2017, Vol. 62. American Physical Society, 2017.","ista":"Polshyn H, Naibert T, Budakian R. 2017. Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. APS March Meeting 2017. APS: American Physical Society, Bulletin of the American Physical Society, vol. 62, P39.00011."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR17/Session/P39.11"}],"alternative_title":["Bulletin of the American Physical Society"],"intvolume":" 62","month":"03","abstract":[{"text":"New ways to investigate and manipulate fluxoid and vortex states of mesoscopic superconducting structures are of great interest. The states with multiple vortices or winding numbers could be useful for the study of vortex interactions and interference effects, the braiding of Majorana bound states by winding vortices, and the development of novel superconducting devices. We demonstrate a methodology based on magnetic force microscopy that allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. By using micro-magnet as a source of inhomogeneous magnetic field, we can efficiently explore the configuration space of fluxoid states. Scanning over the structure reveals the energy crossing points of the lowest laying fluxoid states. This is due the strong interaction of cantilever with thermally activated fluxoid transitions at points of degeneracy. We show that measured patterns of fluxoid transitions allow to identify the states, investigate their energetics, and manipulate them. Further, we show that the dynamics of driven fluxoid transitions can be described by stochastic resonance model, which provides a unique way of measuring fluxoid transition rate and related energy barrier for chosen transitions even in complicated structures","lang":"eng"}],"oa_version":"Published Version","issue":"4","volume":62,"publication_status":"published","publication_identifier":{"issn":["0003-0503"]},"language":[{"iso":"eng"}],"conference":{"name":"APS: American Physical Society","end_date":"2017-03-17","location":"New Orleans, LA, United States","start_date":"2017-03-13"},"type":"conference","status":"public","_id":"10745","date_updated":"2022-02-08T10:44:35Z","extern":"1"},{"volume":15,"publication_status":"published","publication_identifier":{"isbn":["978-3643908124"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4666","creator":"system","file_size":380624,"date_updated":"2018-12-12T10:08:06Z","file_name":"IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf","date_created":"2018-12-12T10:08:06Z"}],"alternative_title":["American Studies in Austria"],"intvolume":" 15","month":"02","oa_version":"None","file_date_updated":"2018-12-12T10:08:06Z","date_updated":"2021-01-12T06:48:06Z","ddc":["001"],"extern":"1","type":"book_chapter","status":"public","_id":"1075","page":"73 - 80","date_created":"2018-12-11T11:50:00Z","date_published":"2017-02-01T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Austria and America: 20th-Century Cross-Cultural Encounters","day":"01","oa":1,"publisher":"LIT Verlag Berlin-Münster-Wien-Zürich-London","author":[{"first_name":"Bernhard","id":"479E9046-F248-11E8-B48F-1D18A9856A87","last_name":"Wenzl","full_name":"Wenzl, Bernhard"}],"publist_id":"6306","editor":[{"first_name":"Joshua","last_name":"Parker","full_name":"Parker, Joshua"},{"first_name":"Ralph","last_name":"Poole","full_name":"Poole, Ralph"}],"title":"An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier"","citation":{"chicago":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on "The Vienna Frontier"” In Austria and America: 20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017.","ista":"Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier" In: Austria and America: 20th-Century Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.","mla":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on "The Vienna Frontier"” Austria and America: 20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, vol. 15, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","ama":"Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier" In: Parker J, Poole R, eds. Austria and America: 20th-Century Cross-Cultural Encounters. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London; 2017:73-80.","apa":"Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier" In J. Parker & R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters (Vol. 15, pp. 73–80). LIT Verlag Berlin-Münster-Wien-Zürich-London.","ieee":"B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier",” in Austria and America: 20th-Century Cross-Cultural Encounters, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","short":"B. Wenzl, in:, J. Parker, R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80."},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"},{"external_id":{"pmid":["29269482"]},"article_processing_charge":"No","author":[{"last_name":"Franks","full_name":"Franks, Tobias M.","first_name":"Tobias M."},{"first_name":"Asako","full_name":"McCloskey, Asako","last_name":"McCloskey"},{"full_name":"Shokhirev, Maxim Nikolaievich","last_name":"Shokhirev","first_name":"Maxim Nikolaievich"},{"first_name":"Chris","full_name":"Benner, Chris","last_name":"Benner"},{"first_name":"Annie","full_name":"Rathore, Annie","last_name":"Rathore"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"title":"Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells","citation":{"apa":"Franks, T. M., McCloskey, A., Shokhirev, M. N., Benner, C., Rathore, A., & Hetzer, M. (2017). Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.306753.117","ama":"Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes & Development. 2017;31(22):2222-2234. doi:10.1101/gad.306753.117","short":"T.M. Franks, A. McCloskey, M.N. Shokhirev, C. Benner, A. Rathore, M. Hetzer, Genes & Development 31 (2017) 2222–2234.","ieee":"T. M. Franks, A. McCloskey, M. N. Shokhirev, C. Benner, A. Rathore, and M. Hetzer, “Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells,” Genes & Development, vol. 31, no. 22. Cold Spring Harbor Laboratory, pp. 2222–2234, 2017.","mla":"Franks, Tobias M., et al. “Nup98 Recruits the Wdr82–Set1A/COMPASS Complex to Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor Cells.” Genes & Development, vol. 31, no. 22, Cold Spring Harbor Laboratory, 2017, pp. 2222–34, doi:10.1101/gad.306753.117.","ista":"Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. 2017. Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes & Development. 31(22), 2222–2234.","chicago":"Franks, Tobias M., Asako McCloskey, Maxim Nikolaievich Shokhirev, Chris Benner, Annie Rathore, and Martin Hetzer. “Nup98 Recruits the Wdr82–Set1A/COMPASS Complex to Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor Cells.” Genes & Development. Cold Spring Harbor Laboratory, 2017. https://doi.org/10.1101/gad.306753.117."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","page":"2222-2234","date_created":"2022-04-07T07:45:59Z","doi":"10.1101/gad.306753.117","date_published":"2017-12-21T00:00:00Z","year":"2017","publication":"Genes & Development","day":"21","oa":1,"publisher":"Cold Spring Harbor Laboratory","quality_controlled":"1","date_updated":"2022-07-18T08:33:05Z","extern":"1","type":"journal_article","article_type":"original","keyword":["Developmental Biology","Genetics"],"status":"public","_id":"11066","volume":31,"issue":"22","publication_status":"published","publication_identifier":{"issn":["0890-9369","1549-5477"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.306753.117"}],"scopus_import":"1","intvolume":" 31","month":"12","abstract":[{"text":"Recent studies have shown that a subset of nucleoporins (Nups) can detach from the nuclear pore complex and move into the nuclear interior to regulate transcription. One such dynamic Nup, called Nup98, has been implicated in gene activation in healthy cells and has been shown to drive leukemogenesis when mutated in patients with acute myeloid leukemia (AML). Here we show that in hematopoietic cells, Nup98 binds predominantly to transcription start sites to recruit the Wdr82–Set1A/COMPASS (complex of proteins associated with Set1) complex, which is required for deposition of the histone 3 Lys4 trimethyl (H3K4me3)-activating mark. Depletion of Nup98 or Wdr82 abolishes Set1A recruitment to chromatin and subsequently ablates H3K4me3 at adjacent promoters. Furthermore, expression of a Nup98 fusion protein implicated in aggressive AML causes mislocalization of H3K4me3 at abnormal regions and up-regulation of associated genes. Our findings establish a function of Nup98 in hematopoietic gene activation and provide mechanistic insight into which Nup98 leukemic fusion proteins promote AML.","lang":"eng"}],"oa_version":"Published Version","pmid":1},{"publication_status":"published","publication_identifier":{"issn":["1934-5909"]},"language":[{"iso":"eng"}],"volume":21,"issue":"5","abstract":[{"lang":"eng","text":"Neural progenitor cells (NeuPCs) possess a unique nuclear architecture that changes during differentiation. Nucleoporins are linked with cell-type-specific gene regulation, coupling physical changes in nuclear structure to transcriptional output; but, whether and how they coordinate with key fate-determining transcription factors is unclear. Here we show that the nucleoporin Nup153 interacts with Sox2 in adult NeuPCs, where it is indispensable for their maintenance and controls neuronal differentiation. Genome-wide analyses show that Nup153 and Sox2 bind and co-regulate hundreds of genes. Binding of Nup153 to gene promoters or transcriptional end sites correlates with increased or decreased gene expression, respectively, and inhibiting Nup153 expression alters open chromatin configurations at its target genes, disrupts genomic localization of Sox2, and promotes differentiation in vitro and a gliogenic fate switch in vivo. Together, these findings reveal that nuclear structural proteins may exert bimodal transcriptional effects to control cell fate."}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1016/j.stem.2017.08.012","open_access":"1"}],"scopus_import":"1","intvolume":" 21","month":"11","date_updated":"2022-07-18T08:33:07Z","extern":"1","_id":"11067","article_type":"original","type":"journal_article","keyword":["Cell Biology","Genetics","Molecular Medicine"],"status":"public","year":"2017","publication":"Cell Stem Cell","day":"02","page":"618-634.e7","date_created":"2022-04-07T07:46:12Z","doi":"10.1016/j.stem.2017.08.012","date_published":"2017-11-02T00:00:00Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","citation":{"chicago":"Toda, Tomohisa, Jonathan Y. Hsu, Sara B. Linker, Lauren Hu, Simon T. Schafer, Jerome Mertens, Filipe V. Jacinto, Martin Hetzer, and Fred H. Gage. “Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells.” Cell Stem Cell. Elsevier, 2017. https://doi.org/10.1016/j.stem.2017.08.012.","ista":"Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer M, Gage FH. 2017. Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell. 21(5), 618–634.e7.","mla":"Toda, Tomohisa, et al. “Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells.” Cell Stem Cell, vol. 21, no. 5, Elsevier, 2017, p. 618–634.e7, doi:10.1016/j.stem.2017.08.012.","apa":"Toda, T., Hsu, J. Y., Linker, S. B., Hu, L., Schafer, S. T., Mertens, J., … Gage, F. H. (2017). Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell. Elsevier. https://doi.org/10.1016/j.stem.2017.08.012","ama":"Toda T, Hsu JY, Linker SB, et al. Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell. 2017;21(5):618-634.e7. doi:10.1016/j.stem.2017.08.012","short":"T. Toda, J.Y. Hsu, S.B. Linker, L. Hu, S.T. Schafer, J. Mertens, F.V. Jacinto, M. Hetzer, F.H. Gage, Cell Stem Cell 21 (2017) 618–634.e7.","ieee":"T. Toda et al., “Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells,” Cell Stem Cell, vol. 21, no. 5. Elsevier, p. 618–634.e7, 2017."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","external_id":{"pmid":["28919367"]},"article_processing_charge":"No","author":[{"full_name":"Toda, Tomohisa","last_name":"Toda","first_name":"Tomohisa"},{"first_name":"Jonathan Y.","full_name":"Hsu, Jonathan Y.","last_name":"Hsu"},{"last_name":"Linker","full_name":"Linker, Sara B.","first_name":"Sara B."},{"full_name":"Hu, Lauren","last_name":"Hu","first_name":"Lauren"},{"first_name":"Simon T.","full_name":"Schafer, Simon T.","last_name":"Schafer"},{"first_name":"Jerome","last_name":"Mertens","full_name":"Mertens, Jerome"},{"first_name":"Filipe V.","last_name":"Jacinto","full_name":"Jacinto, Filipe V."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER"},{"first_name":"Fred H.","full_name":"Gage, Fred H.","last_name":"Gage"}],"title":"Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells"},{"publication":"Nature Communications","day":"30","year":"2017","date_created":"2022-04-07T07:45:50Z","date_published":"2017-08-30T00:00:00Z","doi":"10.1038/s41467-017-00322-z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"short":"A. Buchwalter, M. Hetzer, Nature Communications 8 (2017).","ieee":"A. Buchwalter and M. Hetzer, “Nucleolar expansion and elevated protein translation in premature aging,” Nature Communications, vol. 8. Springer Nature, 2017.","apa":"Buchwalter, A., & Hetzer, M. (2017). Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-00322-z","ama":"Buchwalter A, Hetzer M. Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. 2017;8. doi:10.1038/s41467-017-00322-z","mla":"Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein Translation in Premature Aging.” Nature Communications, vol. 8, 328, Springer Nature, 2017, doi:10.1038/s41467-017-00322-z.","ista":"Buchwalter A, Hetzer M. 2017. Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. 8, 328.","chicago":"Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein Translation in Premature Aging.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/s41467-017-00322-z."},"title":"Nucleolar expansion and elevated protein translation in premature aging","article_processing_charge":"No","external_id":{"pmid":["28855503"]},"author":[{"first_name":"Abigail","last_name":"Buchwalter","full_name":"Buchwalter, Abigail"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"article_number":"328","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"volume":8,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Premature aging disorders provide an opportunity to study the mechanisms that drive aging. In Hutchinson-Gilford progeria syndrome (HGPS), a mutant form of the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins. We sought to investigate protein homeostasis in this disease. Here, we report a widespread increase in protein turnover in HGPS-derived cells compared to normal cells. We determine that global protein synthesis is elevated as a consequence of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts. Depleting normal lamin A or inducing mutant lamin A expression are each sufficient to drive nucleolar expansion. We further show that nucleolar size correlates with donor age in primary fibroblasts derived from healthy individuals and that ribosomal RNA production increases with age, indicating that nucleolar size and activity can serve as aging biomarkers. While limiting ribosome biogenesis extends lifespan in several systems, we show that increased ribosome biogenesis and activity are a hallmark of premature aging.","lang":"eng"}],"intvolume":" 8","month":"08","main_file_link":[{"url":"https://doi.org/10.1038/s41467-017-00322-z","open_access":"1"}],"scopus_import":"1","extern":"1","date_updated":"2022-07-18T08:33:03Z","_id":"11065","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"status":"public","article_type":"original","type":"journal_article"},{"abstract":[{"lang":"eng","text":"We present spectroscopic follow-up observations of CR7 with ALMA, targeted at constraining the infrared (IR) continuum and [C II]158 mm line-emission at high spatial resolution matched to the HST/WFC3 imaging. CR7 is a luminous Lyα emitting galaxy at z = 6.6 that consists of three separated UV-continuum components. Our observations reveal several well-separated components of [C II] emission. The two most luminous components in [C II] coincide with the brightest UV components (A and B), blueshifted by »150 km s−1 with respect to the\r\npeak of Lyα emission. Other [C II] components are observed close to UV clumps B and C and are blueshifted by »300 and ≈80 km s−1 with respect to the systemic redshift. We do not detect FIR continuum emission due to dust with a 3σ limiting luminosity LIR T L d 35 K 3.1 10 = <´ 10 ( ) . This allows us to mitigate uncertainties in the dust-corrected SFR and derive SFRs for the three UV clumps A, B, and C of 28, 5, and 7 M yr−1. All clumps have [C II] luminosities consistent within the scatter observed in the local relation between SFR and L[ ] C II , implying that strong Lyα emission does not necessarily anti-correlate with [C II] luminosity. Combining\r\nour measurements with the literature, we show that galaxies with blue UV slopes have weaker [C II] emission at fixed SFR, potentially due to their lower metallicities and/or higher photoionization. Comparison with hydrodynamical simulations suggests that CR7ʼs clumps have metallicities of 0.1 Z Z 0.2 < < . The observed ISM structure of CR7 indicates that we are likely witnessing the build up of a central galaxy in the early universe through complex accretion of satellites."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.06569"}],"month":"12","intvolume":" 851","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":851,"_id":"11518","type":"journal_article","article_type":"original","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","dark ages","reionization","first stars – galaxies: formation – galaxies: high-redshift – galaxies: ISM – galaxies: kinematics and dynamics"],"date_updated":"2022-08-18T10:23:35Z","extern":"1","acknowledgement":"We thank the referee for their constructive comments, which have helped improve the quality and clarity of this work. We thank Raffaella Schneider for comments on an earlier version of this paper. We thank Leindert Boogaard, Steven Bos, Rychard Bouwens, and Renske Smit for discussions. J.M. acknowledges the support of a Huygens PhD fellowship from Leiden University. D.S. acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. A.F. acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120. B.D. acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 294.A-5018. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2015.1.00122.S. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ.","publisher":"IOP Publishing","quality_controlled":"1","oa":1,"year":"2017","day":"21","publication":"The Astrophysical Journal","date_published":"2017-12-21T00:00:00Z","doi":"10.3847/1538-4357/aa9931","date_created":"2022-07-07T08:48:04Z","article_number":"145","citation":{"chicago":"Matthee, Jorryt J, D. Sobral, F. Boone, H. Röttgering, D. Schaerer, M. Girard, A. Pallottini, et al. “ALMA Reveals Metals yet No Dust within Multiple Components in CR7.” The Astrophysical Journal. IOP Publishing, 2017. https://doi.org/10.3847/1538-4357/aa9931.","ista":"Matthee JJ, Sobral D, Boone F, Röttgering H, Schaerer D, Girard M, Pallottini A, Vallini L, Ferrara A, Darvish B, Mobasher B. 2017. ALMA reveals metals yet no dust within multiple components in CR7. The Astrophysical Journal. 851(2), 145.","mla":"Matthee, Jorryt J., et al. “ALMA Reveals Metals yet No Dust within Multiple Components in CR7.” The Astrophysical Journal, vol. 851, no. 2, 145, IOP Publishing, 2017, doi:10.3847/1538-4357/aa9931.","apa":"Matthee, J. J., Sobral, D., Boone, F., Röttgering, H., Schaerer, D., Girard, M., … Mobasher, B. (2017). ALMA reveals metals yet no dust within multiple components in CR7. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/aa9931","ama":"Matthee JJ, Sobral D, Boone F, et al. ALMA reveals metals yet no dust within multiple components in CR7. The Astrophysical Journal. 2017;851(2). doi:10.3847/1538-4357/aa9931","ieee":"J. J. Matthee et al., “ALMA reveals metals yet no dust within multiple components in CR7,” The Astrophysical Journal, vol. 851, no. 2. IOP Publishing, 2017.","short":"J.J. Matthee, D. Sobral, F. Boone, H. Röttgering, D. Schaerer, M. Girard, A. Pallottini, L. Vallini, A. Ferrara, B. Darvish, B. Mobasher, The Astrophysical Journal 851 (2017)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"last_name":"Sobral","full_name":"Sobral, D.","first_name":"D."},{"last_name":"Boone","full_name":"Boone, F.","first_name":"F."},{"last_name":"Röttgering","full_name":"Röttgering, H.","first_name":"H."},{"first_name":"D.","full_name":"Schaerer, D.","last_name":"Schaerer"},{"last_name":"Girard","full_name":"Girard, M.","first_name":"M."},{"first_name":"A.","full_name":"Pallottini, A.","last_name":"Pallottini"},{"first_name":"L.","full_name":"Vallini, L.","last_name":"Vallini"},{"first_name":"A.","last_name":"Ferrara","full_name":"Ferrara, A."},{"first_name":"B.","full_name":"Darvish, B.","last_name":"Darvish"},{"first_name":"B.","full_name":"Mobasher, B.","last_name":"Mobasher"}],"article_processing_charge":"No","external_id":{"arxiv":["1709.06569"]},"title":"ALMA reveals metals yet no dust within multiple components in CR7"},{"year":"2017","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","page":"1242-1258","date_created":"2022-07-12T12:04:16Z","doi":"10.1093/mnras/stw3090","date_published":"2017-04-01T00:00:00Z","acknowledgement":"We thank the reviewer for his/her helpful comments and suggestions that have greatly improved this work. DS and JM acknowledge financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship. DS also acknowledges funding from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). PNB is grateful for support from the UK STFC via grant ST/M001229/1. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson merit award. We thank Matthew Hayes, Ryan Trainor, Kimihiko Nakajima and Anne Verhamme for many helpful discussions and Ana Sobral, Carolina Duarte and Miguel Domingos for taking part in observations with the NB392 filter. We also thank Sergio Santos for helpful comments. This research is based on observations obtained on the Isaac Newton Telescope (INT), programs: I13AN002, I14AN002, 088-INT7/14A, I14BN006, 118-INT13/14B & I15AN008. The authors acknowledge the award of time from programmes: I13AN002, I14AN002, 088-INT7/14A, I14BN006, 118-INT13/14B, I15AN008 on the INT. INT is operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 098.A 0819. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY and ASTROPY packages, the astronomical imaging tools SEXTRACTOR, SWARP (Bertin & Arnouts 1996; Bertin 2010), SCAMP (Bertin 2006) and TOPCAT (Taylor 2005). Dedicated to the memory of M. L. Nicolau and M. C. Serrano.","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","citation":{"mla":"Sobral, David, et al. “The CALYMHA Survey: Lyα Luminosity Function and Global Escape Fraction of Lyα Photons at z = 2.23.” Monthly Notices of the Royal Astronomical Society, vol. 466, no. 1, Oxford University Press, 2017, pp. 1242–58, doi:10.1093/mnras/stw3090.","ieee":"D. Sobral et al., “The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23,” Monthly Notices of the Royal Astronomical Society, vol. 466, no. 1. Oxford University Press, pp. 1242–1258, 2017.","short":"D. Sobral, J.J. Matthee, P. Best, A. Stroe, H. Röttgering, I. Oteo, I. Smail, L. Morabito, A. Paulino-Afonso, Monthly Notices of the Royal Astronomical Society 466 (2017) 1242–1258.","ama":"Sobral D, Matthee JJ, Best P, et al. The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23. Monthly Notices of the Royal Astronomical Society. 2017;466(1):1242-1258. doi:10.1093/mnras/stw3090","apa":"Sobral, D., Matthee, J. J., Best, P., Stroe, A., Röttgering, H., Oteo, I., … Paulino-Afonso, A. (2017). The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw3090","chicago":"Sobral, David, Jorryt J Matthee, Philip Best, Andra Stroe, Huub Röttgering, Iván Oteo, Ian Smail, Leah Morabito, and Ana Paulino-Afonso. “The CALYMHA Survey: Lyα Luminosity Function and Global Escape Fraction of Lyα Photons at z = 2.23.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw3090.","ista":"Sobral D, Matthee JJ, Best P, Stroe A, Röttgering H, Oteo I, Smail I, Morabito L, Paulino-Afonso A. 2017. The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23. Monthly Notices of the Royal Astronomical Society. 466(1), 1242–1258."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1609.05897"]},"article_processing_charge":"No","author":[{"last_name":"Sobral","full_name":"Sobral, David","first_name":"David"},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee"},{"first_name":"Philip","full_name":"Best, Philip","last_name":"Best"},{"first_name":"Andra","full_name":"Stroe, Andra","last_name":"Stroe"},{"full_name":"Röttgering, Huub","last_name":"Röttgering","first_name":"Huub"},{"last_name":"Oteo","full_name":"Oteo, Iván","first_name":"Iván"},{"first_name":"Ian","last_name":"Smail","full_name":"Smail, Ian"},{"last_name":"Morabito","full_name":"Morabito, Leah","first_name":"Leah"},{"first_name":"Ana","full_name":"Paulino-Afonso, Ana","last_name":"Paulino-Afonso"}],"title":"The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23","publication_status":"published","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"language":[{"iso":"eng"}],"issue":"1","volume":466,"abstract":[{"text":"We present the CAlibrating LYMan-α with Hα (CALYMHA) pilot survey and new results on Lyman α (Lyα) selected galaxies at z ∼ 2. We use a custom-built Lyα narrow-band filter at the Isaac Newton Telescope, designed to provide a matched volume coverage to the z = 2.23 Hα HiZELS survey. Here, we present the first results for the COSMOS and UDS fields. Our survey currently reaches a 3σ line flux limit of ∼4 × 10−17 erg s−1 cm−2, and a Lyα luminosity limit of ∼1042.3 erg s−1. We find 188 Lyα emitters over 7.3 × 105 Mpc3, but also find significant numbers of other line-emitting sources corresponding to He II, C III] and C IV emission lines. These sources are important contaminants, and we carefully remove them, unlike most previous studies. We find that the Lyα luminosity function at z = 2.23 is very well described by a Schechter function up to LLy α ≈ 1043 erg s−1 with L∗=1042.59+0.16−0.08 erg s−1, ϕ∗=10−3.09+0.14−0.34 Mpc−3 and α = −1.75 ± 0.25. Above LLy α ≈ 1043 erg s−1, the Lyα luminosity function becomes power-law like, driven by X-ray AGN. We find that Lyα-selected emitters have a high escape fraction of 37 ± 7 per cent, anticorrelated with Lyα luminosity and correlated with Lyα equivalent width. Lyα emitters have ubiquitous large (≈40 kpc) Lyα haloes, ∼2 times larger than their Hα extents. By directly comparing our Lyα and Hα luminosity functions, we find that the global/overall escape fraction of Lyα photons (within a 13 kpc radius) from the full population of star-forming galaxies is 5.1 ± 0.2 per cent at the peak of the star formation history. An extra 3.3 ± 0.3 per cent of Lyα photons likely still escape, but at larger radii.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1609.05897","open_access":"1"}],"scopus_import":"1","intvolume":" 466","month":"04","date_updated":"2022-08-19T07:18:20Z","extern":"1","_id":"11562","type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: haloes","galaxies: high-redshift","galaxies: luminosity function","mass function","galaxies: statistics","cosmology: observations"],"status":"public"},{"date_updated":"2022-08-19T07:59:57Z","extern":"1","_id":"11566","type":"journal_article","article_type":"original","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: high-redshift","quasars: emission lines","galaxies: star formation","cosmology: observations"],"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":471,"issue":"3","abstract":[{"lang":"eng","text":"While traditionally associated with active galactic nuclei (AGN), the properties of the C II] (λ = 2326 Å), C III] (λ, λ = 1907, 1909 Å) and C IV (λ, λ = 1549, 1551 Å) emission lines are still uncertain as large, unbiased samples of sources are scarce. We present the first blind, statistical study of C II], C III] and C IV emitters at z ∼ 0.68, 1.05, 1.53, respectively, uniformly selected down to a flux limit of ∼4 × 10−17 erg s−1 cm−1 through a narrow-band survey covering an area of ∼1.4 deg2 over COSMOS and UDS. We detect 16 C II], 35 C III] and 17 C IV emitters, whose nature we investigate using optical colours as well as Hubble Space Telescope (HST), X-ray, radio and far-infrared data. We find that z ∼ 0.7 C II] emitters are consistent with a mixture of blue (UV slope β = −2.0 ± 0.4) star-forming (SF) galaxies with discy HST structure and AGN with Seyfert-like morphologies. Bright C II] emitters have individual X-ray detections as well as high average black hole accretion rates (BHARs) of ∼0.1 M⊙ yr−1. C III] emitters at z ∼ 1.05 trace a general population of SF galaxies, with β = −0.8 ± 1.1, a variety of optical morphologies, including isolated and interacting galaxies and low BHAR (<0.02 M⊙ yr−1). Our C IV emitters at z ∼ 1.5 are consistent with young, blue quasars (β ∼ −1.9) with point-like optical morphologies, bright X-ray counterparts and large BHAR (0.8 M⊙ yr−1). We also find some surprising C II], C III] and C IV emitters with rest-frame equivalent widths (EWs) that could be as large as 50–100 Å. AGN or spatial offsets between the UV continuum stellar disc and the line-emitting regions may explain the large EW. These bright C II], C III] and C IV emitters are ideal candidates for spectroscopic follow-up to fully unveil their nature."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.10169","open_access":"1"}],"month":"11","intvolume":" 471","citation":{"mla":"Stroe, Andra, et al. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, Morphologies and Equivalent Widths .” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3, Oxford University Press, 2017, pp. 2558–74, doi:10.1093/mnras/stx1712.","ieee":"A. Stroe, D. Sobral, J. J. Matthee, J. Calhau, and I. Oteo, “A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths ,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3. Oxford University Press, pp. 2558–2574, 2017.","short":"A. Stroe, D. Sobral, J.J. Matthee, J. Calhau, I. Oteo, Monthly Notices of the Royal Astronomical Society 471 (2017) 2558–2574.","ama":"Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths . Monthly Notices of the Royal Astronomical Society. 2017;471(3):2558-2574. doi:10.1093/mnras/stx1712","apa":"Stroe, A., Sobral, D., Matthee, J. J., Calhau, J., & Oteo, I. (2017). A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths . Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1712","chicago":"Stroe, Andra, David Sobral, Jorryt J Matthee, João Calhau, and Ivan Oteo. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, Morphologies and Equivalent Widths .” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1712.","ista":"Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. 2017. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths . Monthly Notices of the Royal Astronomical Society. 471(3), 2558–2574."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Andra","full_name":"Stroe, Andra","last_name":"Stroe"},{"first_name":"David","full_name":"Sobral, David","last_name":"Sobral"},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee"},{"last_name":"Calhau","full_name":"Calhau, João","first_name":"João"},{"first_name":"Ivan","full_name":"Oteo, Ivan","last_name":"Oteo"}],"article_processing_charge":"No","external_id":{"arxiv":["1703.10169"]},"title":"A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths ","year":"2017","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","page":"2558-2574","date_published":"2017-11-01T00:00:00Z","doi":"10.1093/mnras/stx1712","date_created":"2022-07-12T12:33:16Z","acknowledgement":"We would like to thank the anonymous referee for her/his valuable input that helped improve the clarity and interpretation of our results. DS acknowledges financial support from the Netherlands Organisation for Scientific research (NWO), through a Veni fellowship. IO acknowledges support from the European Research Council in the form of the Advanced Investigator Programme, 321302, COSMICISM. CALYMHA data are based on observations made with the Isaac Newton Telescope (proposals 13AN002, I14AN002, 088-INT7/14A, I14BN006, 118-INT13/14B, I15AN008) operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias. Also based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 098.A-0819 and 179.A-2005. We are grateful to E. L. Wright and J. Schombert for their cosmology calculator. We would like to thank the authors of NUMPY (van der Walt et al. 2011), SCIPY (Jones et al. 2001), MATPLOTLIB (Hunter 2007) and ASTROPY (Astropy Collaboration et al. 2013) for making these packages publicly available. This research has made use of the NASA/IPAC Extragalactic Database (NED), which is ","quality_controlled":"1","publisher":"Oxford University Press","oa":1},{"article_processing_charge":"No","external_id":{"arxiv":["1605.08782"]},"author":[{"last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"last_name":"Sobral","full_name":"Sobral, David","first_name":"David"},{"first_name":"Philip","last_name":"Best","full_name":"Best, Philip"},{"first_name":"Ali Ahmad","full_name":"Khostovan, Ali Ahmad","last_name":"Khostovan"},{"last_name":"Oteo","full_name":"Oteo, Iván","first_name":"Iván"},{"last_name":"Bouwens","full_name":"Bouwens, Rychard","first_name":"Rychard"},{"last_name":"Röttgering","full_name":"Röttgering, Huub","first_name":"Huub"}],"title":"The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution","citation":{"mla":"Matthee, Jorryt J., et al. “The Production and Escape of Lyman-Continuum Radiation from Star-Forming Galaxies at z ∼ 2 and Their Redshift Evolution.” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 3, Oxford University Press, 2017, pp. 3637–55, doi:10.1093/mnras/stw2973.","apa":"Matthee, J. J., Sobral, D., Best, P., Khostovan, A. A., Oteo, I., Bouwens, R., & Röttgering, H. (2017). The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2973","ama":"Matthee JJ, Sobral D, Best P, et al. The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution. Monthly Notices of the Royal Astronomical Society. 2017;465(3):3637-3655. doi:10.1093/mnras/stw2973","ieee":"J. J. Matthee et al., “The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution,” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 3. Oxford University Press, pp. 3637–3655, 2017.","short":"J.J. Matthee, D. Sobral, P. Best, A.A. Khostovan, I. Oteo, R. Bouwens, H. Röttgering, Monthly Notices of the Royal Astronomical Society 465 (2017) 3637–3655.","chicago":"Matthee, Jorryt J, David Sobral, Philip Best, Ali Ahmad Khostovan, Iván Oteo, Rychard Bouwens, and Huub Röttgering. “The Production and Escape of Lyman-Continuum Radiation from Star-Forming Galaxies at z ∼ 2 and Their Redshift Evolution.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2973.","ista":"Matthee JJ, Sobral D, Best P, Khostovan AA, Oteo I, Bouwens R, Röttgering H. 2017. The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution. Monthly Notices of the Royal Astronomical Society. 465(3), 3637–3655."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3637-3655","date_created":"2022-07-12T12:12:14Z","doi":"10.1093/mnras/stw2973","date_published":"2017-03-01T00:00:00Z","year":"2017","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"We thank the referee for the many helpful and constructive comments which have significantly improved this paper. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). PNB is grateful for support from the UK STFC via grant ST/M001229/1. IO acknowledges support from the European Research Council in the form of the Advanced Investigator Programme, 321302, COSMICISM. The authors thank Andreas Faisst, Michael Rutkowski and Andreas Sandberg for answering questions related to this work and Daniel Schaerer and Mark Dijkstra for discussions. We acknowledge the work that has been done by both the COSMOS team in assembling such large, state-of-the-art multi-wavelength data set, as this has been crucial for the results presented in this paper. We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY (Jones et al. 2001; Hunter 2007; Van Der Walt, Colbert & Varoquaux 2011) and ASTROPY (Astropy Collaboration et al. 2013) packages, the astronomical imaging tools SEXTRACTOR and SWARP (Bertin & Arnouts 1996;\r\nBertin 2010) and the TOPCAT analysis program (Taylor 2013).","date_updated":"2022-08-19T07:53:04Z","extern":"1","type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","cosmology: observations","dark ages","reionization","first stars"],"status":"public","_id":"11564","issue":"3","volume":465,"publication_status":"published","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.08782"}],"scopus_import":"1","intvolume":" 465","month":"03","abstract":[{"lang":"eng","text":"We study the production rate of ionizing photons of a sample of 588 Hα emitters (HAEs) and 160 Lyman-α emitters (LAEs) at z = 2.2 in the COSMOS field in order to assess the implied emissivity from galaxies, based on their ultraviolet (UV) luminosity. By exploring the rest-frame Lyman Continuum (LyC) with GALEX/NUV data, we find fesc < 2.8 (6.4) per cent through median (mean) stacking. By combining the Hα luminosity density with intergalactic medium emissivity measurements from absorption studies, we find a globally averaged 〈fesc〉 of 5.9+14.5−4.2 per cent at z = 2.2 if we assume HAEs are the only source of ionizing photons. We find similarly low values of the global 〈fesc〉 at z ≈ 3–5, also ruling out a high 〈fesc〉 at z < 5. These low escape fractions allow us to measure ξion, the number of produced ionizing photons per unit UV luminosity, and investigate how this depends on galaxy properties. We find a typical ξion ≈ 1024.77 ± 0.04 Hz erg−1 for HAEs and ξion ≈ 1025.14 ± 0.09 Hz erg−1 for LAEs. LAEs and low-mass HAEs at z = 2.2 show similar values of ξion as typically assumed in the reionization era, while the typical HAE is three times less ionizing. Due to an increasing ξion with increasing EW(Hα), ξion likely increases with redshift. This evolution alone is fully in line with the observed evolution of ξion between z ≈ 2 and 5, indicating a typical value of ξion ≈ 1025.4 Hz erg−1 in the reionization era."}],"oa_version":"Preprint"},{"type":"journal_article","article_type":"original","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: high redshift","galaxies: luminosity function","mass function","quasars: emission lines","star formation","cosmology: observations"],"_id":"11567","date_updated":"2022-08-19T08:02:04Z","extern":"1","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.10169","open_access":"1"}],"month":"11","intvolume":" 471","abstract":[{"lang":"eng","text":"Recently, the C III] and C IV emission lines have been observed in galaxies in the early Universe (z > 5), providing new ways to measure their redshift and study their stellar populations and active galactic nuclei (AGN). We explore the first blind C II], C III] and C IV survey (z ∼ 0.68, 1.05, 1.53, respectively) presented in Stroe et al. (2017). We derive luminosity functions (LF) and study properties of C II], C III] and C IV line emitters through comparisons to the LFs of H α and Ly α emitters, UV selected star-forming (SF) galaxies and quasars at similar redshifts. The C II] LF at z ∼ 0.68 is equally well described by a Schechter or a power-law LF, characteristic of a mixture of SF and AGN activity. The C III] LF (z ∼ 1.05) is consistent to a scaled down version of the Schechter H α and Ly α LF at their redshift, indicating a SF origin. In stark contrast, the C IV LF at z ∼ 1.53 is well fit by a power-law, quasar-like LF. We find that the brightest UV sources (MUV < −22) will universally have C III] and C IV emission. However, on average, C III] and C IV are not as abundant as H α or Ly α emitters at the same redshift, with cosmic average ratios of ∼0.02–0.06 to H α and ∼0.01–0.1 to intrinsic Ly α. We predict that the C III] and C IV lines can only be truly competitive in confirming high-redshift candidates when the hosts are intrinsically bright and the effective Ly α escape fraction is below 1 per cent. While C III] and C IV were proposed as good tracers of young, relatively low-metallicity galaxies typical of the early Universe, we find that, at least at z ∼ 1.5, C IV is exclusively hosted by AGN/quasars, especially at large line equivalent widths."}],"oa_version":"Preprint","volume":471,"issue":"3","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"last_name":"Stroe","full_name":"Stroe, Andra","first_name":"Andra"},{"last_name":"Sobral","full_name":"Sobral, David","first_name":"David"},{"last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"last_name":"Calhau","full_name":"Calhau, João","first_name":"João"},{"first_name":"Ivan","last_name":"Oteo","full_name":"Oteo, Ivan"}],"external_id":{"arxiv":["1703.10169"]},"article_processing_charge":"No","title":"A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios","citation":{"chicago":"Stroe, Andra, David Sobral, Jorryt J Matthee, João Calhau, and Ivan Oteo. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity Functions and Cosmic Average Line Ratios.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1713.","ista":"Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. 2017. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios. Monthly Notices of the Royal Astronomical Society. 471(3), 2575–2586.","mla":"Stroe, Andra, et al. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity Functions and Cosmic Average Line Ratios.” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3, Oxford University Press, 2017, pp. 2575–86, doi:10.1093/mnras/stx1713.","ama":"Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios. Monthly Notices of the Royal Astronomical Society. 2017;471(3):2575-2586. doi:10.1093/mnras/stx1713","apa":"Stroe, A., Sobral, D., Matthee, J. J., Calhau, J., & Oteo, I. (2017). A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1713","short":"A. Stroe, D. Sobral, J.J. Matthee, J. Calhau, I. Oteo, Monthly Notices of the Royal Astronomical Society 471 (2017) 2575–2586.","ieee":"A. Stroe, D. Sobral, J. J. Matthee, J. Calhau, and I. Oteo, “A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3. Oxford University Press, pp. 2575–2586, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"page":"2575-2586","doi":"10.1093/mnras/stx1713","date_published":"2017-11-01T00:00:00Z","date_created":"2022-07-12T12:54:57Z","year":"2017","day":"01","publication":"Monthly Notices of the Royal Astronomical Society"},{"acknowledgement":"We thank the anonymous referee for their comments. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. JM thanks David Sobral for useful discussions and help with fitting routines and Jonas Chavez Montero and Ying Zu for providing data. We thank PRACE for the access to the Curie facility in France. We have used the DiRAC system which is a part of National E-Infrastructure at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk); the equipment was funded by BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/H008519/1, STFC DiRAC Operations grant ST/K003267/1 and Durham University. The study was sponsored by the Dutch National Computing Facilities Foundation (NCF) for the use of supercomputer facilities, with financial support from the Netherlands Organisation for Scientific Research (NWO), through VICI grant 639.043.409, and the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement 278594- GasAroundGalaxies, and from the Belgian Science Policy Office ([AP P7/08 CHARM]). We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY, H5PY and RPY2 packages, and the TOPCAT analysis program (Taylor 2005).","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"year":"2017","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","page":"2381-2396","doi":"10.1093/mnras/stw2884","date_published":"2017-02-01T00:00:00Z","date_created":"2022-07-12T12:25:08Z","citation":{"mla":"Matthee, Jorryt J., et al. “The Origin of Scatter in the Stellar Mass–Halo Mass Relation of Central Galaxies in the EAGLE Simulation.” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 2, Oxford University Press, 2017, pp. 2381–96, doi:10.1093/mnras/stw2884.","apa":"Matthee, J. J., Schaye, J., Crain, R. A., Schaller, M., Bower, R., & Theuns, T. (2017). The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2884","ama":"Matthee JJ, Schaye J, Crain RA, Schaller M, Bower R, Theuns T. The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation. Monthly Notices of the Royal Astronomical Society. 2017;465(2):2381-2396. doi:10.1093/mnras/stw2884","ieee":"J. J. Matthee, J. Schaye, R. A. Crain, M. Schaller, R. Bower, and T. Theuns, “The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation,” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 2. Oxford University Press, pp. 2381–2396, 2017.","short":"J.J. Matthee, J. Schaye, R.A. Crain, M. Schaller, R. Bower, T. Theuns, Monthly Notices of the Royal Astronomical Society 465 (2017) 2381–2396.","chicago":"Matthee, Jorryt J, Joop Schaye, Robert A. Crain, Matthieu Schaller, Richard Bower, and Tom Theuns. “The Origin of Scatter in the Stellar Mass–Halo Mass Relation of Central Galaxies in the EAGLE Simulation.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2884.","ista":"Matthee JJ, Schaye J, Crain RA, Schaller M, Bower R, Theuns T. 2017. The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation. Monthly Notices of the Royal Astronomical Society. 465(2), 2381–2396."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Matthee","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"last_name":"Schaye","full_name":"Schaye, Joop","first_name":"Joop"},{"full_name":"Crain, Robert A.","last_name":"Crain","first_name":"Robert A."},{"first_name":"Matthieu","full_name":"Schaller, Matthieu","last_name":"Schaller"},{"first_name":"Richard","last_name":"Bower","full_name":"Bower, Richard"},{"first_name":"Tom","full_name":"Theuns, Tom","last_name":"Theuns"}],"article_processing_charge":"No","external_id":{"arxiv":["1608.08218"]},"title":"The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation","abstract":[{"lang":"eng","text":"We use the hydrodynamical EAGLE simulation to study the magnitude and origin of the scatter in the stellar mass–halo mass relation for central galaxies. We separate cause and effect by correlating stellar masses in the baryonic simulation with halo properties in a matched dark matter only (DMO) simulation. The scatter in stellar mass increases with redshift and decreases with halo mass. At z = 0.1, it declines from 0.25 dex at M200, DMO ≈ 1011 M⊙ to 0.12 dex at M200, DMO ≈ 1013 M⊙, but the trend is weak above 1012 M⊙. For M200, DMO < 1012.5 M⊙ up to 0.04 dex of the scatter is due to scatter in the halo concentration. At fixed halo mass, a larger stellar mass corresponds to a more concentrated halo. This is likely because higher concentrations imply earlier formation times and hence more time for accretion and star formation, and/or because feedback is less efficient in haloes with higher binding energies. The maximum circular velocity, Vmax, DMO, and binding energy are therefore more fundamental properties than halo mass, meaning that they are more accurate predictors of stellar mass, and we provide fitting formulae for their relations with stellar mass. However, concentration alone cannot explain the total scatter in the Mstar−M200,DMO relation, and it does not explain the scatter in Mstar–Vmax, DMO. Halo spin, sphericity, triaxiality, substructure and environment are also not responsible for the remaining scatter, which thus could be due to more complex halo properties or non-linear/stochastic baryonic effects."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.08218"}],"month":"02","intvolume":" 465","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":465,"_id":"11565","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: formation","galaxies: haloes","cosmology: theory"],"date_updated":"2022-08-19T07:56:07Z","extern":"1"},{"date_updated":"2022-08-19T07:15:14Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics galaxies","active","galaxies","evolution","galaxies","high-redshift","galaxies","luminosity function","mass function","galaxies: star formation"],"_id":"11561","volume":471,"issue":"1","publication_identifier":{"issn":["0035-8711","1365-2966"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.04721"}],"month":"10","intvolume":" 471","abstract":[{"lang":"eng","text":"We present a sample of ∼1000 emission-line galaxies at z = 0.4–4.7 from the ∼0.7deg2 High-z Emission-Line Survey in the Boötes field identified with a suite of six narrow-band filters at ≈0.4–2.1 μm. These galaxies have been selected on their Ly α (73), [O II] (285), H β/[O III] (387) or H α (362) emission line, and have been classified with optical to near-infrared colours. A subsample of 98 sources have reliable redshifts from multiple narrow-band (e.g. [O II]–H α) detections and/or spectroscopy. In this survey paper, we present the observations, selection and catalogues of emitters. We measure number densities of Ly α, [O II], H β/[O III] and H α and confirm strong luminosity evolution in star-forming galaxies from z ∼ 0.4 to ∼5, in agreement with previous results. To demonstrate the usefulness of dual-line emitters, we use the sample of dual [O II]–H α emitters to measure the observed [O II]/H α ratio at z = 1.47. The observed [O II]/H α ratio increases significantly from 0.40 ± 0.01 at z = 0.1 to 0.52 ± 0.05 at z = 1.47, which we attribute to either decreasing dust attenuation with redshift, or due to a bias in the (typically) fibre measurements in the local Universe that only measure the central kpc regions. At the bright end, we find that both the H α and Ly α number densities at z ≈ 2.2 deviate significantly from a Schechter form, following a power law. We show that this is driven entirely by an increasing X-ray/active galactic nucleus fraction with line luminosity, which reaches ≈100 per cent at line luminosities L ≳ 3 × 1044 erg s−1."}],"oa_version":"Preprint","author":[{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee"},{"last_name":"Sobral","full_name":"Sobral, David","first_name":"David"},{"last_name":"Best","full_name":"Best, Philip","first_name":"Philip"},{"last_name":"Smail","full_name":"Smail, Ian","first_name":"Ian"},{"last_name":"Bian","full_name":"Bian, Fuyan","first_name":"Fuyan"},{"first_name":"Behnam","last_name":"Darvish","full_name":"Darvish, Behnam"},{"first_name":"Huub","last_name":"Röttgering","full_name":"Röttgering, Huub"},{"last_name":"Fan","full_name":"Fan, Xiaohui","first_name":"Xiaohui"}],"article_processing_charge":"No","external_id":{"arxiv":["1702.04721"]},"title":"Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7","citation":{"short":"J.J. Matthee, D. Sobral, P. Best, I. Smail, F. Bian, B. Darvish, H. Röttgering, X. Fan, Monthly Notices of the Royal Astronomical Society 471 (2017) 629–649.","ieee":"J. J. Matthee et al., “Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 1. Oxford University Press, pp. 629–649, 2017.","apa":"Matthee, J. J., Sobral, D., Best, P., Smail, I., Bian, F., Darvish, B., … Fan, X. (2017). Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1569","ama":"Matthee JJ, Sobral D, Best P, et al. Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7. Monthly Notices of the Royal Astronomical Society. 2017;471(1):629-649. doi:10.1093/mnras/stx1569","mla":"Matthee, Jorryt J., et al. “Boötes-HiZELS: An Optical to near-Infrared Survey of Emission-Line Galaxies at z = 0.4–4.7.” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 1, Oxford University Press, 2017, pp. 629–49, doi:10.1093/mnras/stx1569.","ista":"Matthee JJ, Sobral D, Best P, Smail I, Bian F, Darvish B, Röttgering H, Fan X. 2017. Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7. Monthly Notices of the Royal Astronomical Society. 471(1), 629–649.","chicago":"Matthee, Jorryt J, David Sobral, Philip Best, Ian Smail, Fuyan Bian, Behnam Darvish, Huub Röttgering, and Xiaohui Fan. “Boötes-HiZELS: An Optical to near-Infrared Survey of Emission-Line Galaxies at z = 0.4–4.7.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1569."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"629-649","date_published":"2017-10-01T00:00:00Z","doi":"10.1093/mnras/stx1569","date_created":"2022-07-12T11:01:35Z","year":"2017","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","quality_controlled":"1","publisher":"Oxford University Press","oa":1},{"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":472,"abstract":[{"lang":"eng","text":"We present spectroscopic follow-up of candidate luminous Ly α emitters (LAEs) at z = 5.7–6.6 in the SA22 field with VLT/X-SHOOTER. We confirm two new luminous LAEs at z = 5.676 (SR6) and z = 6.532 (VR7), and also present HST follow-up of both sources. These sources have luminosities LLy α ≈ 3 × 1043 erg s−1, very high rest-frame equivalent widths of EW0 ≳ 200 Å and narrow Ly α lines (200–340 km s−1). VR7 is the most UV-luminous LAE at z > 6.5, with M1500 = −22.5, even brighter in the UV than CR7. Besides Ly α, we do not detect any other rest-frame UV lines in the spectra of SR6 and VR7, and argue that rest-frame UV lines are easier to observe in bright galaxies with low Ly α equivalent widths. We confirm that Ly α line widths increase with Ly α luminosity at z = 5.7, while there are indications that Ly α lines of faint LAEs become broader at z = 6.6, potentially due to reionization. We find a large spread of up to 3 dex in UV luminosity for >L⋆ LAEs, but find that the Ly α luminosity of the brightest LAEs is strongly related to UV luminosity at z = 6.6. Under basic assumptions, we find that several LAEs at z ≈ 6–7 have Ly α escape fractions ≳ 100 per cent, indicating bursty star formation histories, alternative Ly α production mechanisms, or dust attenuating Ly α emission differently than UV emission. Finally, we present a method to compute ξion, the production efficiency of ionizing photons, and find that LAEs at z ≈ 6–7 have high values of log10(ξion/Hz erg−1) ≈ 25.51 ± 0.09 that may alleviate the need for high Lyman-Continuum escape fractions required for reionization."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.06591"}],"month":"11","intvolume":" 472","date_updated":"2022-08-19T08:05:37Z","extern":"1","_id":"11572","type":"journal_article","article_type":"original","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution – galaxies: high-redshift","dark ages","reionization","first stars","cosmology: observations"],"year":"2017","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","page":"772-787","doi":"10.1093/mnras/stx2061","date_published":"2017-11-01T00:00:00Z","date_created":"2022-07-13T09:47:39Z","acknowledgement":"We thank the referee for a constructive report that has improved the quality and clarity of this work. The authors thank Grecco Oyarzún for discussions. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G. We thank Kasper Schmidt for providing measurements. Based on observations with the W.M. Keck Observatory through programme C267D. The W.M. Keck Observatory is operated as a scientific partnership amongst the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 097.A-0943, 294.A 5018 and 098.A-0819 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. The authors acknowledge the award of observing time (W16AN004) and of service time (SW2014b20) on the William Herschel Telescope (WHT). WHT and its service programme are operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. Based on observations made with the NASA/ESA HST, obtained (from the Data Archive) at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with programme #14699. We are grateful for the excellent data sets from the COSMOS, UltraVISTA, SXDS, UDS and CFHTLS survey teams; without these legacy surveys, this research would have been impossible. We have benefited from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY and ASTROPY packages, the astronomical imaging tools SEXTRACTOR, SWARP and SCAMP and the TOPCAT analysis tool (Taylor 2013).","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"citation":{"mla":"Matthee, Jorryt J., et al. “Spectroscopic Properties of Luminous Ly α Emitters at z ≈ 6–7 and Comparison to the Lyman-Break Population.” Monthly Notices of the Royal Astronomical Society, vol. 472, no. 1, Oxford University Press, 2017, pp. 772–87, doi:10.1093/mnras/stx2061.","ieee":"J. J. Matthee et al., “Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population,” Monthly Notices of the Royal Astronomical Society, vol. 472, no. 1. Oxford University Press, pp. 772–787, 2017.","short":"J.J. Matthee, D. Sobral, B. Darvish, S. Santos, B. Mobasher, A. Paulino-Afonso, H. Röttgering, L. Alegre, Monthly Notices of the Royal Astronomical Society 472 (2017) 772–787.","ama":"Matthee JJ, Sobral D, Darvish B, et al. Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population. Monthly Notices of the Royal Astronomical Society. 2017;472(1):772-787. doi:10.1093/mnras/stx2061","apa":"Matthee, J. J., Sobral, D., Darvish, B., Santos, S., Mobasher, B., Paulino-Afonso, A., … Alegre, L. (2017). Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx2061","chicago":"Matthee, Jorryt J, David Sobral, Behnam Darvish, Sérgio Santos, Bahram Mobasher, Ana Paulino-Afonso, Huub Röttgering, and Lara Alegre. “Spectroscopic Properties of Luminous Ly α Emitters at z ≈ 6–7 and Comparison to the Lyman-Break Population.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx2061.","ista":"Matthee JJ, Sobral D, Darvish B, Santos S, Mobasher B, Paulino-Afonso A, Röttgering H, Alegre L. 2017. Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population. Monthly Notices of the Royal Astronomical Society. 472(1), 772–787."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee"},{"last_name":"Sobral","full_name":"Sobral, David","first_name":"David"},{"full_name":"Darvish, Behnam","last_name":"Darvish","first_name":"Behnam"},{"first_name":"Sérgio","last_name":"Santos","full_name":"Santos, Sérgio"},{"first_name":"Bahram","last_name":"Mobasher","full_name":"Mobasher, Bahram"},{"first_name":"Ana","full_name":"Paulino-Afonso, Ana","last_name":"Paulino-Afonso"},{"full_name":"Röttgering, Huub","last_name":"Röttgering","first_name":"Huub"},{"last_name":"Alegre","full_name":"Alegre, Lara","first_name":"Lara"}],"external_id":{"arxiv":["1706.06591"]},"article_processing_charge":"No","title":"Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population"},{"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: kinematics and dynamics"],"status":"public","article_type":"original","type":"journal_article","_id":"11573","extern":"1","date_updated":"2022-08-19T08:07:31Z","intvolume":" 471","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1704.06263","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We present dynamical measurements from the KMOS (K-band multi-object spectrograph) Deep Survey (KDS), which comprises 77 typical star-forming galaxies at z ≃ 3.5 in the mass range 9.0 < log (M⋆/M⊙) < 10.5. These measurements constrain the internal dynamics, the intrinsic velocity dispersions (σint) and rotation velocities (VC) of galaxies in the high-redshift Universe. The mean velocity dispersion of the galaxies in our sample is σint=70.8+3.3−3.1kms−1, revealing that the increasing average σint with increasing redshift, reported for z ≲ 2, continues out to z ≃ 3.5. Only 36 ± 8 per cent of our galaxies are rotation-dominated (VC/σint > 1), with the sample average VC/σint value much smaller than at lower redshift. After carefully selecting comparable star-forming samples at multiple epochs, we find that the rotation-dominated fraction evolves with redshift with a z−0.2 dependence. The rotation-dominated KDS galaxies show no clear offset from the local rotation velocity–stellar mass (i.e. VC–M⋆) relation, although a smaller fraction of the galaxies are on the relation due to the increase in the dispersion-dominated fraction. These observations are consistent with a simple equilibrium model picture, in which random motions are boosted in high-redshift galaxies by a combination of the increasing gas fractions, accretion efficiency, specific star formation rate and stellar feedback and which may provide significant pressure support against gravity on the galactic disc scale.","lang":"eng"}],"volume":471,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"title":"The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5","article_processing_charge":"No","external_id":{"arxiv":["1704.06263"]},"author":[{"first_name":"O. J.","full_name":"Turner, O. J.","last_name":"Turner"},{"last_name":"Cirasuolo","full_name":"Cirasuolo, M.","first_name":"M."},{"full_name":"Harrison, C. M.","last_name":"Harrison","first_name":"C. M."},{"first_name":"R. J.","full_name":"McLure, R. J.","last_name":"McLure"},{"full_name":"Dunlop, J. S.","last_name":"Dunlop","first_name":"J. S."},{"last_name":"Swinbank","full_name":"Swinbank, A. M.","first_name":"A. M."},{"first_name":"H. L.","last_name":"Johnson","full_name":"Johnson, H. L."},{"first_name":"D.","last_name":"Sobral","full_name":"Sobral, D."},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee"},{"last_name":"Sharples","full_name":"Sharples, R. M.","first_name":"R. M."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Turner OJ, Cirasuolo M, Harrison CM, McLure RJ, Dunlop JS, Swinbank AM, Johnson HL, Sobral D, Matthee JJ, Sharples RM. 2017. The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5. Monthly Notices of the Royal Astronomical Society. 471(2), 1280–1320.","chicago":"Turner, O. J., M. Cirasuolo, C. M. Harrison, R. J. McLure, J. S. Dunlop, A. M. Swinbank, H. L. Johnson, D. Sobral, Jorryt J Matthee, and R. M. Sharples. “The KMOS Deep Survey (KDS) – I. Dynamical Measurements of Typical Star-Forming Galaxies at z ≃ 3.5.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1366.","short":"O.J. Turner, M. Cirasuolo, C.M. Harrison, R.J. McLure, J.S. Dunlop, A.M. Swinbank, H.L. Johnson, D. Sobral, J.J. Matthee, R.M. Sharples, Monthly Notices of the Royal Astronomical Society 471 (2017) 1280–1320.","ieee":"O. J. Turner et al., “The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 2. Oxford University Press, pp. 1280–1320, 2017.","ama":"Turner OJ, Cirasuolo M, Harrison CM, et al. The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5. Monthly Notices of the Royal Astronomical Society. 2017;471(2):1280-1320. doi:10.1093/mnras/stx1366","apa":"Turner, O. J., Cirasuolo, M., Harrison, C. M., McLure, R. J., Dunlop, J. S., Swinbank, A. M., … Sharples, R. M. (2017). The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1366","mla":"Turner, O. J., et al. “The KMOS Deep Survey (KDS) – I. Dynamical Measurements of Typical Star-Forming Galaxies at z ≃ 3.5.” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 2, Oxford University Press, 2017, pp. 1280–320, doi:10.1093/mnras/stx1366."},"oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"We wish to thank the anonymous referee for their comments, which have improved the quality and clarity of this work. OJT acknowledges the financial support of the Science and Technology Facilities Council through a studentship award. MC and OJT acknowledge the KMOS team and all the personnel of the European Southern Observatory Very Large Telescope for outstanding support during the KMOS GTO observations. CMH, AMS and RMS acknowledge the Science and Technology Facilities Council through grant code ST/L00075X/1. RJM acknowledges the support of the European Research Council via the award of a Consolidator Grant (PI: McLure). JSD acknowledges the support of the European Research Council via the award of an Advanced Grant (PI J. Dunlop), and the contribution of the EC FP7 SPACE project ASTRODEEP (Ref.No: 312725). AMS acknowledges the Leverhulme Foundation. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). This work is based on observations taken by the CANDELS Multi-Cycle Treasury Program with the NASA/ESA HST, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. This work is based on observations taken by the 3D HST Treasury Program (GO 12177 and 12328) with the NASA/ESA HST, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. Based on data obtained with the European Southern Observatory Very Large Telescope, Paranal, Chile, under Large Program 185.A-0791, and made available by the VUDS team at the CESAM data centre, Laboratoire d’Astrophysique de Marseille, France. Based on observations obtained at the Very Large Telescope of the European Southern Observatory. Programme IDs: 092.A 0399(A), 093.A-0122(A,B), 094.A-0214(A,B),095.A0680(A,B),096.A-0315(A,B,C).","date_created":"2022-07-13T10:03:01Z","doi":"10.1093/mnras/stx1366","date_published":"2017-10-01T00:00:00Z","page":"1280-1320","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","year":"2017"},{"_id":"11633","article_number":"1711.02890","type":"preprint","status":"public","keyword":["asteroseismology - methods","data analysis - stars","oscillations"],"date_updated":"2022-08-22T08:45:42Z","citation":{"mla":"Bugnet, Lisa Annabelle, et al. “FliPer: Checking the Reliability of Global Seismic Parameters from Automatic Pipelines.” ArXiv, 1711.02890, doi:10.48550/arXiv.1711.02890.","apa":"Bugnet, L. A., Garcia, R. A., Davies, G. R., Mathur, S., & Corsaro, E. (n.d.). FliPer: Checking the reliability of global seismic parameters from automatic pipelines. arXiv. https://doi.org/10.48550/arXiv.1711.02890","ama":"Bugnet LA, Garcia RA, Davies GR, Mathur S, Corsaro E. FliPer: Checking the reliability of global seismic parameters from automatic pipelines. arXiv. doi:10.48550/arXiv.1711.02890","short":"L.A. Bugnet, R.A. Garcia, G.R. Davies, S. Mathur, E. Corsaro, ArXiv (n.d.).","ieee":"L. A. Bugnet, R. A. Garcia, G. R. Davies, S. Mathur, and E. Corsaro, “FliPer: Checking the reliability of global seismic parameters from automatic pipelines,” arXiv. .","chicago":"Bugnet, Lisa Annabelle, R. A. Garcia, G. R. Davies, S. Mathur, and E. Corsaro. “FliPer: Checking the Reliability of Global Seismic Parameters from Automatic Pipelines.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1711.02890.","ista":"Bugnet LA, Garcia RA, Davies GR, Mathur S, Corsaro E. FliPer: Checking the reliability of global seismic parameters from automatic pipelines. arXiv, 1711.02890."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"},{"first_name":"R. A.","last_name":"Garcia","full_name":"Garcia, R. A."},{"first_name":"G. R.","last_name":"Davies","full_name":"Davies, G. R."},{"last_name":"Mathur","full_name":"Mathur, S.","first_name":"S."},{"first_name":"E.","last_name":"Corsaro","full_name":"Corsaro, E."}],"external_id":{"arxiv":["1711.02890"]},"article_processing_charge":"No","title":"FliPer: Checking the reliability of global seismic parameters from automatic pipelines","abstract":[{"lang":"eng","text":"Our understanding of stars through asteroseismic data analysis is limited by our ability to take advantage of the huge amount of observed stars provided by space missions such as CoRoT, Kepler , K2, and soon TESS and PLATO. Global seismic pipelines provide global stellar parameters such as mass and radius using the mean seismic parameters, as well as the effective temperature. These pipelines are commonly used automatically on thousands of stars observed by K2 for 3 months (and soon TESS for at least ∼ 1 month). However, pipelines are not immune from misidentifying noise peaks and stellar oscillations. Therefore, new validation techniques are required to assess the quality of these results. We present a new metric called FliPer (Flicker in Power), which takes into account the average variability at all measured time scales. The proper calibration of FliPer enables us to obtain good estimations of global stellar parameters such as surface gravity that are robust against the influence of noise peaks and hence are an excellent way to find faults in asteroseismic pipelines."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1711.02890"}],"oa":1,"month":"11","publication_status":"submitted","year":"2017","day":"08","language":[{"iso":"eng"}],"publication":"arXiv","doi":"10.48550/arXiv.1711.02890","date_published":"2017-11-08T00:00:00Z","date_created":"2022-07-21T07:13:13Z"},{"title":"Capacity releasing diffusion for speed and locality","external_id":{"arxiv":["1706.05826"]},"article_processing_charge":"No","author":[{"first_name":"Di","last_name":"Wang","full_name":"Wang, Di"},{"full_name":"Fountoulakis, Kimon","last_name":"Fountoulakis","first_name":"Kimon"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"first_name":"Michael W.","full_name":"Mahoney, Michael W.","last_name":"Mahoney"},{"first_name":" Satish","last_name":"Rao ","full_name":"Rao , Satish"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Wang, Di, Kimon Fountoulakis, Monika H Henzinger, Michael W. Mahoney, and Satish Rao . “Capacity Releasing Diffusion for Speed and Locality.” In Proceedings of the 34th International Conference on Machine Learning, 70:3598–3607. ML Research Press, 2017.","ista":"Wang D, Fountoulakis K, Henzinger MH, Mahoney MW, Rao Satish. 2017. Capacity releasing diffusion for speed and locality. Proceedings of the 34th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 70, 3598–3607.","mla":"Wang, Di, et al. “Capacity Releasing Diffusion for Speed and Locality.” Proceedings of the 34th International Conference on Machine Learning, vol. 70, ML Research Press, 2017, pp. 3598–607.","short":"D. Wang, K. Fountoulakis, M.H. Henzinger, M.W. Mahoney, Satish Rao , in:, Proceedings of the 34th International Conference on Machine Learning, ML Research Press, 2017, pp. 3598–3607.","ieee":"D. Wang, K. Fountoulakis, M. H. Henzinger, M. W. Mahoney, and Satish Rao , “Capacity releasing diffusion for speed and locality,” in Proceedings of the 34th International Conference on Machine Learning, Sydney, Australia, 2017, vol. 70, pp. 3598–3607.","apa":"Wang, D., Fountoulakis, K., Henzinger, M. H., Mahoney, M. W., & Rao , Satish. (2017). Capacity releasing diffusion for speed and locality. In Proceedings of the 34th International Conference on Machine Learning (Vol. 70, pp. 3598–3607). Sydney, Australia: ML Research Press.","ama":"Wang D, Fountoulakis K, Henzinger MH, Mahoney MW, Rao Satish. Capacity releasing diffusion for speed and locality. In: Proceedings of the 34th International Conference on Machine Learning. Vol 70. ML Research Press; 2017:3598-3607."},"date_created":"2022-07-25T13:59:21Z","date_published":"2017-09-01T00:00:00Z","page":"3598-3607","publication":"Proceedings of the 34th International Conference on Machine Learning","day":"01","year":"2017","oa":1,"publisher":"ML Research Press","quality_controlled":"1","extern":"1","date_updated":"2023-02-09T09:15:31Z","status":"public","conference":{"start_date":"2017-08-06","end_date":"2017-08-11","location":"Sydney, Australia","name":"International Conference on Machine Learning"},"type":"conference","_id":"11651","volume":70,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2640-3498"]},"intvolume":" 70","month":"09","main_file_link":[{"url":"http://proceedings.mlr.press/v70/wang17b/wang17b.pdf","open_access":"1"}],"alternative_title":["PMLR"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Diffusions and related random walk procedures are of central importance in many areas of machine learning, data analysis, and applied mathematics. Because they spread mass agnostically at each step in an iterative manner, they can sometimes spread mass “too aggressively,” thereby failing to find the “right” clusters. We introduce a novel Capacity Releasing Diffusion (CRD) Process, which is both faster and stays more local than the classical spectral diffusion process. As an application, we use our CRD Process to develop an improved local algorithm for graph clustering. Our local graph clustering method can find local clusters in a model of clustering where one begins the CRD Process in a cluster whose vertices are connected better internally than externally by an O(log2n) factor, where n is the number of nodes in the cluster. Thus, our CRD Process is the first local graph clustering algorithm that is not subject to the well-known quadratic Cheeger barrier. Our result requires a certain smoothness condition, which we expect to be an artifact of our analysis. Our empirical evaluation demonstrates improved results, in particular for realistic social graphs where there are moderately good—but not very good—clusters."}]}]