--- _id: '5586' abstract: - lang: eng text: Input files and scripts from "Evolution of gene dosage on the Z-chromosome of schistosome parasites" by Picard M.A.L., et al (2018). article_processing_charge: No author: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109 apa: Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109 chicago: Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109. ieee: B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018. ista: Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, 10.15479/AT:ISTA:109. mla: Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018). Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109. short: B. Vicoso, (2018). contributor: - first_name: Marion A id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 datarep_id: '109' date_created: 2018-12-12T12:31:40Z date_published: 2018-07-24T00:00:00Z date_updated: 2024-02-21T13:45:12Z day: '24' ddc: - '570' department: - _id: BeVi doi: 10.15479/AT:ISTA:109 file: - access_level: open_access checksum: e60b484bd6f55c08eb66a189cb72c923 content_type: application/zip creator: system date_created: 2018-12-12T13:02:35Z date_updated: 2020-07-14T12:47:08Z file_id: '5601' file_name: IST-2018-109-v1+1_SupplementaryMethods.zip file_size: 11918144 relation: main_file file_date_updated: 2020-07-14T12:47:08Z has_accepted_license: '1' keyword: - schistosoma - Z-chromosome - gene expression month: '07' oa: 1 oa_version: Published Version project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publisher: Institute of Science and Technology Austria related_material: record: - id: '131' relation: research_paper status: public status: public title: Input files and scripts from "Evolution of gene dosage on the Z-chromosome of schistosome parasites" by Picard M.A.L., et al (2018) tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '5583' abstract: - lang: eng text: "Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone." article_processing_charge: No author: - first_name: Thomas full_name: Ellis, Thomas id: 3153D6D4-F248-11E8-B48F-1D18A9856A87 last_name: Ellis orcid: 0000-0002-8511-0254 citation: ama: Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95 apa: Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95 chicago: Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95. ieee: T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018. ista: Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95. mla: Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95. short: T. Ellis, (2018). contributor: - first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field - first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton datarep_id: '95' date_created: 2018-12-12T12:31:39Z date_published: 2018-02-12T00:00:00Z date_updated: 2024-02-21T13:45:01Z day: '12' department: - _id: NiBa doi: 10.15479/AT:ISTA:95 file: - access_level: open_access checksum: fc6aab51439f2622ba6df8632e66fd4f content_type: text/csv creator: system date_created: 2018-12-12T13:02:41Z date_updated: 2020-07-14T12:47:07Z file_id: '5606' file_name: IST-2018-95-v1+1_amajus_GPS_2012.csv file_size: 122048 relation: main_file - access_level: open_access checksum: 92347586ae4f8a6eb7c04354797bf314 content_type: text/csv creator: system date_created: 2018-12-12T13:02:42Z date_updated: 2020-07-14T12:47:07Z file_id: '5607' file_name: IST-2018-95-v1+2_offspring_SNPs_2012.csv file_size: 235980 relation: main_file - access_level: open_access checksum: 3300813645a54e6c5c39f41917228354 content_type: text/csv creator: system date_created: 2018-12-12T13:02:43Z date_updated: 2020-07-14T12:47:07Z file_id: '5608' file_name: IST-2018-95-v1+3_parents_SNPs_2012.csv file_size: 311712 relation: main_file - access_level: open_access checksum: e739fc473567fd8f39438b445fc46147 content_type: application/zip creator: system date_created: 2018-12-12T13:02:44Z date_updated: 2020-07-14T12:47:07Z file_id: '5609' file_name: IST-2018-95-v1+4_faps_scripts.zip file_size: 342090 relation: main_file file_date_updated: 2020-07-14T12:47:07Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '286' relation: research_paper status: public status: public title: Data and Python scripts supporting Python package FAPS tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '5569' abstract: - lang: eng text: "Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic." article_processing_charge: No author: - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 citation: ama: Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74 apa: Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74 chicago: Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74. ieee: T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018. ista: Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74. mla: Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74. short: T. Bergmiller, N. Nikolic, (2018). datarep_id: '74' date_created: 2018-12-12T12:31:35Z date_published: 2018-02-07T00:00:00Z date_updated: 2024-02-21T13:44:45Z day: '07' ddc: - '579' department: - _id: CaGu doi: 10.15479/AT:ISTA:74 file: - access_level: open_access checksum: 61ebb92213cfffeba3ddbaff984b81af content_type: application/zip creator: system date_created: 2018-12-12T13:04:39Z date_updated: 2020-07-14T12:47:04Z file_id: '5637' file_name: IST-2018-74-v1+2_15-11-05.zip file_size: 3558703796 relation: main_file - access_level: open_access checksum: bf26649af310ef6892d68576515cde6d content_type: application/zip creator: system date_created: 2018-12-12T13:04:55Z date_updated: 2020-07-14T12:47:04Z file_id: '5638' file_name: IST-2018-74-v1+3_15-07-31.zip file_size: 1830422606 relation: main_file - access_level: open_access checksum: 8e46eedce06f22acb2be1a9b9d3f56bd content_type: application/zip creator: system date_created: 2018-12-12T13:05:11Z date_updated: 2020-07-14T12:47:04Z file_id: '5639' file_name: IST-2018-74-v1+4_Images_for_analysis.zip file_size: 2140849248 relation: main_file file_date_updated: 2020-07-14T12:47:04Z has_accepted_license: '1' keyword: - microscopy - microfluidics month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria publist_id: '7385' related_material: record: - id: '438' relation: research_paper status: public status: public title: Time-lapse microscopy 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) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '161' abstract: - lang: eng text: 'Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells.' article_number: '2988' article_processing_charge: No author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Andersson Anna full_name: Mc, Andersson Anna last_name: Mc - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9 apa: De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9 chicago: De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9. ieee: D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018. ista: De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988. mla: De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9. short: D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018). date_created: 2018-12-11T11:44:57Z date_published: 2018-07-30T00:00:00Z date_updated: 2024-02-21T13:45:39Z day: '30' ddc: - '570' department: - _id: GaTk - _id: CaGu doi: 10.1038/s41467-018-05417-9 ec_funded: 1 external_id: isi: - '000440149300021' file: - access_level: open_access checksum: 3ba7ab27b27723c7dcf633e8fc1f8f18 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:44:28Z date_updated: 2020-07-14T12:45:06Z file_id: '5728' file_name: 2018_NatureComm_DeMartino.pdf file_size: 1043205 relation: main_file file_date_updated: 2020-07-14T12:45:06Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Communications publication_status: published publisher: Springer Nature publist_id: '7760' quality_controlled: '1' related_material: record: - id: '5587' relation: popular_science status: public scopus_import: '1' status: public title: Statistical mechanics for metabolic networks during steady state growth tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 9 year: '2018' ... --- _id: '5587' abstract: - lang: eng text: "Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015)." article_processing_charge: No author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62 apa: De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:62 chicago: De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62. ieee: D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. ista: De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:62. mla: De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62. short: D. De Martino, G. Tkačik, (2018). datarep_id: '111' date_created: 2018-12-12T12:31:41Z date_published: 2018-09-21T00:00:00Z date_updated: 2024-02-21T13:45:39Z day: '21' ddc: - '530' department: - _id: GaTk doi: 10.15479/AT:ISTA:62 ec_funded: 1 file: - access_level: open_access checksum: 97992e3e8cf8544ec985a48971708726 content_type: application/zip creator: system date_created: 2018-12-12T13:05:13Z date_updated: 2020-07-14T12:47:08Z file_id: '5641' file_name: IST-2018-111-v1+1_CODES.zip file_size: 14376 relation: main_file file_date_updated: 2020-07-14T12:47:08Z has_accepted_license: '1' keyword: - metabolic networks - e.coli core - maximum entropy - monte carlo markov chain sampling - ellipsoidal rounding month: '09' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publisher: Institute of Science and Technology Austria related_material: record: - id: '161' relation: research_paper status: public status: public title: Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH" tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '542' abstract: - lang: eng text: The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter. article_processing_charge: No article_type: original author: - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513 apa: Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300513 chicago: Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300513. ieee: R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018. ista: Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375. mla: Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513. short: R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375. date_created: 2018-12-11T11:47:04Z date_published: 2018-01-01T00:00:00Z date_updated: 2024-02-21T13:48:27Z day: '01' ddc: - '576' department: - _id: BeVi doi: 10.1534/genetics.117.300513 ec_funded: 1 external_id: isi: - '000419356300024' file: - access_level: open_access checksum: 2123845e7031a0cf043905be160f9e69 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:14Z date_updated: 2020-07-14T12:46:50Z file_id: '5132' file_name: IST-2018-1058-v1+1_365.full__1_.pdf file_size: 1311661 relation: main_file file_date_updated: 2020-07-14T12:46:50Z has_accepted_license: '1' intvolume: ' 208' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 365 - 375 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '7274' pubrep_id: '1058' quality_controlled: '1' related_material: record: - id: '5571' relation: popular_science status: public - id: '5572' relation: popular_science status: public scopus_import: '1' status: public title: Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 208 year: '2018' ... --- _id: '5751' abstract: - lang: eng text: 'Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures.' article_number: '71' article_processing_charge: No author: - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7 apa: Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7 chicago: Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology. Springer Nature, 2018. https://doi.org/10.1038/s42003-018-0078-7. ieee: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018. ista: Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71. mla: Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology, vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7. short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018). date_created: 2018-12-18T13:22:58Z date_published: 2018-06-14T00:00:00Z date_updated: 2024-02-21T13:48:42Z day: '14' ddc: - '004' - '519' - '576' department: - _id: KrCh doi: 10.1038/s42003-018-0078-7 ec_funded: 1 external_id: isi: - '000461126500071' file: - access_level: open_access checksum: a9db825fa3b64a51ff3de035ec973b3e content_type: application/pdf creator: dernst date_created: 2018-12-18T13:37:04Z date_updated: 2020-07-14T12:47:10Z file_id: '5752' file_name: 2018_CommBiology_Pavlogiannis.pdf file_size: 1804194 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 1' isi: 1 issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Communications Biology publication_identifier: issn: - 2399-3642 publication_status: published publisher: Springer Nature pubrep_id: '1045' quality_controlled: '1' related_material: record: - id: '7196' relation: part_of_dissertation status: public - id: '5559' relation: popular_science status: public scopus_import: '1' status: public title: Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 1 year: '2018' ... --- _id: '5757' abstract: - lang: eng text: "File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants." article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 citation: ama: Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757 apa: Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757 chicago: Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757. ieee: C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018. ista: Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757. mla: Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757. short: C. Fraisse, (2018). contributor: - first_name: Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse - first_name: Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala - first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 date_created: 2018-12-19T14:22:35Z date_published: 2018-12-19T00:00:00Z date_updated: 2024-02-21T13:59:18Z day: '19' ddc: - '576' department: - _id: BeVi - _id: NiBa doi: 10.15479/at:ista:/5757 ec_funded: 1 file: - access_level: open_access checksum: aed7ee9ca3f4dc07d8a66945f68e13cd content_type: application/zip creator: cfraisse date_created: 2018-12-19T14:19:52Z date_updated: 2020-07-14T12:47:11Z file_id: '5758' file_name: FileS1.zip file_size: 369837892 relation: main_file - access_level: open_access checksum: 3592e467b4d8206650860b612d6e12f3 content_type: application/zip creator: cfraisse date_created: 2018-12-19T14:19:49Z date_updated: 2020-07-14T12:47:11Z file_id: '5759' file_name: FileS2.zip file_size: 84856909 relation: main_file - access_level: open_access checksum: c37ac5d5437c457338afc128c1240655 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:49Z date_updated: 2020-07-14T12:47:11Z file_id: '5760' file_name: FileS3.txt file_size: 881133 relation: main_file - access_level: open_access checksum: 943dfd14da61817441e33e3e3cb8cdb9 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:49Z date_updated: 2020-07-14T12:47:11Z file_id: '5761' file_name: FileS4.txt file_size: 883742 relation: main_file - access_level: open_access checksum: 1c669b6c4690ec1bbca3e2da9f566d17 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:49Z date_updated: 2020-07-14T12:47:11Z file_id: '5762' file_name: FileS5.txt file_size: 2495437 relation: main_file - access_level: open_access checksum: f40f661b987ca6fb6b47f650cbbb04e6 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:50Z date_updated: 2020-07-14T12:47:11Z file_id: '5763' file_name: FileS6.txt file_size: 15913457 relation: main_file - access_level: open_access checksum: 25f41e5b8a075669c6c88d4c6713bf6f content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:50Z date_updated: 2020-07-14T12:47:11Z file_id: '5764' file_name: FileS7.txt file_size: 2584120 relation: main_file - access_level: open_access checksum: f6c0bd3e63e14ddf5445bd69b43a9152 content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:50Z date_updated: 2020-07-14T12:47:11Z file_id: '5765' file_name: FileS8.txt file_size: 2446059 relation: main_file - access_level: open_access checksum: 0fe7a58a030b11bf3b9c8ff7a7addcae content_type: text/plain creator: cfraisse date_created: 2018-12-19T14:19:50Z date_updated: 2020-07-14T12:47:11Z file_id: '5766' file_name: FileS9.txt file_size: 100737 relation: main_file file_date_updated: 2020-07-14T12:47:11Z has_accepted_license: '1' keyword: - (mal)adaptation - pleiotropy - selective constraint - evo-devo - gene expression - Drosophila melanogaster month: '12' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publisher: Institute of Science and Technology Austria related_material: record: - id: '6089' relation: research_paper status: public status: public title: Supplementary Files for "Pleiotropy modulates the efficacy of selection in Drosophila melanogaster" type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '149' abstract: - lang: eng text: The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt citation: ama: Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040 apa: Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040 chicago: Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040. ieee: J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018. ista: Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. mla: Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040. short: J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:53Z date_published: 2018-07-12T00:00:00Z date_updated: 2024-02-22T14:34:33Z day: '12' ddc: - '515' - '519' degree_awarded: PhD department: - _id: LaEr doi: 10.15479/AT:ISTA:TH_1040 ec_funded: 1 file: - access_level: open_access checksum: d4dad55a7513f345706aaaba90cb1bb8 content_type: application/pdf creator: dernst date_created: 2019-04-08T13:55:20Z date_updated: 2020-07-14T12:44:57Z file_id: '6241' file_name: 2018_thesis_Alt.pdf file_size: 5801709 relation: main_file - access_level: closed checksum: d73fcf46300dce74c403f2b491148ab4 content_type: application/zip creator: dernst date_created: 2019-04-08T13:55:20Z date_updated: 2020-07-14T12:44:57Z file_id: '6242' file_name: 2018_thesis_Alt_source.zip file_size: 3802059 relation: source_file file_date_updated: 2020-07-14T12:44:57Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '456' project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7772' pubrep_id: '1040' related_material: record: - id: '1677' relation: part_of_dissertation status: public - id: '550' relation: part_of_dissertation status: public - id: '6183' relation: part_of_dissertation status: public - id: '566' relation: part_of_dissertation status: public - id: '1010' relation: part_of_dissertation status: public - id: '6240' relation: part_of_dissertation status: public - id: '6184' relation: part_of_dissertation status: public status: public supervisor: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 title: Dyson equation and eigenvalue statistics of random matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '415' abstract: - lang: eng text: Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field. acknowledgement: "We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n" article_number: '104307' article_processing_charge: No article_type: original author: - first_name: Wojciech full_name: Rzadkowski, Wojciech id: 48C55298-F248-11E8-B48F-1D18A9856A87 last_name: Rzadkowski orcid: 0000-0002-1106-4419 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591 apa: Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5017591 chicago: Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5017591. ieee: W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” The Journal of Chemical Physics, vol. 148, no. 10. AIP Publishing, 2018. ista: Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307. mla: Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591. short: W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018). date_created: 2018-12-11T11:46:21Z date_published: 2018-03-14T00:00:00Z date_updated: 2024-02-28T13:01:59Z day: '14' department: - _id: MiLe doi: 10.1063/1.5017591 ec_funded: 1 external_id: arxiv: - '1711.09904' isi: - '000427517200065' intvolume: ' 148' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.09904 month: '03' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: The Journal of Chemical Physics publication_status: published publisher: AIP Publishing publist_id: '7408' quality_controlled: '1' related_material: record: - id: '10759' relation: dissertation_contains status: public scopus_import: '1' status: public title: Effect of a magnetic field on molecule–solvent angular momentum transfer type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 148 year: '2018' ... --- _id: '134' abstract: - lang: eng text: "The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface." acknowledged_ssus: - _id: ScienComp alternative_title: - SIGGRAPH article_number: '94' article_processing_charge: No author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Tomas full_name: Skrivan, Tomas id: 486A5A46-F248-11E8-B48F-1D18A9856A87 last_name: Skrivan - first_name: Matthias full_name: Mueller Fischer, Matthias last_name: Mueller Fischer - first_name: Nuttapong full_name: Chentanez, Nuttapong last_name: Chentanez - first_name: Miles full_name: Macklin, Miles last_name: Macklin - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336 apa: Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336 chicago: Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336. ieee: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018. ista: Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94. mla: Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336. short: S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018). date_created: 2018-12-11T11:44:48Z date_published: 2018-07-30T00:00:00Z date_updated: 2024-02-28T13:58:51Z day: '30' ddc: - '000' department: - _id: ChWo doi: 10.1145/3197517.3201336 ec_funded: 1 external_id: isi: - '000448185000055' file: - access_level: open_access checksum: db75ebabe2ec432bf41389e614d6ef62 content_type: application/pdf creator: dernst date_created: 2018-12-18T09:59:23Z date_updated: 2020-07-14T12:44:45Z file_id: '5744' file_name: 2018_ACM_Jeschke.pdf file_size: 22185016 relation: main_file file_date_updated: 2020-07-14T12:44:45Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '7789' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/ scopus_import: '1' status: public title: Water surface wavelets tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2018' ... --- _id: '6339' abstract: - lang: eng text: We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment. article_number: '165301' article_processing_charge: No author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Timur full_name: Tscherbul, Timur last_name: Tscherbul - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301 apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301 chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301. ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018. ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301. mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301. short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018). date_created: 2019-04-17T10:53:38Z date_published: 2018-10-16T00:00:00Z date_updated: 2024-02-28T13:15:09Z day: '16' department: - _id: MiLe doi: 10.1103/physrevlett.121.165301 external_id: arxiv: - '1803.07990' isi: - '000447468400008' intvolume: ' 121' isi: 1 issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.07990 month: '10' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review Letters publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/ scopus_import: '1' status: public title: Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2018' ... --- _id: '417' abstract: - lang: eng text: 'We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. ' article_number: '165301' article_processing_charge: No author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Timur full_name: Tscherbul, Timur last_name: Tscherbul - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301 apa: Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301 chicago: Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301. ieee: G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018. ista: Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301. mla: Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301. short: G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018). date_created: 2018-12-11T11:46:22Z date_published: 2018-10-16T00:00:00Z date_updated: 2024-02-28T13:14:53Z day: '16' department: - _id: MiLe doi: 10.1103/PhysRevLett.121.165301 external_id: arxiv: - '1803.07990' intvolume: ' 121' issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.07990 month: '10' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '8025' quality_controlled: '1' scopus_import: '1' status: public title: Diagrammatic Monte Carlo approach to rotating molecular impurities type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2018' ... --- _id: '6665' abstract: - lang: eng text: We prove that, at least for the binary erasure channel, the polar-coding paradigm gives rise to codes that not only approach the Shannon limit but, in fact, do so under the best possible scaling of their block length as a function of the gap to capacity. This result exhibits the first known family of binary codes that attain both optimal scaling and quasi-linear complexity of encoding and decoding. Specifically, for any fixed δ > 0, we exhibit binary linear codes that ensure reliable communication at rates within ε > 0 of capacity with block length n = O(1/ε 2+δ ), construction complexity Θ(n), and encoding/decoding complexity Θ(n log n). author: - first_name: Arman full_name: Fazeli, Arman last_name: Fazeli - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Alexander full_name: Vardy, Alexander last_name: Vardy citation: ama: 'Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal scaling: Polar codes with large kernels. In: 2018 IEEE Information Theory Workshop. IEEE; 2018:1-5. doi:10.1109/itw.2018.8613428' apa: 'Fazeli, A., Hassani, H., Mondelli, M., & Vardy, A. (2018). Binary linear codes with optimal scaling: Polar codes with large kernels. In 2018 IEEE Information Theory Workshop (pp. 1–5). Guangzhou, China: IEEE. https://doi.org/10.1109/itw.2018.8613428' chicago: 'Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” In 2018 IEEE Information Theory Workshop, 1–5. IEEE, 2018. https://doi.org/10.1109/itw.2018.8613428.' ieee: 'A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with optimal scaling: Polar codes with large kernels,” in 2018 IEEE Information Theory Workshop, Guangzhou, China, 2018, pp. 1–5.' ista: 'Fazeli A, Hassani H, Mondelli M, Vardy A. 2018. Binary linear codes with optimal scaling: Polar codes with large kernels. 2018 IEEE Information Theory Workshop. ITW: Information Theory Workshop, 1–5.' mla: 'Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” 2018 IEEE Information Theory Workshop, IEEE, 2018, pp. 1–5, doi:10.1109/itw.2018.8613428.' short: A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, in:, 2018 IEEE Information Theory Workshop, IEEE, 2018, pp. 1–5. conference: end_date: 2018-11-29 location: Guangzhou, China name: 'ITW: Information Theory Workshop' start_date: 2018-11-25 date_created: 2019-07-23T11:01:42Z date_published: 2018-11-01T00:00:00Z date_updated: 2024-03-07T12:18:50Z day: '01' doi: 10.1109/itw.2018.8613428 extern: '1' external_id: arxiv: - '1711.01339' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.01339 month: '11' oa: 1 oa_version: Preprint page: 1-5 publication: 2018 IEEE Information Theory Workshop publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '9002' relation: later_version status: public status: public title: 'Binary linear codes with optimal scaling: Polar codes with large kernels' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '15143' abstract: - lang: eng text: To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome assembly involves multiple sequence-specific RNA–RNA interactions between single-stranded RNA segment precursors. These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus σNS. Here, we compared the abilities of NSP2 and σNS to mediate sequence-specific interactions between RV genomic segment precursors. Despite their similar activities, NSP2 successfully promotes inter-segment association, while σNS fails to do so. To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity, resulting in efficient intramolecular RNA helix disruption. Hexameric σNS oligomerizes into an octamer that binds two RNAs, yet it exhibits only limited RNA-unwinding activity compared to NSP2. Thus, the formation of intersegment RNA–RNA interactions is governed by both helix-unwinding capacity of the chaperones and stability of RNA structure. We propose that this protein-mediated RNA selection mechanism may underpin the high fidelity assembly of multi-segmented RNA genomes in Reoviridae. article_processing_charge: Yes article_type: original author: - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Alexander full_name: Borodavka, Alexander last_name: Borodavka - first_name: Anders full_name: Barth, Anders last_name: Barth - first_name: Antonio N full_name: Calabrese, Antonio N last_name: Calabrese - first_name: Peter full_name: Mojzes, Peter last_name: Mojzes - first_name: Joseph J B full_name: Cockburn, Joseph J B last_name: Cockburn - first_name: Don C full_name: Lamb, Don C last_name: Lamb - first_name: Roman full_name: Tuma, Roman last_name: Tuma citation: ama: Bravo JPK, Borodavka A, Barth A, et al. Stability of local secondary structure determines selectivity of viral RNA chaperones. Nucleic Acids Research. 2018;46(15):7924-7937. doi:10.1093/nar/gky394 apa: Bravo, J. P. K., Borodavka, A., Barth, A., Calabrese, A. N., Mojzes, P., Cockburn, J. J. B., … Tuma, R. (2018). Stability of local secondary structure determines selectivity of viral RNA chaperones. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gky394 chicago: Bravo, Jack Peter Kelly, Alexander Borodavka, Anders Barth, Antonio N Calabrese, Peter Mojzes, Joseph J B Cockburn, Don C Lamb, and Roman Tuma. “Stability of Local Secondary Structure Determines Selectivity of Viral RNA Chaperones.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky394. ieee: J. P. K. Bravo et al., “Stability of local secondary structure determines selectivity of viral RNA chaperones,” Nucleic Acids Research, vol. 46, no. 15. Oxford University Press, pp. 7924–7937, 2018. ista: Bravo JPK, Borodavka A, Barth A, Calabrese AN, Mojzes P, Cockburn JJB, Lamb DC, Tuma R. 2018. Stability of local secondary structure determines selectivity of viral RNA chaperones. Nucleic Acids Research. 46(15), 7924–7937. mla: Bravo, Jack Peter Kelly, et al. “Stability of Local Secondary Structure Determines Selectivity of Viral RNA Chaperones.” Nucleic Acids Research, vol. 46, no. 15, Oxford University Press, 2018, pp. 7924–37, doi:10.1093/nar/gky394. short: J.P.K. Bravo, A. Borodavka, A. Barth, A.N. Calabrese, P. Mojzes, J.J.B. Cockburn, D.C. Lamb, R. Tuma, Nucleic Acids Research 46 (2018) 7924–7937. date_created: 2024-03-20T10:43:13Z date_published: 2018-09-06T00:00:00Z date_updated: 2024-03-20T11:10:56Z day: '06' doi: 10.1093/nar/gky394 extern: '1' external_id: pmid: - '29796667' intvolume: ' 46' issue: '15' keyword: - Genetics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/nar/gky394 month: '09' oa: 1 oa_version: Published Version page: 7924-7937 pmid: 1 publication: Nucleic Acids Research publication_identifier: eissn: - 1362-4962 issn: - 0305-1048 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Stability of local secondary structure determines selectivity of viral RNA chaperones type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2018' ... --- _id: '412' abstract: - lang: eng text: Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana. acknowledgement: We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417. article_processing_charge: No article_type: original author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Madhumitha full_name: Narasimhan, Madhumitha id: 44BF24D0-F248-11E8-B48F-1D18A9856A87 last_name: Narasimhan orcid: 0000-0002-8600-0671 - first_name: Urszula full_name: Kania, Urszula id: 4AE5C486-F248-11E8-B48F-1D18A9856A87 last_name: Kania - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785 apa: Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785 chicago: Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785. ieee: M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018. ista: Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716. mla: Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785. short: M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716. date_created: 2018-12-11T11:46:20Z date_published: 2018-04-09T00:00:00Z date_updated: 2024-03-27T23:30:06Z day: '09' ddc: - '580' department: - _id: JiFr doi: 10.1105/tpc.17.00785 ec_funded: 1 external_id: isi: - '000429441400018' pmid: - '29511054' file: - access_level: open_access checksum: 4e165e653b67d3f0684697f21aace5a1 content_type: application/pdf creator: dernst date_created: 2022-05-23T09:12:38Z date_updated: 2022-05-23T09:12:38Z file_id: '11406' file_name: 2018_PlantCell_Adamowski.pdf file_size: 4407538 relation: main_file success: 1 file_date_updated: 2022-05-23T09:12:38Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 700 - 716 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: The Plant Cell publication_identifier: eissn: - 1532-298X issn: - 1040-4651 publication_status: published publisher: American Society of Plant Biologists publist_id: '7417' quality_controlled: '1' related_material: record: - id: '6269' relation: dissertation_contains status: public scopus_import: '1' status: public title: A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2018' ... --- _id: '5914' abstract: - lang: eng text: With the advent of optogenetics, it became possible to change the activity of a targeted population of neurons in a temporally controlled manner. To combine the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics, we have developed a closed-loop recording system that allows for the actual electrophysiological signal to be used as a trigger for the laser light mediating the optogenetic intervention. We have optimized the weight, size, and shape of the corresponding implant to make it compatible with the size, force, and movements of a behaving mouse, and we have shown that the system can efficiently block sharp wave ripple (SWR) events using those events themselves as a trigger. To demonstrate the full potential of the optogenetic recording system we present a pilot study addressing the contribution of SWR events to learning in a complex behavioral task. article_number: e0087 article_processing_charge: No author: - first_name: Dámaris K full_name: Rangel Guerrero, Dámaris K id: 4871BCE6-F248-11E8-B48F-1D18A9856A87 last_name: Rangel Guerrero orcid: 0000-0002-8602-4374 - first_name: James G. full_name: Donnett, James G. last_name: Donnett - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Krisztián full_name: Kovács, Krisztián id: 2AB5821E-F248-11E8-B48F-1D18A9856A87 last_name: Kovács orcid: 0000-0001-6251-1007 citation: ama: 'Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018' apa: 'Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K. (2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018' chicago: 'Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.' ieee: 'D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience, 2018.' ista: 'Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 5(4), e0087.' mla: 'Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.' short: D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018). date_created: 2019-02-03T22:59:16Z date_published: 2018-07-27T00:00:00Z date_updated: 2024-03-27T23:30:10Z day: '27' ddc: - '570' department: - _id: JoCs doi: 10.1523/ENEURO.0087-18.2018 ec_funded: 1 external_id: isi: - '000443994700007' file: - access_level: open_access checksum: f4915d45fc7ad4648b7b7a13fdecca01 content_type: application/pdf creator: dernst date_created: 2019-02-05T12:48:36Z date_updated: 2020-07-14T12:47:13Z file_id: '5921' file_name: 2018_ENeuro_Guerrero.pdf file_size: 3746884 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 257D4372-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I2072-B27 name: Interneuron plasticity during spatial learning publication: eNeuro publication_status: published publisher: Society of Neuroscience quality_controlled: '1' related_material: record: - id: '6849' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 5 year: '2018' ... --- _id: '402' abstract: - lang: eng text: During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined. acknowledged_ssus: - _id: Bio acknowledgement: "M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line." article_processing_charge: No article_type: original author: - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Frank P full_name: Assen, Frank P id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87 last_name: Assen orcid: 0000-0003-3470-6119 - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Jun full_name: Abe, Jun last_name: Abe - first_name: Helga full_name: Schachner, Helga last_name: Schachner - first_name: Gabriele full_name: Asfour, Gabriele last_name: Asfour - first_name: Zsuzsanna full_name: Bagó Horváth, Zsuzsanna last_name: Bagó Horváth - first_name: Jens full_name: Stein, Jens last_name: Stein - first_name: Pavel full_name: Uhrin, Pavel last_name: Uhrin - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Dontscho full_name: Kerjaschki, Dontscho last_name: Kerjaschki citation: ama: Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411. doi:10.1126/science.aal3662 apa: Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aal3662 chicago: Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662. ieee: M. Brown et al., “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018. ista: Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411. mla: Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662. short: M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411. date_created: 2018-12-11T11:46:16Z date_published: 2018-03-23T00:00:00Z date_updated: 2024-03-27T23:30:09Z day: '23' department: - _id: MiSi doi: 10.1126/science.aal3662 ec_funded: 1 external_id: isi: - '000428043600047' pmid: - '29567714' intvolume: ' 359' isi: 1 issue: '6382' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/science.aal3662 month: '03' oa: 1 oa_version: Published Version page: 1408 - 1411 pmid: 1 project: - _id: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and transduction of leukocytes (FWF) - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '7428' quality_controlled: '1' related_material: record: - id: '6947' relation: dissertation_contains status: public scopus_import: '1' status: public title: Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 359 year: '2018' ... --- _id: '395' abstract: - lang: eng text: 'Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. ' acknowledged_ssus: - _id: PreCl - _id: EM-Fac - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dora-Clara full_name: Tarlungeanu, Dora-Clara id: 2ABCE612-F248-11E8-B48F-1D18A9856A87 last_name: Tarlungeanu citation: ama: Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:10.15479/AT:ISTA:th_992 apa: Tarlungeanu, D.-C. (2018). The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992 chicago: Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_992. ieee: D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018. ista: Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria. mla: Tarlungeanu, Dora-Clara. The Branched Chain Amino Acids in Autism Spectrum Disorders . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_992. short: D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:46:14Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-09-07T12:38:59Z day: '01' ddc: - '570' - '616' degree_awarded: PhD department: - _id: GaNo doi: 10.15479/AT:ISTA:th_992 file: - access_level: closed checksum: 9f5231c96e0ad945040841a8630232da content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T09:19:17Z date_updated: 2021-02-11T23:30:15Z embargo_to: open_access file_id: '6217' file_name: 2018_Thesis_Tarlungeanu_source.docx file_size: 43684035 relation: source_file - access_level: open_access checksum: 0c33c370aa2010df5c552db57a6d01e9 content_type: application/pdf creator: dernst date_created: 2019-04-05T09:19:17Z date_updated: 2021-02-11T11:17:16Z embargo: 2018-03-15 file_id: '6218' file_name: 2018_Thesis_Tarlungeanu.pdf file_size: 30511532 relation: main_file file_date_updated: 2021-02-11T23:30:15Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '88' project: - _id: 25473368-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F03523 name: Transmembrane Transporters in Health and Disease publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7434' pubrep_id: '992' related_material: record: - id: '1183' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: 'The branched chain amino acids in autism spectrum disorders ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '51' abstract: - lang: eng text: Asymmetries have long been known about in the central nervous system. From gross anatomical differences, such as the presence of the parapineal organ in only one hemisphere of the developing zebrafish, to more subtle differences in activity between both hemispheres, as seen in freely roaming animals or human participants under PET and fMRI imaging analysis. The presence of asymmetries has been demonstrated to have huge behavioural implications, with their disruption often leading to the generation of neurological disorders, memory problems, changes in personality, and in an organism's health and well-being. For my Ph.D. work I aimed to tackle two important avenues of research. The first being the process of input-side dependency in the hippocampus, with the goal of finding a key gene responsible for its development (Gene X). The second project was to do with experience-induced laterality formation in the hippocampus. Specifically, how laterality in the synapse density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental enrichment. Through unilateral tracer injections into the CA3, I was able to selectively measure the properties of synapses within the CA1 and investigate how they differed based upon which hemisphere the presynaptic neurone originated. Having found the existence of a previously unreported reversed (left-isomerism) i.v. mutant, through morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate a key gene responsible for the process of left or right determination of inputs to the CA1 s.r.. This work relates to the previous finding of input-side dependent asymmetry in the wild-type rodent, where the origin of the projecting neurone to the CA1 will determine the morphology of a synapse, to a greater degree than the hemisphere in which the projection terminates. Using left- and right-isomerism i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like (Evl) as a potential target for Gene X. In relation to this topic, I also highlight my work in the recently published paper of how knockout of PirB can lead to a lack of input-side dependency in the murine hippocampus. For the second question, I show that the environmental enrichment paradigm will lead to an asymmetry in the synapse densities in the hippocampus of mice. I also highlight that the nature of the enrichment is of less consequence than the process of enrichment itself. I demonstrate that the CA3 region will dramatically alter its projection targets, in relation to environmental stimulation, with the asymmetry in synaptic density, caused by enrichment, relying heavily on commissural fibres. I also highlight the vital importance of input-side dependent asymmetry, as a necessary component of experience-dependent laterality formation in the CA1 s.r.. However, my results suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism also at play. Upon further investigation, I highlight the significant, and highly important, finding that the changes seen in the CA1 s.r. were predominantly caused through projections from the left-CA3, with the right-CA3 having less involvement in this mechanism. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Matthew J full_name: Case, Matthew J id: 44B7CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Case citation: ama: 'Case MJ. From the left to the right: A tale of asymmetries, environments, and hippocampal development. 2018. doi:10.15479/AT:ISTA:th_1032' apa: 'Case, M. J. (2018). From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1032' chicago: 'Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1032.' ieee: 'M. J. Case, “From the left to the right: A tale of asymmetries, environments, and hippocampal development,” Institute of Science and Technology Austria, 2018.' ista: 'Case MJ. 2018. From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria.' mla: 'Case, Matthew J. From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1032.' short: 'M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development, Institute of Science and Technology Austria, 2018.' date_created: 2018-12-11T11:44:22Z date_published: 2018-06-27T00:00:00Z date_updated: 2023-09-07T12:39:22Z day: '27' ddc: - '571' - '576' degree_awarded: PhD department: - _id: RySh doi: 10.15479/AT:ISTA:th_1032 file: - access_level: closed checksum: dcc7b55619d8509dd62b8e99d6cdee44 content_type: application/msword creator: dernst date_created: 2019-04-09T07:16:26Z date_updated: 2021-02-11T23:30:13Z embargo_to: open_access file_id: '6251' file_name: 2018_Thesis_Case_Source.doc file_size: 141270528 relation: source_file - access_level: open_access checksum: f69fdd5c8709c4e618aa8c1a1221153d content_type: application/pdf creator: dernst date_created: 2019-04-09T07:16:23Z date_updated: 2021-02-11T11:17:14Z embargo: 2019-07-05 file_id: '6252' file_name: 2018_Thesis_Case.pdf file_size: 15193621 relation: main_file file_date_updated: 2021-02-11T23:30:13Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '186' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '8003' pubrep_id: '1032' related_material: record: - id: '682' relation: part_of_dissertation status: public status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: 'From the left to the right: A tale of asymmetries, environments, and hippocampal development' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '10' abstract: - lang: eng text: Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Susanne full_name: Laukoter, Susanne id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87 last_name: Laukoter orcid: 0000-0002-7903-3010 citation: ama: Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:10.15479/AT:ISTA:th1057 apa: Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057 chicago: Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057. ieee: S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018. ista: Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria. mla: Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057. short: S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:08Z date_published: 2018-11-21T00:00:00Z date_updated: 2023-09-07T12:40:44Z day: '21' ddc: - '570' degree_awarded: PhD department: - _id: SiHi doi: 10.15479/AT:ISTA:th1057 file: - access_level: closed checksum: 41fdbf5fdce312802935d88a8ad9932c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-05-10T07:47:04Z date_updated: 2019-11-23T23:30:03Z embargo_to: open_access file_id: '6396' file_name: Thesis_LaukoterSusanne_FINAL.docx file_size: 17949175 relation: source_file - access_level: open_access checksum: 53001a9a0c9e570e598d861bb0af28aa content_type: application/pdf creator: dernst date_created: 2019-05-10T07:47:04Z date_updated: 2021-02-11T11:17:16Z embargo: 2019-11-21 file_id: '6397' file_name: Thesis_LaukoterSusanne_FINAL.pdf file_size: 21187245 relation: main_file file_date_updated: 2021-02-11T11:17:16Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1 - 139 publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '8046' pubrep_id: '1057' status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: Role of genomic imprinting in cerebral cortex development type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '323' abstract: - lang: eng text: 'In the here presented thesis, we explore the role of branched actin networks in cell migration and antigen presentation, the two most relevant processes in dendritic cell biology. Branched actin networks construct lamellipodial protrusions at the leading edge of migrating cells. These are typically seen as adhesive structures, which mediate force transduction to the extracellular matrix that leads to forward locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found that the resulting cells lack lamellipodial protrusions. Instead, depending on the maturation state, one or multiple filopodia were formed. By challenging these cells in a variety of migration assays we found that lamellipodial protrusions are dispensable for the locomotion of leukocytes and actually dampen the speed of migration. However, lamellipodia are critically required to negotiate complex environments that DCs experience while they travel to the next draining lymph node. Taken together our results suggest that leukocyte lamellipodia have rather a sensory- than a force transducing function. Furthermore, we show for the first time structure and dynamics of dendritic cell F-actin at the immunological synapse with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension, leading to an altered ultrastructure of the immunological synapse and severe T cell priming defects. These results point towards a previously unappreciated role of the cellular mechanics of dendritic cells in T cell activation. Additionally, we present a novel cell culture based system for the differentiation of dendritic cells from conditionally immortalized hematopoietic precursors. These precursor cells are genetically tractable via the CRISPR/Cas9 system while they retain their ability to differentiate into highly migratory dendritic cells and other immune cells. This will foster the study of all aspects of dendritic cell biology and beyond. ' acknowledged_ssus: - _id: NanoFab - _id: Bio - _id: PreCl - _id: EM-Fac acknowledgement: "First of all I would like to thank Michael Sixt for giving me the opportunity to work in \r\nhis group and for his support throughout the years. He is a truly inspiring person and \r\nthe best boss one can imagine. I would \ also like to thank all current and past \r\nmembers of the Sixt group for their help and the great working atmosphere in the lab. \r\nIt is a true privilege to work with such a bright, funny and friendly group of people and \r\nI’m proud \ that I could be part of it. Furthermore, I would like to say ‘thank \ you’ to Daria Siekhaus for all the meetings and discussion we had throughout the years \r\nand to Federica Benvenuti for being part of my committee. \ I am also grateful to Jack \r\nMerrin in the nanofabrication facility \ and all the people working in the bioimaging-\r\n, the electron microscopy- and the preclinical facilities." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X citation: ama: Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:10.15479/AT:ISTA:th_998 apa: Leithner, A. F. (2018). Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_998 chicago: Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_998. ieee: A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute of Science and Technology Austria, 2018. ista: Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria. mla: Leithner, Alexander F. Branched Actin Networks in Dendritic Cell Biology. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_998. short: A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:45:49Z date_published: 2018-04-12T00:00:00Z date_updated: 2023-09-07T12:39:44Z day: '12' ddc: - '571' - '599' - '610' degree_awarded: PhD department: - _id: MiSi doi: 10.15479/AT:ISTA:th_998 file: - access_level: closed checksum: d5e3edbac548c26c1fa43a4b37a54a4c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T09:23:11Z date_updated: 2021-02-11T23:30:17Z embargo_to: open_access file_id: '6219' file_name: PhD_thesis_AlexLeithner_final_version.docx file_size: 29027671 relation: source_file - access_level: open_access checksum: 071f7476db29e41146824ebd0697cb10 content_type: application/pdf creator: dernst date_created: 2019-04-05T09:23:11Z date_updated: 2021-02-11T11:17:16Z embargo: 2019-04-15 file_id: '6220' file_name: PhD_thesis_AlexLeithner.pdf file_size: 66045341 relation: main_file file_date_updated: 2021-02-11T23:30:17Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '99' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7542' pubrep_id: '998' related_material: record: - id: '1321' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 title: Branched actin networks in dendritic cell biology tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '539' abstract: - lang: eng text: The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andrej full_name: Hurny, Andrej id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87 last_name: Hurny orcid: 0000-0003-3638-1426 citation: ama: Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:10.15479/AT:ISTA:th_930 apa: Hurny, A. (2018). Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_930 chicago: Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_930. ieee: A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018. ista: Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria. mla: Hurny, Andrej. Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_930. short: A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:47:03Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-07T12:41:06Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: EvBe doi: 10.15479/AT:ISTA:th_930 file: - access_level: closed checksum: 0c9d6d1c80d9857e6e545213467bbcb2 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T09:37:56Z date_updated: 2020-12-02T23:30:08Z embargo_to: open_access file_id: '6226' file_name: 2018_Hurny_thesis_source.docx file_size: 28112114 relation: source_file - access_level: open_access checksum: ecbe481a1413d270bd501b872c7ed54f content_type: application/pdf creator: dernst date_created: 2019-04-05T09:37:55Z date_updated: 2020-12-02T09:52:16Z embargo: 2019-07-10 file_id: '6227' file_name: 2018_Hurny_thesis.pdf file_size: 12524427 relation: main_file file_date_updated: 2020-12-02T23:30:08Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '147' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7277' pubrep_id: '930' related_material: record: - id: '1024' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Identification and characterization of novel auxin-cytokinin cross-talk components tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '48' abstract: - lang: eng text: 'The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Igor full_name: Gridchyn, Igor id: 4B60654C-F248-11E8-B48F-1D18A9856A87 last_name: Gridchyn orcid: 0000-0002-1807-1929 citation: ama: Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:10.15479/AT:ISTA:th_1042 apa: Gridchyn, I. (2018). Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1042 chicago: Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1042. ieee: I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018. ista: Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria. mla: Gridchyn, Igor. Reactivation Content Is Important for Consolidation of Spatial Memory. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1042. short: I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:21Z date_published: 2018-08-27T00:00:00Z date_updated: 2023-09-07T12:42:44Z day: '27' ddc: - '573' degree_awarded: PhD department: - _id: JoCs doi: 10.15479/AT:ISTA:th_1042 file: - access_level: closed checksum: 7db4415e435590fa33542c7b0a0321d7 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-08T13:36:01Z date_updated: 2021-02-11T23:30:22Z embargo_to: open_access file_id: '6236' file_name: 2018_Thesis_Gridchyn_source.docx file_size: 7666687 relation: source_file - access_level: open_access checksum: f96f3fe8979f7b1e6db6acaca962b10c content_type: application/pdf creator: dernst date_created: 2019-04-08T13:36:01Z date_updated: 2021-02-11T11:17:18Z embargo: 2019-08-29 file_id: '6237' file_name: 2018_Thesis_Gridchyn.pdf file_size: 6034153 relation: main_file file_date_updated: 2021-02-11T23:30:22Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '104' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '8006' pubrep_id: '1042' status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Reactivation content is important for consolidation of spatial memory tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '9' abstract: - lang: eng text: 'Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vera full_name: Belyaeva, Vera id: 47F080FE-F248-11E8-B48F-1D18A9856A87 last_name: Belyaeva citation: ama: Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:10.15479/AT:ISTA:th1064 apa: Belyaeva, V. (2018). Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1064 chicago: Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1064. ieee: V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018. ista: Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria. mla: Belyaeva, Vera. Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1064. short: V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:08Z date_published: 2018-07-01T00:00:00Z date_updated: 2023-09-07T12:43:10Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: DaSi doi: 10.15479/AT:ISTA:th1064 file: - access_level: closed checksum: d27b2465cb70d0c9678a0381b9b6ced1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-08T14:13:12Z date_updated: 2020-07-14T12:48:14Z embargo_to: open_access file_id: '6243' file_name: 2018_Thesis_Belyaeva_source.docx file_size: 102737483 relation: source_file - access_level: open_access checksum: a2939b61bde2de7b8ced77bbae0eaaed content_type: application/pdf creator: dernst date_created: 2019-04-08T14:14:08Z date_updated: 2021-02-11T11:17:16Z embargo: 2019-11-19 file_id: '6244' file_name: 2018_Thesis_Belyaeva.pdf file_size: 88077843 relation: main_file file_date_updated: 2021-02-11T11:17:16Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '96' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '8047' pubrep_id: '1064' status: public supervisor: - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 title: 'Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '6266' abstract: - lang: eng 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. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Catherine full_name: Mckenzie, Catherine id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87 last_name: Mckenzie citation: 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 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. ieee: C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018. ista: Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria. mla: Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission . Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:th_1055. short: C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018. date_created: 2019-04-09T14:13:39Z date_published: 2018-10-31T00:00:00Z date_updated: 2023-09-07T13:02:37Z day: '31' ddc: - '571' - '573' degree_awarded: PhD department: - _id: HaJa doi: 10.15479/at:ista:th_1055 file: - access_level: open_access checksum: 9d2c2dca04b00e485470c28b262af59a content_type: application/pdf creator: dernst date_created: 2019-04-09T14:12:40Z date_updated: 2021-02-11T11:17:16Z embargo: 2019-11-24 file_id: '6267' file_name: 2018_Thesis_McKenzie.pdf file_size: 4906420 relation: main_file - access_level: closed checksum: 50b58c272899601bc6fd9642c4dc97f1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-09T14:12:40Z date_updated: 2020-07-14T12:47:25Z embargo_to: open_access file_id: '6268' file_name: 2018_Thesis_McKenzie_source.docx file_size: 5053545 relation: source_file file_date_updated: 2021-02-11T11:17:16Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '95' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria pubrep_id: '1055' related_material: record: - id: '7132' relation: new_edition status: public status: public supervisor: - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 title: 'Design and characterization of methods and biological components to realize synthetic neurotransmission ' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '50' abstract: - lang: eng text: The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Daniel full_name: Capek, Daniel id: 31C42484-F248-11E8-B48F-1D18A9856A87 last_name: Capek orcid: 0000-0001-5199-9940 citation: 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 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. 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. 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. 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. date_created: 2018-12-11T11:44:21Z date_published: 2018-06-22T00:00:00Z date_updated: 2023-09-07T12:48:16Z day: '22' ddc: - '570' - '591' - '596' degree_awarded: PhD department: - _id: CaHe doi: 10.15479/AT:ISTA:TH_1031 file: - access_level: open_access checksum: d3eca3dcacb67bffdde6e6609c31cdd0 content_type: application/pdf creator: dernst date_created: 2019-04-08T13:42:26Z date_updated: 2021-02-11T11:17:17Z embargo: 2019-06-25 file_id: '6238' file_name: 2018_Thesis_Capek.pdf file_size: 31576521 relation: main_file - access_level: closed checksum: 876deb14067e638aba65d209668bd821 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-08T13:42:27Z date_updated: 2021-02-11T23:30:21Z embargo_to: open_access file_id: '6239' file_name: 2018_Thesis_Capek_source.docx file_size: 38992956 relation: source_file file_date_updated: 2021-02-11T23:30:21Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '95' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '8004' pubrep_id: '1031' related_material: record: - id: '1100' relation: part_of_dissertation status: public - id: '661' relation: part_of_dissertation status: public - id: '676' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '26' 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Magdalena full_name: Steinrück, Magdalena id: 2C023F40-F248-11E8-B48F-1D18A9856A87 last_name: Steinrück orcid: 0000-0003-1229-9719 citation: ama: Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:10.15479/AT:ISTA:th1059 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 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. ieee: M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018. ista: Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria. mla: Steinrück, Magdalena. The Influence of Sequence Context on the Evolution of Bacterial Gene Expression. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1059. short: M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:14Z date_published: 2018-10-30T00:00:00Z date_updated: 2023-09-07T12:48:43Z day: '30' ddc: - '576' - '579' degree_awarded: PhD department: - _id: CaGu doi: 10.15479/AT:ISTA:th1059 file: - access_level: closed checksum: 413cbce1cd1debeae3abe2a25dbc70d1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-02-08T10:51:22Z date_updated: 2020-07-14T12:45:43Z embargo_to: open_access file_id: '5941' file_name: Thesis_Steinrueck_final.docx file_size: 9190845 relation: source_file - access_level: open_access checksum: 3def8b7854c8b42d643597ce0215efac content_type: application/pdf creator: dernst date_created: 2019-02-08T10:51:22Z date_updated: 2021-02-11T11:17:14Z embargo: 2019-11-02 file_id: '5942' file_name: Thesis_Steinrueck_final.pdf file_size: 7521973 relation: main_file file_date_updated: 2021-02-11T11:17:14Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '109' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '8029' pubrep_id: '1059' related_material: record: - id: '704' relation: part_of_dissertation status: public status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: The influence of sequence context on the evolution of bacterial gene expression type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5816' abstract: - lang: eng text: Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field. article_number: '114701' article_processing_charge: No author: - first_name: Arne full_name: Hollmann, Arne last_name: Hollmann - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Maciej full_name: Kucharski, Maciej last_name: Kucharski - first_name: Dietmar full_name: Kissinger, Dietmar last_name: Kissinger - first_name: Gunter full_name: Fischer, Gunter last_name: Fischer - first_name: Lars R. full_name: Schreiber, Lars R. last_name: Schreiber citation: ama: Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 2018;89(11). doi:10.1063/1.5038258 apa: Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., & Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258 chicago: Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments. AIP Publishing, 2018. https://doi.org/10.1063/1.5038258. ieee: A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R. Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” Review of Scientific Instruments, vol. 89, no. 11. AIP Publishing, 2018. ista: Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 89(11), 114701. mla: Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments, vol. 89, no. 11, 114701, AIP Publishing, 2018, doi:10.1063/1.5038258. short: A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018). date_created: 2019-01-10T14:22:23Z date_published: 2018-11-01T00:00:00Z date_updated: 2024-03-27T23:30:26Z day: '01' department: - _id: GeKa doi: 10.1063/1.5038258 external_id: arxiv: - '1804.09522' isi: - '000451735700054' intvolume: ' 89' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.09522 month: '11' oa: 1 oa_version: Preprint publication: Review of Scientific Instruments publication_identifier: issn: - '00346748' publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: record: - id: '10058' relation: dissertation_contains status: public scopus_import: '1' status: public title: 30 GHz-voltage controlled oscillator operating at 4 K type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 89 year: '2018' ... --- _id: '6263' abstract: - lang: eng text: 'Antibiotic resistance can emerge spontaneously through genomic mutation and render treatment ineffective. To counteract this process, in addition to the discovery and description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand its determinantsis needed. To address this challenge, this thesisuncoversnew genetic determinants of resistance evolvability using a customized robotic setup, exploressystematic ways in which resistance evolution is perturbed due to dose-responsecharacteristics of drugs and mutation rate differences,and mathematically investigates the evolutionary fate of one specific type of evolvability modifier -a stress-induced mutagenesis allele.We find severalgenes which strongly inhibit or potentiate resistance evolution. In order to identify them, we first developedan automated high-throughput feedback-controlled protocol whichkeeps the population size and selection pressure approximately constant for hundreds of cultures by dynamically re-diluting the cultures and adjusting the antibiotic concentration. We implementedthis protocol on a customized liquid handling robot and propagated 100 different gene deletion strains of Escherichia coliin triplicate for over 100 generations in tetracycline and in chloramphenicol, and comparedtheir adaptation rates.We find a diminishing returns pattern, where initially sensitive strains adapted more compared to less sensitive ones. Our data uncover that deletions of certain genes which do not affect mutation rate,including efflux pump components, a chaperone and severalstructural and regulatory genes can strongly and reproducibly alterresistance evolution. Sequencing analysis of evolved populations indicates that epistasis with resistance mutations is the most likelyexplanation. This work could inspire treatment strategies in which targeted inhibitors of evolvability mechanisms will be given alongside antibiotics to slow down resistance evolution and extend theefficacy of antibiotics.We implemented astochasticpopulation genetics model, toverifyways in which general properties, namely, dose-response characteristics of drugs and mutation rates, influence evolutionary dynamics. In particular, under the exposure to antibiotics with shallow dose-response curves,bacteria have narrower distributions of fitness effects of new mutations. We show that in silicothis also leads to slower resistance evolution. We see and confirm with experiments that increased mutation rates, apart from speeding up evolution, also leadto high reproducibility of phenotypic adaptation in a context of continually strong selection pressure.Knowledge of these patterns can aid in predicting the dynamics of antibiotic resistance evolutionand adapting treatment schemes accordingly.Focusing on a previously described type of evolvability modifier –a stress-induced mutagenesis allele –we find conditions under which it can persist in a population under periodic selectionakin to clinical treatment. We set up a deterministic infinite populationcontinuous time model tracking the frequencies of a mutator and resistance allele and evaluate various treatment schemes in how well they maintain a stress-induced mutator allele. In particular,a high diversity of stresses is crucial for the persistence of the mutator allele. This leads to a general trade-off where exactly those diversifying treatment schemes which are likely to decrease levels of resistance could lead to stronger selection of highly evolvable genotypes.In the long run, this work will lead to a deeper understanding of the genetic and cellular mechanisms involved in antibiotic resistance evolution and could inspire new strategies for slowing down its rate. ' acknowledged_ssus: - _id: M-Shop - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 citation: ama: Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:10.15479/AT:ISTA:th1072 apa: Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072 chicago: Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072. ieee: M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018. ista: Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. mla: Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072. short: M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018. date_created: 2019-04-09T13:57:15Z date_published: 2018-12-28T00:00:00Z date_updated: 2023-09-22T09:20:37Z day: '28' ddc: - '570' - '576' - '579' degree_awarded: PhD department: - _id: ToBo doi: 10.15479/AT:ISTA:th1072 file: - access_level: open_access checksum: fc60585c9eaad868ac007004ef130908 content_type: application/pdf creator: dernst date_created: 2019-04-09T13:49:24Z date_updated: 2021-02-11T11:17:17Z embargo: 2020-01-25 file_id: '6264' file_name: 2018_Thesis_Lukacisinova.pdf file_size: 5656866 relation: main_file - access_level: closed checksum: 264057ec0a92ab348cc83b41f021ba92 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-09T13:49:23Z date_updated: 2020-07-14T12:47:25Z embargo_to: open_access file_id: '6265' file_name: 2018_Thesis_Lukacisinova_source.docx file_size: 5168054 relation: source_file file_date_updated: 2021-02-11T11:17:17Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '91' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1619' relation: part_of_dissertation status: public - id: '696' relation: part_of_dissertation status: public - id: '1027' relation: part_of_dissertation status: public status: public supervisor: - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X title: Genetic determinants of antibiotic resistance evolution type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '544' abstract: - lang: eng text: Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult. acknowledged_ssus: - _id: LifeSc acknowledgement: ' A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner by DOC Fellowships from the Austrian Academy of Sciences, ' article_processing_charge: No author: - first_name: Attila full_name: György, Attila id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87 last_name: György orcid: 0000-0002-1819-198X - first_name: Marko full_name: Roblek, Marko id: 3047D808-F248-11E8-B48F-1D18A9856A87 last_name: Roblek orcid: 0000-0001-9588-1389 - first_name: Aparna full_name: Ratheesh, Aparna id: 2F064CFE-F248-11E8-B48F-1D18A9856A87 last_name: Ratheesh orcid: 0000-0001-7190-0776 - first_name: Katarina full_name: Valosková, Katarina id: 46F146FC-F248-11E8-B48F-1D18A9856A87 last_name: Valosková - first_name: Vera full_name: Belyaeva, Vera id: 47F080FE-F248-11E8-B48F-1D18A9856A87 last_name: Belyaeva - first_name: Stephanie full_name: Wachner, Stephanie id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87 last_name: Wachner - first_name: Yutaka full_name: Matsubayashi, Yutaka last_name: Matsubayashi - first_name: Besaiz full_name: Sanchez Sanchez, Besaiz last_name: Sanchez Sanchez - first_name: Brian full_name: Stramer, Brian last_name: Stramer - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 citation: ama: 'György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 2018;8(3):845-857. doi:10.1534/g3.117.300452' apa: 'György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.117.300452' chicago: 'György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/g3.117.300452.' ieee: 'A. György et al., “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” G3: Genes, Genomes, Genetics, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.' ista: 'György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857.' mla: 'György, Attila, et al. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics, vol. 8, no. 3, Genetics Society of America, 2018, pp. 845–57, doi:10.1534/g3.117.300452.' short: 'A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner, Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes, Genetics 8 (2018) 845–857.' date_created: 2018-12-11T11:47:05Z date_published: 2018-03-01T00:00:00Z date_updated: 2024-03-27T23:30:29Z day: '01' ddc: - '570' department: - _id: DaSi doi: 10.1534/g3.117.300452 ec_funded: 1 external_id: isi: - '000426693300011' file: - access_level: open_access checksum: 7d9d28b915159078a4ca7add568010e8 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:48Z date_updated: 2020-07-14T12:46:56Z file_id: '4905' file_name: IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf file_size: 2251222 relation: main_file file_date_updated: 2020-07-14T12:46:56Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 845 - 857 project: - _id: 253B6E48-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29638 name: Drosophila TNFa´s Funktion in Immunzellen - _id: 253B6E48-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29638 name: The role of Drosophila TNF alpha in immune cell invasion - _id: 2637E9C0-B435-11E9-9278-68D0E5697425 grant_number: 'LSC16-021 ' name: Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis - _id: 2536F660-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '334077' name: Investigating the role of transporters in invasive migration through junctions publication: 'G3: Genes, Genomes, Genetics' publication_status: published publisher: Genetics Society of America publist_id: '7271' pubrep_id: '990' quality_controlled: '1' related_material: record: - id: '6530' relation: research_paper - id: '6543' relation: research_paper - id: '11193' relation: dissertation_contains status: public - id: '6546' relation: dissertation_contains status: public scopus_import: '1' status: public title: Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2018' ... --- _id: '612' abstract: - lang: eng text: Metabotropic GABAB receptors mediate slow inhibitory effects presynaptically and postsynaptically through the modulation of different effector signalling pathways. Here, we analysed the distribution of GABAB receptors using highly sensitive SDS-digested freeze-fracture replica labelling in mouse cerebellar Purkinje cells. Immunoreactivity for GABAB1 was observed on presynaptic and, more abundantly, on postsynaptic compartments, showing both scattered and clustered distribution patterns. Quantitative analysis of immunoparticles revealed a somato-dendritic gradient, with the density of immunoparticles increasing 26-fold from somata to dendritic spines. To understand the spatial relationship of GABAB receptors with two key effector ion channels, the G protein-gated inwardly rectifying K+ (GIRK/Kir3) channel and the voltage-dependent Ca2+ channel, biochemical and immunohistochemical approaches were performed. Co-immunoprecipitation analysis demonstrated that GABAB receptors co-assembled with GIRK and CaV2.1 channels in the cerebellum. Using double-labelling immunoelectron microscopic techniques, co-clustering between GABAB1 and GIRK2 was detected in dendritic spines, whereas they were mainly segregated in the dendritic shafts. In contrast, co-clustering of GABAB1 and CaV2.1 was detected in dendritic shafts but not spines. Presynaptically, although no significant co-clustering of GABAB1 and GIRK2 or CaV2.1 channels was detected, inter-cluster distance for GABAB1 and GIRK2 was significantly smaller in the active zone than in the dendritic shafts, and that for GABAB1 and CaV2.1 was significantly smaller in the active zone than in the dendritic shafts and spines. Thus, GABAB receptors are associated with GIRK and CaV2.1 channels in different subcellular compartments. These data provide a better framework for understanding the different roles played by GABAB receptors and their effector ion channels in the cerebellar network. article_processing_charge: No article_type: original author: - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Carolina full_name: Aguado, Carolina last_name: Aguado - first_name: Francisco full_name: Ciruela, Francisco last_name: Ciruela - first_name: Javier full_name: Cózar, Javier last_name: Cózar - first_name: David full_name: Kleindienst, David id: 42E121A4-F248-11E8-B48F-1D18A9856A87 last_name: Kleindienst - first_name: Luis full_name: De La Ossa, Luis last_name: De La Ossa - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler - first_name: Kevin full_name: Wickman, Kevin last_name: Wickman - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa citation: ama: Luján R, Aguado C, Ciruela F, et al. Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. 2018;223(3):1565-1587. doi:10.1007/s00429-017-1568-y apa: Luján, R., Aguado, C., Ciruela, F., Cózar, J., Kleindienst, D., De La Ossa, L., … Fukazawa, Y. (2018). Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. Springer. https://doi.org/10.1007/s00429-017-1568-y chicago: Luján, Rafael, Carolina Aguado, Francisco Ciruela, Javier Cózar, David Kleindienst, Luis De La Ossa, Bernhard Bettler, et al. “Differential Association of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain Structure and Function. Springer, 2018. https://doi.org/10.1007/s00429-017-1568-y. ieee: R. Luján et al., “Differential association of GABAB receptors with their effector ion channels in Purkinje cells,” Brain Structure and Function, vol. 223, no. 3. Springer, pp. 1565–1587, 2018. ista: Luján R, Aguado C, Ciruela F, Cózar J, Kleindienst D, De La Ossa L, Bettler B, Wickman K, Watanabe M, Shigemoto R, Fukazawa Y. 2018. Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. 223(3), 1565–1587. mla: Luján, Rafael, et al. “Differential Association of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain Structure and Function, vol. 223, no. 3, Springer, 2018, pp. 1565–87, doi:10.1007/s00429-017-1568-y. short: R. Luján, C. Aguado, F. Ciruela, J. Cózar, D. Kleindienst, L. De La Ossa, B. Bettler, K. Wickman, M. Watanabe, R. Shigemoto, Y. Fukazawa, Brain Structure and Function 223 (2018) 1565–1587. date_created: 2018-12-11T11:47:29Z date_published: 2018-04-01T00:00:00Z date_updated: 2024-03-27T23:30:30Z day: '01' ddc: - '571' department: - _id: RySh doi: 10.1007/s00429-017-1568-y ec_funded: 1 external_id: isi: - '000428419500030' file: - access_level: open_access checksum: a55b3103476ecb5f4f983d8801807e8b content_type: application/pdf creator: system date_created: 2018-12-12T10:15:36Z date_updated: 2020-07-14T12:47:20Z file_id: '5157' file_name: IST-2018-1013-v1+1_2018_Kleindienst_Differential.pdf file_size: 5542926 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 223' isi: 1 issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1565 - 1587 project: - _id: 25CBA828-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '720270' name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1) - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Brain Structure and Function publication_status: published publisher: Springer publist_id: '7192' pubrep_id: '1013' quality_controlled: '1' related_material: record: - id: '9562' relation: dissertation_contains status: public scopus_import: '1' status: public title: Differential association of GABAB receptors with their effector ion channels in Purkinje cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 223 year: '2018' ... --- _id: '21' abstract: - lang: eng text: Parvalbumin-positive (PV+) GABAergic interneurons in hippocampal microcircuits are thought to play a key role in several higher network functions, such as feedforward and feedback inhibition, network oscillations, and pattern separation. Fast lateral inhibition mediated by GABAergic interneurons may implement a winner-takes-all mechanism in the hippocampal input layer. However, it is not clear whether the functional connectivity rules of granule cells (GCs) and interneurons in the dentate gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings from up to seven GCs and up to four PV+ interneurons in the dentate gyrus, we find that connectivity is structured in space, synapse-specific, and enriched in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV+ interneuron) is ~ 10-times more abundant than recurrent inhibition (in which a GC inhibits itself). Thus, unique connectivity rules may enable the dentate gyrus to perform specific higher-order computations acknowledgement: This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.. article_number: '4605' article_processing_charge: No article_type: original author: - first_name: 'Claudia ' full_name: 'Espinoza Martinez, Claudia ' id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87 last_name: Espinoza Martinez orcid: 0000-0003-4710-2082 - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán orcid: 0000-0003-2209-5242 - first_name: Xiaomin full_name: Zhang, Xiaomin id: 423EC9C2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-06899-3 apa: Espinoza Martinez, C., Guzmán, J., Zhang, X., & Jonas, P. M. (2018). Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06899-3 chicago: Espinoza Martinez, Claudia , José Guzmán, Xiaomin Zhang, and Peter M Jonas. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06899-3. ieee: C. Espinoza Martinez, J. Guzmán, X. Zhang, and P. M. Jonas, “Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018. ista: Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. 2018. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 9(1), 4605. mla: Espinoza Martinez, Claudia, et al. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” Nature Communications, vol. 9, no. 1, 4605, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06899-3. short: C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications 9 (2018). date_created: 2018-12-11T11:44:12Z date_published: 2018-11-02T00:00:00Z date_updated: 2024-03-27T23:30:31Z day: '02' ddc: - '570' department: - _id: PeJo doi: 10.1038/s41467-018-06899-3 ec_funded: 1 external_id: isi: - '000449069700009' file: - access_level: open_access checksum: 9fe2a63bd95a5067d896c087d07998f3 content_type: application/pdf creator: dernst date_created: 2018-12-17T15:41:57Z date_updated: 2020-07-14T12:45:28Z file_id: '5715' file_name: 2018_NatureComm_Espinoza.pdf file_size: 4651930 relation: main_file file_date_updated: 2020-07-14T12:45:28Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '8034' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/ record: - id: '6363' relation: dissertation_contains status: public scopus_import: '1' status: public title: Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 9 year: '2018' ... --- _id: '66' abstract: - lang: eng text: 'Crypto-currencies are digital assets designed to work as a medium of exchange, e.g., Bitcoin, but they are susceptible to attacks (dishonest behavior of participants). A framework for the analysis of attacks in crypto-currencies requires (a) modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior; (b) concurrent interactions between participants; and (c) analysis of long-term monetary gains. Traditional game-theoretic approaches for the analysis of security protocols consider either qualitative temporal properties such as safety and termination, or the very special class of one-shot (stateless) games. However, to analyze general attacks on protocols for crypto-currencies, both stateful analysis and quantitative objectives are necessary. In this work our main contributions are as follows: (a) we show how a class of concurrent mean-payo games, namely ergodic games, can model various attacks that arise naturally in crypto-currencies; (b) we present the first practical implementation of algorithms for ergodic games that scales to model realistic problems for crypto-currencies; and (c) we present experimental results showing that our framework can handle games with thousands of states and millions of transitions.' alternative_title: - LIPIcs article_number: '11' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.11' apa: 'Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Velner, Y. (2018). Ergodic mean-payoff games for the analysis of attacks in crypto-currencies (Vol. 118). Presented at the CONCUR: Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11' chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Yaron Velner. “Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11. ieee: 'K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and Y. Velner, “Ergodic mean-payoff games for the analysis of attacks in crypto-currencies,” presented at the CONCUR: Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.' ista: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. 2018. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 118, 11.' mla: Chatterjee, Krishnendu, et al. Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies. Vol. 118, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.11. short: K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, Y. Velner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-09-07 location: Beijing, China name: 'CONCUR: Conference on Concurrency Theory' start_date: 2018-09-04 date_created: 2018-12-11T11:44:27Z date_published: 2018-09-01T00:00:00Z date_updated: 2024-03-27T23:30:33Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPIcs.CONCUR.2018.11 ec_funded: 1 external_id: arxiv: - '1806.03108' file: - access_level: open_access checksum: 68a055b1aaa241cc38375083cf832a7d content_type: application/pdf creator: dernst date_created: 2018-12-17T12:08:00Z date_updated: 2020-07-14T12:47:34Z file_id: '5696' file_name: 2018_CONCUR_Chatterjee.pdf file_size: 1078309 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 118' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 266EEEC0-B435-11E9-9278-68D0E5697425 name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts publication_identifier: isbn: - 978-3-95977-087-3 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7988' quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Ergodic mean-payoff games for the analysis of attacks in crypto-currencies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2018' ... --- _id: '311' abstract: - lang: eng text: 'Smart contracts are computer programs that are executed by a network of mutually distrusting agents, without the need of an external trusted authority. Smart contracts handle and transfer assets of considerable value (in the form of crypto-currency like Bitcoin). Hence, it is crucial that their implementation is bug-free. We identify the utility (or expected payoff) of interacting with such smart contracts as the basic and canonical quantitative property for such contracts. We present a framework for such quantitative analysis of smart contracts. Such a formal framework poses new and novel research challenges in programming languages, as it requires modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior and modeling utilities which are not specified as standard temporal properties such as safety and termination. While game-theoretic incentives have been analyzed in the security community, their analysis has been restricted to the very special case of stateless games. However, to analyze smart contracts, stateful analysis is required as it must account for the different program states of the protocol. Our main contributions are as follows: we present (i)~a simplified programming language for smart contracts; (ii)~an automatic translation of the programs to state-based games; (iii)~an abstraction-refinement approach to solve such games; and (iv)~experimental results on real-world-inspired smart contracts.' acknowledgement: 'The research was partially supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games).' alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: 'Chatterjee K, Goharshady AK, Velner Y. Quantitative analysis of smart contracts. In: Vol 10801. Springer; 2018:739-767. doi:10.1007/978-3-319-89884-1_26' apa: 'Chatterjee, K., Goharshady, A. K., & Velner, Y. (2018). Quantitative analysis of smart contracts (Vol. 10801, pp. 739–767). Presented at the ESOP: European Symposium on Programming, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89884-1_26' chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Yaron Velner. “Quantitative Analysis of Smart Contracts,” 10801:739–67. Springer, 2018. https://doi.org/10.1007/978-3-319-89884-1_26. ieee: 'K. Chatterjee, A. K. Goharshady, and Y. Velner, “Quantitative analysis of smart contracts,” presented at the ESOP: European Symposium on Programming, Thessaloniki, Greece, 2018, vol. 10801, pp. 739–767.' ista: 'Chatterjee K, Goharshady AK, Velner Y. 2018. Quantitative analysis of smart contracts. ESOP: European Symposium on Programming, LNCS, vol. 10801, 739–767.' mla: Chatterjee, Krishnendu, et al. Quantitative Analysis of Smart Contracts. Vol. 10801, Springer, 2018, pp. 739–67, doi:10.1007/978-3-319-89884-1_26. short: K. Chatterjee, A.K. Goharshady, Y. Velner, in:, Springer, 2018, pp. 739–767. conference: end_date: 2018-04-19 location: Thessaloniki, Greece name: 'ESOP: European Symposium on Programming' start_date: 2018-04-16 date_created: 2018-12-11T11:45:45Z date_published: 2018-04-01T00:00:00Z date_updated: 2024-03-27T23:30:33Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-319-89884-1_26 ec_funded: 1 file: - access_level: open_access checksum: 9c8a8338c571903b599b6ca93abd2cce content_type: application/pdf creator: dernst date_created: 2018-12-17T15:45:49Z date_updated: 2020-07-14T12:46:00Z file_id: '5716' file_name: 2018_ESOP_Chatterjee.pdf file_size: 1394993 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' intvolume: ' 10801' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 739 - 767 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '7554' quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Quantitative analysis of smart contracts tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10801 year: '2018' ... --- _id: '6340' abstract: - lang: eng text: We present a secure approach for maintaining andreporting credit history records on the Blockchain. Our ap-proach removes third-parties such as credit reporting agen-cies from the lending process and replaces them with smartcontracts. This allows customers to interact directly with thelenders or banks while ensuring the integrity, unmalleabilityand privacy of their credit data. Additionally, each customerhas full control over complete or selective disclosure of hercredit records, eliminating the risk of privacy violations or databreaches. Moreover, our approach provides strong guaranteesfor the lenders as well. A lender can check both correctness andcompleteness of the credit data disclosed to her. This is the firstapproach that can perform all credit reporting tasks withouta central authority or changing the financial mechanisms*. article_processing_charge: No author: - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Ali full_name: Behrouz, Ali last_name: Behrouz - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Goharshady AK, Behrouz A, Chatterjee K. Secure Credit Reporting on the Blockchain. In: Proceedings of the IEEE International Conference on Blockchain. IEEE; 2018:1343-1348. doi:10.1109/Cybermatics_2018.2018.00231' apa: 'Goharshady, A. K., Behrouz, A., & Chatterjee, K. (2018). Secure Credit Reporting on the Blockchain. In Proceedings of the IEEE International Conference on Blockchain (pp. 1343–1348). Halifax, Canada: IEEE. https://doi.org/10.1109/Cybermatics_2018.2018.00231' chicago: Goharshady, Amir Kafshdar, Ali Behrouz, and Krishnendu Chatterjee. “Secure Credit Reporting on the Blockchain.” In Proceedings of the IEEE International Conference on Blockchain, 1343–48. IEEE, 2018. https://doi.org/10.1109/Cybermatics_2018.2018.00231. ieee: A. K. Goharshady, A. Behrouz, and K. Chatterjee, “Secure Credit Reporting on the Blockchain,” in Proceedings of the IEEE International Conference on Blockchain, Halifax, Canada, 2018, pp. 1343–1348. ista: Goharshady AK, Behrouz A, Chatterjee K. 2018. Secure Credit Reporting on the Blockchain. Proceedings of the IEEE International Conference on Blockchain. IEEE International Conference on Blockchain, 1343–1348. mla: Goharshady, Amir Kafshdar, et al. “Secure Credit Reporting on the Blockchain.” Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–48, doi:10.1109/Cybermatics_2018.2018.00231. short: A.K. Goharshady, A. Behrouz, K. Chatterjee, in:, Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–1348. conference: end_date: 2018-08-03 location: Halifax, Canada name: IEEE International Conference on Blockchain start_date: 2018-07-30 date_created: 2019-04-18T10:37:35Z date_published: 2018-09-01T00:00:00Z date_updated: 2024-03-27T23:30:34Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1109/Cybermatics_2018.2018.00231 ec_funded: 1 external_id: arxiv: - '1805.09104' isi: - '000481634500196' file: - access_level: open_access checksum: b25c9bb7cf6e7e6634e692d26d41ead8 content_type: application/pdf creator: akafshda date_created: 2019-04-18T10:36:39Z date_updated: 2020-07-14T12:47:27Z file_id: '6341' file_name: blockchain2018.pdf file_size: 624338 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1343-1348 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 266EEEC0-B435-11E9-9278-68D0E5697425 name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Proceedings of the IEEE International Conference on Blockchain publication_identifier: isbn: - '978-1-5386-7975-3 ' publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Secure Credit Reporting on the Blockchain tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '6009' abstract: - lang: eng text: "We study algorithmic questions wrt algebraic path properties in concurrent systems, where the transitions of the system are labeled from a complete, closed semiring. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.\r\n" article_number: '9' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 2018;40(3). doi:10.1145/3210257 apa: Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A. (2018). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3210257 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3210257. ieee: K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3. Association for Computing Machinery (ACM), 2018. ista: Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2018. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 40(3), 9. mla: Chatterjee, Krishnendu, et al. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3, 9, Association for Computing Machinery (ACM), 2018, doi:10.1145/3210257. short: K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 40 (2018). date_created: 2019-02-14T14:31:52Z date_published: 2018-08-01T00:00:00Z date_updated: 2024-03-27T23:30:34Z day: '01' department: - _id: KrCh doi: 10.1145/3210257 ec_funded: 1 external_id: arxiv: - '1510.07565' isi: - '000444694800001' intvolume: ' 40' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1510.07565 month: '08' oa: 1 oa_version: Preprint project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: ACM Transactions on Programming Languages and Systems publication_identifier: issn: - 0164-0925 publication_status: published publisher: Association for Computing Machinery (ACM) quality_controlled: '1' related_material: record: - id: '1437' relation: earlier_version status: public - id: '5441' relation: earlier_version status: public - id: '5442' relation: earlier_version status: public - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Algorithms for algebraic path properties in concurrent systems of constant treewidth components type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 40 year: '2018' ... --- _id: '5977' abstract: - lang: eng text: 'We consider the stochastic shortest path (SSP)problem for succinct Markov decision processes(MDPs), where the MDP consists of a set of vari-ables, and a set of nondeterministic rules that up-date the variables. First, we show that several ex-amples from the AI literature can be modeled assuccinct MDPs. Then we present computationalapproaches for upper and lower bounds for theSSP problem: (a) for computing upper bounds, ourmethod is polynomial-time in the implicit descrip-tion of the MDP; (b) for lower bounds, we present apolynomial-time (in the size of the implicit descrip-tion) reduction to quadratic programming. Our ap-proach is applicable even to infinite-state MDPs.Finally, we present experimental results to demon-strate the effectiveness of our approach on severalclassical examples from the AI literature.' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Nastaran full_name: Okati, Nastaran last_name: Okati citation: ama: 'Chatterjee K, Fu H, Goharshady AK, Okati N. Computational approaches for stochastic shortest path on succinct MDPs. In: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. Vol 2018. IJCAI; 2018:4700-4707. doi:10.24963/ijcai.2018/653' apa: 'Chatterjee, K., Fu, H., Goharshady, A. K., & Okati, N. (2018). Computational approaches for stochastic shortest path on succinct MDPs. In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence (Vol. 2018, pp. 4700–4707). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/653' chicago: Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Nastaran Okati. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018:4700–4707. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/653. ieee: K. Chatterjee, H. Fu, A. K. Goharshady, and N. Okati, “Computational approaches for stochastic shortest path on succinct MDPs,” in Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4700–4707. ista: 'Chatterjee K, Fu H, Goharshady AK, Okati N. 2018. Computational approaches for stochastic shortest path on succinct MDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4700–4707.' mla: Chatterjee, Krishnendu, et al. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, vol. 2018, IJCAI, 2018, pp. 4700–07, doi:10.24963/ijcai.2018/653. short: K. Chatterjee, H. Fu, A.K. Goharshady, N. Okati, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4700–4707. conference: end_date: 2018-07-19 location: Stockholm, Sweden name: 'IJCAI: International Joint Conference on Artificial Intelligence' start_date: 2018-07-13 date_created: 2019-02-13T13:26:27Z date_published: 2018-07-17T00:00:00Z date_updated: 2024-03-27T23:30:34Z day: '17' department: - _id: KrCh doi: 10.24963/ijcai.2018/653 ec_funded: 1 external_id: arxiv: - '1804.08984' isi: - '000764175404118' intvolume: ' 2018' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.08984 month: '07' oa: 1 oa_version: Preprint page: 4700-4707 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence publication_identifier: isbn: - 978-099924112-7 issn: - '10450823' publication_status: published publisher: IJCAI quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Computational approaches for stochastic shortest path on succinct MDPs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2018 year: '2018' ... --- _id: '422' abstract: - lang: eng text: We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device which injects fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the skin friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant local skin friction drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle. article_processing_charge: Yes (via OA deal) author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Markus full_name: Schaner, Markus id: 316CE034-F248-11E8-B48F-1D18A9856A87 last_name: Schaner - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 2018;100(4):919-942. doi:10.1007/s10494-018-9896-4 apa: Kühnen, J., Scarselli, D., Schaner, M., & Hof, B. (2018). Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. Springer. https://doi.org/10.1007/s10494-018-9896-4 chicago: Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion. Springer, 2018. https://doi.org/10.1007/s10494-018-9896-4. ieee: J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady modification of the streamwise velocity profile in a pipe,” Flow Turbulence and Combustion, vol. 100, no. 4. Springer, pp. 919–942, 2018. ista: Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942. mla: Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion, vol. 100, no. 4, Springer, 2018, pp. 919–42, doi:10.1007/s10494-018-9896-4. short: J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942. date_created: 2018-12-11T11:46:23Z date_published: 2018-01-01T00:00:00Z date_updated: 2024-03-27T23:30:36Z day: '01' ddc: - '530' department: - _id: BjHo doi: 10.1007/s10494-018-9896-4 ec_funded: 1 external_id: isi: - '000433113900004' file: - access_level: open_access checksum: d7c0bade150faabca150b0a9986e60ca content_type: application/pdf creator: dernst date_created: 2018-12-17T15:52:37Z date_updated: 2020-07-14T12:46:25Z file_id: '5717' file_name: 2018_FlowTurbulenceCombust_Kuehnen.pdf file_size: 2210020 relation: main_file file_date_updated: 2020-07-14T12:46:25Z has_accepted_license: '1' intvolume: ' 100' isi: 1 issue: '4' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 919 - 942 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Flow Turbulence and Combustion publication_status: published publisher: Springer publist_id: '7401' quality_controlled: '1' related_material: record: - id: '7258' relation: dissertation_contains status: public scopus_import: '1' status: public title: Relaminarization by steady modification of the streamwise velocity profile in a pipe tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 100 year: '2018' ... --- _id: '461' abstract: - lang: eng text: Turbulence is the major cause of friction losses in transport processes and it is responsible for a drastic drag increase in flows over bounding surfaces. While much effort is invested into developing ways to control and reduce turbulence intensities, so far no methods exist to altogether eliminate turbulence if velocities are sufficiently large. We demonstrate for pipe flow that appropriate distortions to the velocity profile lead to a complete collapse of turbulence and subsequently friction losses are reduced by as much as 90%. Counterintuitively, the return to laminar motion is accomplished by initially increasing turbulence intensities or by transiently amplifying wall shear. Since neither the Reynolds number nor the shear stresses decrease (the latter often increase), these measures are not indicative of turbulence collapse. Instead, an amplification mechanism measuring the interaction between eddies and the mean shear is found to set a threshold below which turbulence is suppressed beyond recovery. acknowledgement: We acknowledge the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 737549) and the Deutsche Forschungsgemeinschaft (Project No. FOR 1182) for financial support. We thank our technician P. Maier for providing highly valuable ideas and greatly supporting us in all technical aspects. We thank M. Schaner for technical drawings, construction and design. We thank M. Schwegel for a Matlab code to post-process experimental data. article_processing_charge: No author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 - first_name: Ashley full_name: Willis, Ashley last_name: Willis - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Kühnen J, Song B, Scarselli D, et al. Destabilizing turbulence in pipe flow. Nature Physics. 2018;14:386-390. doi:10.1038/s41567-017-0018-3 apa: Kühnen, J., Song, B., Scarselli, D., Budanur, N. B., Riedl, M., Willis, A., … Hof, B. (2018). Destabilizing turbulence in pipe flow. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-017-0018-3 chicago: Kühnen, Jakob, Baofang Song, Davide Scarselli, Nazmi B Budanur, Michael Riedl, Ashley Willis, Marc Avila, and Björn Hof. “Destabilizing Turbulence in Pipe Flow.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-017-0018-3. ieee: J. Kühnen et al., “Destabilizing turbulence in pipe flow,” Nature Physics, vol. 14. Nature Publishing Group, pp. 386–390, 2018. ista: Kühnen J, Song B, Scarselli D, Budanur NB, Riedl M, Willis A, Avila M, Hof B. 2018. Destabilizing turbulence in pipe flow. Nature Physics. 14, 386–390. mla: Kühnen, Jakob, et al. “Destabilizing Turbulence in Pipe Flow.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 386–90, doi:10.1038/s41567-017-0018-3. short: J. Kühnen, B. Song, D. Scarselli, N.B. Budanur, M. Riedl, A. Willis, M. Avila, B. Hof, Nature Physics 14 (2018) 386–390. date_created: 2018-12-11T11:46:36Z date_published: 2018-01-08T00:00:00Z date_updated: 2024-03-27T23:30:36Z day: '08' department: - _id: BjHo doi: 10.1038/s41567-017-0018-3 ec_funded: 1 external_id: isi: - '000429434100020' intvolume: ' 14' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.06543 month: '01' oa: 1 oa_version: Preprint page: 386-390 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin - _id: 25104D44-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '737549' name: Eliminating turbulence in oil pipelines publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7360' quality_controlled: '1' related_material: record: - id: '12726' relation: dissertation_contains status: public - id: '14530' relation: dissertation_contains status: public - id: '7258' relation: dissertation_contains status: public scopus_import: '1' status: public title: Destabilizing turbulence in pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '449' abstract: - lang: eng text: Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development. article_processing_charge: Yes author: - first_name: Tomas full_name: Prat, Tomas id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87 last_name: Prat - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Mina K full_name: Vasileva, Mina K id: 3407EB18-F248-11E8-B48F-1D18A9856A87 last_name: Vasileva - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Markus full_name: Schmid, Markus last_name: Schmid - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 2018;14(1). doi:10.1371/journal.pgen.1007177 apa: Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007177 chicago: Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007177. ieee: T. Prat et al., “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” PLoS Genetics, vol. 14, no. 1. Public Library of Science, 2018. ista: Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1). mla: Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics, vol. 14, no. 1, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007177. short: T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018). date_created: 2018-12-11T11:46:32Z date_published: 2018-01-29T00:00:00Z date_updated: 2024-03-27T23:30:37Z day: '29' ddc: - '581' department: - _id: JiFr doi: 10.1371/journal.pgen.1007177 ec_funded: 1 external_id: isi: - '000423718600034' file: - access_level: open_access checksum: 0276d66788ec076f4924164a39e6a712 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:52Z date_updated: 2020-07-14T12:46:30Z file_id: '4843' file_name: IST-2018-967-v1+1_journal.pgen.1007177.pdf file_size: 24709062 relation: main_file file_date_updated: 2020-07-14T12:46:30Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '7373' pubrep_id: '967' quality_controlled: '1' related_material: record: - id: '1127' relation: dissertation_contains status: public - id: '7172' relation: dissertation_contains status: public - id: '8822' relation: dissertation_contains status: public scopus_import: '1' status: public title: WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '191' abstract: - lang: eng text: Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals. article_number: '10279' article_processing_charge: No author: - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Melinda F full_name: Abas, Melinda F id: 3CFB3B1C-F248-11E8-B48F-1D18A9856A87 last_name: Abas - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Angharad full_name: Jones, Angharad last_name: Jones - first_name: Sascha full_name: Waidmann, Sascha last_name: Waidmann - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-28188-1 apa: Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., & Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. Springer. https://doi.org/10.1038/s41598-018-28188-1 chicago: Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports. Springer, 2018. https://doi.org/10.1038/s41598-018-28188-1. ieee: P. Grones et al., “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” Scientific Reports, vol. 8, no. 1. Springer, 2018. ista: Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279. mla: Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports, vol. 8, no. 1, 10279, Springer, 2018, doi:10.1038/s41598-018-28188-1. short: P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018). date_created: 2018-12-11T11:45:06Z date_published: 2018-07-06T00:00:00Z date_updated: 2024-03-27T23:30:37Z day: '06' ddc: - '581' department: - _id: JiFr - _id: EvBe doi: 10.1038/s41598-018-28188-1 ec_funded: 1 external_id: isi: - '000437673200053' file: - access_level: open_access checksum: 266b03f4fb8198e83141617aaa99dcab content_type: application/pdf creator: dernst date_created: 2018-12-17T15:38:56Z date_updated: 2020-07-14T12:45:20Z file_id: '5714' file_name: 2018_ScientificReports_Grones.pdf file_size: 2413876 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Scientific Reports publication_status: published publisher: Springer publist_id: '7729' quality_controlled: '1' related_material: record: - id: '8822' relation: dissertation_contains status: public scopus_import: '1' status: public title: PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2018' ... --- _id: '15' abstract: - lang: eng text: Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux. acknowledged_ssus: - _id: SSU acknowledgement: This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014). article_processing_charge: No author: - first_name: Miroslav full_name: Hons, Miroslav id: 4167FE56-F248-11E8-B48F-1D18A9856A87 last_name: Hons orcid: 0000-0002-6625-3348 - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 - first_name: Jun full_name: Abe, Jun last_name: Abe - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Jens full_name: Stein, Jens last_name: Stein - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 2018;19(6):606-616. doi:10.1038/s41590-018-0109-z apa: Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/s41590-018-0109-z chicago: Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41590-018-0109-z. ieee: M. Hons et al., “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” Nature Immunology, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018. ista: Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616. mla: Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:10.1038/s41590-018-0109-z. short: M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616. date_created: 2018-12-11T11:44:10Z date_published: 2018-05-18T00:00:00Z date_updated: 2024-03-27T23:30:39Z day: '18' department: - _id: MiSi - _id: Bio doi: 10.1038/s41590-018-0109-z ec_funded: 1 external_id: isi: - '000433041500026' pmid: - '29777221' intvolume: ' 19' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/29777221 month: '05' oa: 1 oa_version: Published Version page: 606 - 616 pmid: 1 project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells - _id: 25A48D24-B435-11E9-9278-68D0E5697425 grant_number: ALTF 1396-2014 name: Molecular and system level view of immune cell migration - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Nature Immunology publication_status: published publisher: Nature Publishing Group publist_id: '8040' quality_controlled: '1' related_material: record: - id: '6891' relation: dissertation_contains status: public scopus_import: '1' status: public title: Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '442' abstract: - lang: eng text: The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH. acknowledgement: 'This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ' article_processing_charge: No article_type: original author: - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 2018;8(1). doi:10.21769/BioProtoc.2685 apa: Li, L., Krens, G., Fendrych, M., & Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-Protocol. Bio-protocol. https://doi.org/10.21769/BioProtoc.2685 chicago: Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol. Bio-protocol, 2018. https://doi.org/10.21769/BioProtoc.2685. ieee: L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” Bio-protocol, vol. 8, no. 1. Bio-protocol, 2018. ista: Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1). mla: Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol, vol. 8, no. 1, Bio-protocol, 2018, doi:10.21769/BioProtoc.2685. short: L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018). date_created: 2018-12-11T11:46:30Z date_published: 2018-01-05T00:00:00Z date_updated: 2024-03-27T23:30:42Z day: '05' ddc: - '576' - '581' department: - _id: JiFr - _id: Bio doi: 10.21769/BioProtoc.2685 ec_funded: 1 file: - access_level: open_access checksum: 6644ba698206eda32b0abf09128e63e3 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:43Z date_updated: 2020-07-14T12:46:29Z file_id: '5299' file_name: IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf file_size: 11352389 relation: main_file file_date_updated: 2020-07-14T12:46:29Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Bio-protocol publication_identifier: eissn: - 2331-8325 publication_status: published publisher: Bio-protocol publist_id: '7381' pubrep_id: '970' quality_controlled: '1' related_material: record: - id: '10083' relation: dissertation_contains status: public status: public title: Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2018' ... --- _id: '3' abstract: - lang: eng text: SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder. acknowledged_ssus: - _id: M-Shop - _id: PreCl acknowledgement: This work was supported by the Simons Foundation Autism Research Initiative (grant 401299) to G.N. and the DFG (SPP1738 grant NO 1249) to K.-M.N. article_processing_charge: No article_type: original author: - first_name: Elena full_name: Deliu, Elena id: 37A40D7E-F248-11E8-B48F-1D18A9856A87 last_name: Deliu orcid: 0000-0002-7370-5293 - first_name: Niccoló full_name: Arecco, Niccoló last_name: Arecco - first_name: Jasmin full_name: Morandell, Jasmin id: 4739D480-F248-11E8-B48F-1D18A9856A87 last_name: Morandell - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 - first_name: Ximena full_name: Contreras, Ximena id: 475990FE-F248-11E8-B48F-1D18A9856A87 last_name: Contreras - first_name: Charles full_name: Girardot, Charles last_name: Girardot - first_name: Eva full_name: Käsper, Eva last_name: Käsper - first_name: Alena full_name: Kozlova, Alena id: C50A9596-02D0-11E9-976E-E38CFE5CBC1D last_name: Kozlova - first_name: Kasumi full_name: Kishi, Kasumi id: 3065DFC4-F248-11E8-B48F-1D18A9856A87 last_name: Kishi - first_name: Ilaria full_name: Chiaradia, Ilaria id: B6467F20-02D0-11E9-BDA5-E960C241894A last_name: Chiaradia orcid: 0000-0002-9529-4464 - first_name: Kyung full_name: Noh, Kyung last_name: Noh - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Deliu E, Arecco N, Morandell J, et al. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 2018;21(12):1717-1727. doi:10.1038/s41593-018-0266-2 apa: Deliu, E., Arecco, N., Morandell, J., Dotter, C., Contreras, X., Girardot, C., … Novarino, G. (2018). Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/s41593-018-0266-2 chicago: Deliu, Elena, Niccoló Arecco, Jasmin Morandell, Christoph Dotter, Ximena Contreras, Charles Girardot, Eva Käsper, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience. Nature Publishing Group, 2018. https://doi.org/10.1038/s41593-018-0266-2. ieee: E. Deliu et al., “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition,” Nature Neuroscience, vol. 21, no. 12. Nature Publishing Group, pp. 1717–1727, 2018. ista: Deliu E, Arecco N, Morandell J, Dotter C, Contreras X, Girardot C, Käsper E, Kozlova A, Kishi K, Chiaradia I, Noh K, Novarino G. 2018. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 21(12), 1717–1727. mla: Deliu, Elena, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience, vol. 21, no. 12, Nature Publishing Group, 2018, pp. 1717–27, doi:10.1038/s41593-018-0266-2. short: E. Deliu, N. Arecco, J. Morandell, C. Dotter, X. Contreras, C. Girardot, E. Käsper, A. Kozlova, K. Kishi, I. Chiaradia, K. Noh, G. Novarino, Nature Neuroscience 21 (2018) 1717–1727. date_created: 2018-12-11T11:44:05Z date_published: 2018-11-19T00:00:00Z date_updated: 2024-03-27T23:30:44Z day: '19' ddc: - '570' department: - _id: GaNo - _id: EdHa doi: 10.1038/s41593-018-0266-2 external_id: isi: - '000451324700010' file: - access_level: open_access checksum: 60abd0f05b7cdc08a6b0ec460884084f content_type: application/pdf creator: dernst date_created: 2019-04-09T07:41:57Z date_updated: 2020-07-14T12:45:58Z file_id: '6255' file_name: 2017_NatureNeuroscience_Deliu.pdf file_size: 8167169 relation: main_file file_date_updated: 2020-07-14T12:45:58Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '12' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 1717 - 1727 project: - _id: 254BA948-B435-11E9-9278-68D0E5697425 grant_number: '401299' name: Probing development and reversibility of autism spectrum disorders publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '8054' pubrep_id: '1071' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/ record: - id: '6074' relation: popular_science status: public - id: '12364' relation: dissertation_contains status: public scopus_import: '1' status: public title: Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 21 year: '2018' ... --- _id: '2' abstract: - lang: eng text: Indirect reciprocity explores how humans act when their reputation is at stake, and which social norms they use to assess the actions of others. A crucial question in indirect reciprocity is which social norms can maintain stable cooperation in a society. Past research has highlighted eight such norms, called “leading-eight” strategies. This past research, however, is based on the assumption that all relevant information about other population members is publicly available and that everyone agrees on who is good or bad. Instead, here we explore the reputation dynamics when information is private and noisy. We show that under these conditions, most leading-eight strategies fail to evolve. Those leading-eight strategies that do evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other’s reputation, previous research has highlighted eight crucial moral systems. These “leading-eight” strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems. article_processing_charge: No author: - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 2018;115(48):12241-12246. doi:10.1073/pnas.1810565115 apa: Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Indirect reciprocity with private, noisy, and incomplete information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1810565115 chicago: Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1810565115. ieee: C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity with private, noisy, and incomplete information,” PNAS, vol. 115, no. 48. National Academy of Sciences, pp. 12241–12246, 2018. ista: Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246. mla: Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS, vol. 115, no. 48, National Academy of Sciences, 2018, pp. 12241–46, doi:10.1073/pnas.1810565115. short: C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 12241–12246. date_created: 2018-12-11T11:44:05Z date_published: 2018-11-27T00:00:00Z date_updated: 2024-03-27T23:30:44Z day: '27' department: - _id: KrCh doi: 10.1073/pnas.1810565115 ec_funded: 1 external_id: isi: - '000451351000063' pmid: - '30429320' intvolume: ' 115' isi: 1 issue: '48' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30429320 month: '11' oa: 1 oa_version: Submitted Version page: 12241-12246 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PNAS publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/no-cooperation-without-open-communication/ record: - id: '10293' relation: dissertation_contains status: public scopus_import: '1' status: public title: Indirect reciprocity with private, noisy, and incomplete information type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '67' abstract: - lang: eng text: 'Gene regulatory networks evolve through rewiring of individual components—that is, through changes in regulatory connections. However, the mechanistic basis of regulatory rewiring is poorly understood. Using a canonical gene regulatory system, we quantify the properties of transcription factors that determine the evolutionary potential for rewiring of regulatory connections: robustness, tunability and evolvability. In vivo repression measurements of two repressors at mutated operator sites reveal their contrasting evolutionary potential: while robustness and evolvability were positively correlated, both were in trade-off with tunability. Epistatic interactions between adjacent operators alleviated this trade-off. A thermodynamic model explains how the differences in robustness, tunability and evolvability arise from biophysical characteristics of repressor–DNA binding. The model also uncovers that the energy matrix, which describes how mutations affect repressor–DNA binding, encodes crucial information about the evolutionary potential of a repressor. The biophysical determinants of evolutionary potential for regulatory rewiring constitute a mechanistic framework for understanding network evolution.' article_processing_charge: No article_type: original author: - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y apa: Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. Nature Publishing Group. https://doi.org/10.1038/s41559-018-0651-y chicago: Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution. Nature Publishing Group, 2018. https://doi.org/10.1038/s41559-018-0651-y. ieee: C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018. ista: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643. mla: Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y. short: C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643. date_created: 2018-12-11T11:44:27Z date_published: 2018-09-10T00:00:00Z date_updated: 2024-03-27T23:30:48Z day: '10' ddc: - '570' department: - _id: CaGu - _id: GaTk - _id: JoBo doi: 10.1038/s41559-018-0651-y ec_funded: 1 external_id: isi: - '000447947600021' file: - access_level: open_access checksum: 383a2e2c944a856e2e821ec8e7bf71b6 content_type: application/pdf creator: dernst date_created: 2020-05-14T11:28:52Z date_updated: 2020-07-14T12:47:37Z file_id: '7830' file_name: 2018_NatureEcology_Igler.pdf file_size: 1135973 relation: main_file file_date_updated: 2020-07-14T12:47:37Z has_accepted_license: '1' intvolume: ' 2' isi: 1 issue: '10' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1633 - 1643 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer - _id: 251EE76E-B435-11E9-9278-68D0E5697425 grant_number: '24573' name: Design principles underlying genetic switch architecture (DOC Fellowship) publication: Nature Ecology and Evolution publication_status: published publisher: Nature Publishing Group publist_id: '7987' quality_controlled: '1' related_material: record: - id: '5585' relation: popular_science status: public - id: '6371' relation: dissertation_contains status: public scopus_import: '1' status: public title: Evolutionary potential of transcription factors for gene regulatory rewiring type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2 year: '2018' ... --- _id: '5585' abstract: - lang: eng text: Mean repression values and standard error of the mean are given for all operator mutant libraries. article_processing_charge: No author: - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108 apa: Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108 chicago: Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108. ieee: C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018. ista: Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 10.15479/AT:ISTA:108. mla: Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:108. short: C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018). datarep_id: '108' date_created: 2018-12-12T12:31:40Z date_published: 2018-07-20T00:00:00Z date_updated: 2024-03-27T23:30:48Z day: '20' ddc: - '576' department: - _id: CaGu - _id: GaTk doi: 10.15479/AT:ISTA:108 ec_funded: 1 file: - access_level: open_access checksum: 1435781526c77413802adee0d4583cce content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: system date_created: 2018-12-12T13:02:45Z date_updated: 2020-07-14T12:47:07Z file_id: '5611' file_name: IST-2018-108-v1+1_data_figures.xlsx file_size: 16507 relation: main_file file_date_updated: 2020-07-14T12:47:07Z has_accepted_license: '1' month: '07' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer - _id: 251EE76E-B435-11E9-9278-68D0E5697425 grant_number: '24573' name: Design principles underlying genetic switch architecture (DOC Fellowship) publisher: Institute of Science and Technology Austria related_material: record: - id: '67' relation: research_paper status: public - id: '6371' relation: research_paper status: public status: public title: Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '1013' 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. article_processing_charge: No article_type: review author: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: 'Fink JM. Viewpoint: Microwave quantum states beat the heat. Physics. 2017;10(32). 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' chicago: 'Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics. American Physical Society, 2017. https://doi.org/10.1103/Physics.10.32.' ieee: 'J. M. Fink, “Viewpoint: Microwave quantum states beat the heat,” Physics, vol. 10, no. 32. American Physical Society, 2017.' 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.' short: J.M. Fink, Physics 10 (2017). date_created: 2018-12-11T11:49:41Z date_published: 2017-03-27T00:00:00Z date_updated: 2022-06-07T10:58:31Z day: '27' ddc: - '530' department: - _id: JoFi doi: 10.1103/Physics.10.32 file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-10-24T11:38:14Z date_updated: 2019-10-24T11:38:14Z file_id: '6968' file_name: 2017_Physics_Fink.pdf file_size: 193622 relation: main_file success: 1 file_date_updated: 2019-10-24T11:38:14Z has_accepted_license: '1' intvolume: ' 10' issue: '32' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Physics publication_status: published publisher: American Physical Society publist_id: '6382' quality_controlled: '1' status: public title: 'Viewpoint: Microwave quantum states beat the heat' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2017' ... --- _id: '10126' article_number: 391a article_processing_charge: No article_type: letter_note author: - first_name: Afshin full_name: Vahid Belarghou, Afshin last_name: Vahid Belarghou - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Timon full_name: Idema, Timon last_name: Idema citation: 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 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. ieee: A. Vahid Belarghou, A. Šarić, and T. Idema, “Curvature mediated interactions in highly curved membranes,” Biophysical Journal, vol. 112, no. 3. Elsevier , 2017. 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. short: A. Vahid Belarghou, A. Šarić, T. Idema, Biophysical Journal 112 (2017). date_created: 2021-10-12T07:47:55Z date_published: 2017-02-03T00:00:00Z date_updated: 2021-11-03T10:02:45Z day: '03' doi: 10.1016/j.bpj.2016.11.2123 extern: '1' intvolume: ' 112' issue: '3' keyword: - biophysics language: - iso: eng main_file_link: - open_access: '1' url: https://www.cell.com/biophysj/fulltext/S0006-3495(16)33153-8 month: '02' oa: 1 oa_version: Published Version publication: Biophysical Journal publication_identifier: issn: - 0006-3495 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' status: public title: Curvature mediated interactions in highly curved membranes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 112 year: '2017' ... --- _id: '10175' 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. article_processing_charge: No article_type: original author: - first_name: Omar full_name: Anza Hafsa, Omar last_name: Anza Hafsa - first_name: Nicolas full_name: Clozeau, Nicolas id: fea1b376-906f-11eb-847d-b2c0cf46455b last_name: Clozeau - first_name: Jean-Philippe full_name: Mandallena, Jean-Philippe last_name: Mandallena citation: 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 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. 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. 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. short: O. Anza Hafsa, N. Clozeau, J.-P. Mandallena, Annales Mathématiques Blaise Pascal 24 (2017) 135–193. date_created: 2021-10-23T10:54:23Z date_published: 2017-11-20T00:00:00Z date_updated: 2021-10-28T15:16:25Z day: '20' ddc: - '510' doi: 10.5802/ambp.367 extern: '1' file: - access_level: open_access checksum: 18f40d13dc5d1e24438260b1875b886f content_type: application/pdf creator: cziletti date_created: 2021-10-28T15:02:56Z date_updated: 2021-10-28T15:02:56Z file_id: '10194' file_name: 2017_AMBP_AnzaHafsa.pdf file_size: 850726 relation: main_file success: 1 file_date_updated: 2021-10-28T15:02:56Z has_accepted_license: '1' intvolume: ' 24' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/3.0/ month: '11' oa: 1 oa_version: Published Version page: 135-193 publication: Annales mathématiques Blaise Pascal publication_identifier: eissn: - 2118-7436 issn: - 1259-1734 publication_status: published publisher: Université Clermont Auvergne quality_controlled: '1' status: public title: Homogenization of nonconvex unbounded singular integrals tmp: image: /images/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/3.0/legalcode name: Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0) short: CC BY-ND (3.0) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 24 year: '2017' ... --- _id: '103' 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. acknowledgement: Research supported by Microsoft, the Danish National Research Foundation, the Lundbeck Foundation, Carlsberg Foundation, Villum Foundation, and the European Commission. article_number: '137701' author: - first_name: S M full_name: Albrecht, S M last_name: Albrecht - first_name: Esben full_name: Hansen, Esben last_name: Hansen - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Ferdinand full_name: Kuemmeth, Ferdinand last_name: Kuemmeth - first_name: Thomas full_name: Jespersen, Thomas last_name: Jespersen - first_name: Jesper full_name: Nygård, Jesper last_name: Nygård - first_name: Peter full_name: Krogstrup, Peter last_name: Krogstrup - first_name: Jeroen full_name: Danon, Jeroen last_name: Danon - first_name: Karsten full_name: Flensberg, Karsten last_name: Flensberg - first_name: Charles full_name: Marcus, Charles last_name: Marcus citation: 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 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. 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. 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. 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). date_created: 2018-12-11T11:44:39Z date_published: 2017-03-31T00:00:00Z date_updated: 2021-01-12T06:47:47Z day: '31' doi: 10.1103/PhysRevLett.118.137701 extern: '1' external_id: arxiv: - '1612.05748' intvolume: ' 118' issue: '13' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.05748 month: '03' oa: 1 oa_version: Preprint publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7951' quality_controlled: '1' status: public title: Transport signatures of quasiparticle poisoning in a majorana island type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2017' ... --- _id: '10370' abstract: - lang: eng 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. article_number: e30292 article_processing_charge: No article_type: original author: - first_name: Sebastian Carsten Johannes full_name: Helle, Sebastian Carsten Johannes last_name: Helle - first_name: Qian full_name: Feng, Qian last_name: Feng - first_name: Mathias J full_name: Aebersold, Mathias J last_name: Aebersold - first_name: Luca full_name: Hirt, Luca last_name: Hirt - first_name: Raphael R full_name: Grüter, Raphael R last_name: Grüter - first_name: Afshin full_name: Vahid, Afshin last_name: Vahid - first_name: Andrea full_name: Sirianni, Andrea last_name: Sirianni - first_name: Serge full_name: Mostowy, Serge last_name: Mostowy - first_name: Jess G full_name: Snedeker, Jess G last_name: Snedeker - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Timon full_name: Idema, Timon last_name: Idema - first_name: Tomaso full_name: Zambelli, Tomaso last_name: Zambelli - first_name: Benoît full_name: Kornmann, Benoît last_name: Kornmann citation: 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 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. ieee: S. C. J. Helle et al., “Mechanical force induces mitochondrial fission,” eLife, vol. 6. eLife Sciences Publications, 2017. 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). date_created: 2021-11-29T08:51:38Z date_published: 2017-11-09T00:00:00Z date_updated: 2021-11-29T09:28:14Z day: '09' ddc: - '572' doi: 10.7554/elife.30292 extern: '1' external_id: pmid: - '29119945' file: - access_level: open_access checksum: c35f42dcfb007f6d6c761a27e24c26d3 content_type: application/pdf creator: cchlebak date_created: 2021-11-29T09:07:41Z date_updated: 2021-11-29T09:07:41Z file_id: '10372' file_name: 2017_eLife_Helle.pdf file_size: 6120157 relation: main_file success: 1 file_date_updated: 2021-11-29T09:07:41Z has_accepted_license: '1' intvolume: ' 6' keyword: - general immunology and microbiology - general biochemistry - genetics and molecular biology - general medicine - general neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://elifesciences.org/articles/30292 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Mechanical force induces mitochondrial fission tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 6 year: '2017' ... --- _id: '10369' 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. 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. article_processing_charge: No article_type: original author: - first_name: Mijo full_name: Simunovic, Mijo last_name: Simunovic - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: J. Michael full_name: Henderson, J. Michael last_name: Henderson - first_name: Ka Yee C. full_name: Lee, Ka Yee C. last_name: Lee - first_name: Gregory A. full_name: Voth, Gregory A. last_name: Voth citation: 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 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 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. 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. 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. 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. short: M. Simunovic, A. Šarić, J.M. Henderson, K.Y.C. Lee, G.A. Voth, ACS Central Science 3 (2017) 1246–1253. date_created: 2021-11-29T08:49:50Z date_published: 2017-11-21T00:00:00Z date_updated: 2021-11-29T09:28:06Z day: '21' ddc: - '540' doi: 10.1021/acscentsci.7b00392 extern: '1' external_id: pmid: - '29296664' file: - access_level: open_access checksum: 1cf3e5e5342f2d728f47560acc3ec560 content_type: application/pdf creator: cchlebak date_created: 2021-11-29T09:00:40Z date_updated: 2021-11-29T09:00:40Z file_id: '10371' file_name: 2017_ACSCentSci_Simunovic.pdf file_size: 2635263 relation: main_file success: 1 file_date_updated: 2021-11-29T09:00:40Z has_accepted_license: '1' intvolume: ' 3' issue: '12' keyword: - general chemical engineering - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://pubs.acs.org/doi/10.1021/acscentsci.7b00392 month: '11' oa: 1 oa_version: Published Version page: 1246-1253 pmid: 1 publication: ACS Central Science publication_identifier: eissn: - 2374-7951 issn: - 2374-7943 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Long-range organization of membrane-curving proteins tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 3 year: '2017' ... --- _id: '10373' 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.' 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. article_processing_charge: No article_type: original author: - first_name: Peter full_name: Wirnsberger, Peter last_name: Wirnsberger - first_name: Domagoj full_name: Fijan, Domagoj last_name: Fijan - first_name: Roger A. full_name: Lightwood, Roger A. last_name: Lightwood - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Christoph full_name: Dellago, Christoph last_name: Dellago - first_name: Daan full_name: Frenkel, Daan last_name: Frenkel citation: 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 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 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. 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. 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. 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. date_created: 2021-11-29T09:28:24Z date_published: 2017-04-24T00:00:00Z date_updated: 2021-11-29T09:59:12Z day: '24' doi: 10.1073/pnas.1621494114 extern: '1' external_id: arxiv: - '1610.06840' pmid: - '28439003' intvolume: ' 114' issue: '19' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.pnas.org/content/114/19/4911 month: '04' oa: 1 oa_version: Published Version page: 4911-4914 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Numerical evidence for thermally induced monopoles type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 114 year: '2017' ... --- _id: '10374' abstract: - lang: eng 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. 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). article_processing_charge: No article_type: original author: - first_name: Georg full_name: Meisl, Georg last_name: Meisl - first_name: Luke full_name: Rajah, Luke last_name: Rajah - first_name: Samuel A. I. full_name: Cohen, Samuel A. I. last_name: Cohen - first_name: Manuela full_name: Pfammatter, Manuela last_name: Pfammatter - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Erik full_name: Hellstrand, Erik last_name: Hellstrand - first_name: Alexander K. full_name: Buell, Alexander K. last_name: Buell - first_name: Adriano full_name: Aguzzi, Adriano last_name: Aguzzi - first_name: Sara full_name: Linse, Sara last_name: Linse - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo - first_name: Christopher M. full_name: Dobson, Christopher M. last_name: Dobson - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles citation: 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 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 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. 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. 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. 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. date_created: 2021-11-29T09:29:31Z date_published: 2017-08-31T00:00:00Z date_updated: 2021-11-29T10:00:00Z day: '31' ddc: - '540' doi: 10.1039/c7sc01965c extern: '1' external_id: pmid: - '29147538' intvolume: ' 8' issue: '10' keyword: - general chemistry language: - iso: eng license: https://creativecommons.org/licenses/by-nc/3.0/ main_file_link: - open_access: '1' url: https://pubs.rsc.org/en/content/articlelanding/2017/SC/C7SC01965C month: '08' oa: 1 oa_version: Published Version page: 7087-7097 pmid: 1 publication: Chemical Science publication_identifier: eissn: - 2041-6539 issn: - 2041-6520 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Scaling behaviour and rate-determining steps in filamentous self-assembly tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) short: CC BY-NC (3.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2017' ... --- _id: '10375' 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.' acknowledgement: This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program. article_processing_charge: No article_type: original author: - first_name: Afshin full_name: Vahid, Afshin last_name: Vahid - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Timon full_name: Idema, Timon last_name: Idema citation: 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 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. 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. 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. short: A. Vahid, A. Šarić, T. Idema, Soft Matter 13 (2017) 4924–4930. date_created: 2021-11-29T10:00:39Z date_published: 2017-06-15T00:00:00Z date_updated: 2021-11-29T10:33:36Z day: '15' doi: 10.1039/c7sm00433h extern: '1' external_id: arxiv: - '1703.00776' pmid: - '28677712' intvolume: ' 13' issue: '28' keyword: - condensed matter physics - general chemistry language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ main_file_link: - open_access: '1' url: https://pubs.rsc.org/en/content/articlelanding/2017/SM/C7SM00433H month: '06' oa: 1 oa_version: Published Version page: 4924-4930 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Curvature variation controls particle aggregation on fluid vesicles tmp: 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) short: CC BY (3.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 13 year: '2017' ... --- _id: '10418' abstract: - lang: eng 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. 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." article_number: '33' article_processing_charge: No article_type: original author: - first_name: Annabelle full_name: Mciver, Annabelle last_name: Mciver - first_name: Carroll full_name: Morgan, Carroll last_name: Morgan - first_name: Benjamin Lucien full_name: Kaminski, Benjamin Lucien last_name: Kaminski - first_name: Joost P full_name: Katoen, Joost P id: 4524F760-F248-11E8-B48F-1D18A9856A87 last_name: Katoen citation: 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' 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. 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. 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. 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. short: A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017). conference: end_date: 2018-01-13 location: Los Angeles, CA, United States name: 'POPL: Programming Languages' start_date: 2018-01-07 date_created: 2021-12-05T23:01:49Z date_published: 2017-12-07T00:00:00Z date_updated: 2021-12-07T08:04:14Z day: '07' department: - _id: KrCh - _id: ToHe doi: 10.1145/3158121 external_id: arxiv: - '1711.03588' intvolume: ' 2' issue: POPL language: - iso: eng main_file_link: - open_access: '1' url: https://dl.acm.org/doi/10.1145/3158121 month: '12' oa: 1 oa_version: Published Version publication: Proceedings of the ACM on Programming Languages publication_identifier: eissn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: A new proof rule for almost-sure termination type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 2 year: '2017' ... --- _id: '10663' abstract: - lang: eng 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.' alternative_title: - Graduate Dissertations and Theses at Illinois article_processing_charge: No author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 citation: ama: Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting structures. 2017. apa: Polshyn, H. (2017). Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign. chicago: Polshyn, Hryhoriy. “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. ista: Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign. 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. date_created: 2022-01-25T14:54:14Z date_published: 2017-09-18T00:00:00Z date_updated: 2022-01-25T15:00:26Z day: '18' degree_awarded: PhD extern: '1' keyword: - physics - superconductivity - magnetic force microscopy - phase slips language: - iso: eng main_file_link: - open_access: '1' url: http://hdl.handle.net/2142/99178 month: '09' oa: 1 oa_version: Published Version page: '103' publication_status: published publisher: University of Illinois at Urbana-Champaign status: public supervisor: - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian title: Magnetic force microscopy studies of mesoscopic superconducting structures type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2017' ... --- _id: '10745' abstract: - lang: eng 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 alternative_title: - Bulletin of the American Physical Society article_number: P39.00011 article_processing_charge: No author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Tyler full_name: Naibert, Tyler last_name: Naibert - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian citation: 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.' 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.' 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. 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. 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.' 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. short: H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American Physical Society, 2017. conference: end_date: 2017-03-17 location: New Orleans, LA, United States name: 'APS: American Physical Society' start_date: 2017-03-13 date_created: 2022-02-08T09:49:17Z date_published: 2017-03-01T00:00:00Z date_updated: 2022-02-08T10:44:35Z day: '01' extern: '1' intvolume: ' 62' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR17/Session/P39.11 month: '03' oa: 1 oa_version: Published Version publication: APS March Meeting 2017 publication_identifier: issn: - 0003-0503 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: ' Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures' type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 62 year: '2017' ... --- _id: '1075' alternative_title: - American Studies in Austria author: - first_name: Bernhard full_name: Wenzl, Bernhard id: 479E9046-F248-11E8-B48F-1D18A9856A87 last_name: Wenzl citation: ama: 'Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot; 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 &quot;The Vienna Frontier&quot; 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.' chicago: 'Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;” 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.' ieee: 'B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;,” 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.' ista: 'Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot; 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 &quot;The Vienna Frontier&quot;” 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.' 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.' date_created: 2018-12-11T11:50:00Z date_published: 2017-02-01T00:00:00Z date_updated: 2021-01-12T06:48:06Z day: '01' ddc: - '001' editor: - first_name: Joshua full_name: Parker, Joshua last_name: Parker - first_name: Ralph full_name: Poole, Ralph last_name: Poole extern: '1' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:08:06Z date_updated: 2018-12-12T10:08:06Z file_id: '4666' file_name: IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf file_size: 380624 relation: main_file file_date_updated: 2018-12-12T10:08:06Z has_accepted_license: '1' intvolume: ' 15' language: - iso: eng month: '02' oa: 1 oa_version: None page: 73 - 80 publication: 'Austria and America: 20th-Century Cross-Cultural Encounters' publication_identifier: isbn: - 978-3643908124 publication_status: published publisher: LIT Verlag Berlin-Münster-Wien-Zürich-London publist_id: '6306' status: public title: 'An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier"' type: book_chapter user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2017' ... --- _id: '11066' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Tobias M. full_name: Franks, Tobias M. last_name: Franks - first_name: Asako full_name: McCloskey, Asako last_name: McCloskey - first_name: Maxim Nikolaievich full_name: Shokhirev, Maxim Nikolaievich last_name: Shokhirev - first_name: Chris full_name: Benner, Chris last_name: Benner - first_name: Annie full_name: Rathore, Annie last_name: Rathore - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: 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 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 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. 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. 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. 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. short: T.M. Franks, A. McCloskey, M.N. Shokhirev, C. Benner, A. Rathore, M. Hetzer, Genes & Development 31 (2017) 2222–2234. date_created: 2022-04-07T07:45:59Z date_published: 2017-12-21T00:00:00Z date_updated: 2022-07-18T08:33:05Z day: '21' doi: 10.1101/gad.306753.117 extern: '1' external_id: pmid: - '29269482' intvolume: ' 31' issue: '22' keyword: - Developmental Biology - Genetics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/gad.306753.117 month: '12' oa: 1 oa_version: Published Version page: 2222-2234 pmid: 1 publication: Genes & Development publication_identifier: issn: - 0890-9369 - 1549-5477 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 31 year: '2017' ... --- _id: '11067' 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. article_processing_charge: No article_type: original author: - first_name: Tomohisa full_name: Toda, Tomohisa last_name: Toda - first_name: Jonathan Y. full_name: Hsu, Jonathan Y. last_name: Hsu - first_name: Sara B. full_name: Linker, Sara B. last_name: Linker - first_name: Lauren full_name: Hu, Lauren last_name: Hu - first_name: Simon T. full_name: Schafer, Simon T. last_name: Schafer - first_name: Jerome full_name: Mertens, Jerome last_name: Mertens - first_name: Filipe V. full_name: Jacinto, Filipe V. last_name: Jacinto - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X - first_name: Fred H. full_name: Gage, Fred H. last_name: Gage citation: 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 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 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. 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. 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. 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. date_created: 2022-04-07T07:46:12Z date_published: 2017-11-02T00:00:00Z date_updated: 2022-07-18T08:33:07Z day: '02' doi: 10.1016/j.stem.2017.08.012 extern: '1' external_id: pmid: - '28919367' intvolume: ' 21' issue: '5' keyword: - Cell Biology - Genetics - Molecular Medicine language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.stem.2017.08.012 month: '11' oa: 1 oa_version: Published Version page: 618-634.e7 pmid: 1 publication: Cell Stem Cell publication_identifier: issn: - 1934-5909 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 21 year: '2017' ... --- _id: '11065' abstract: - lang: eng 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. article_number: '328' article_processing_charge: No article_type: original author: - first_name: Abigail full_name: Buchwalter, Abigail last_name: Buchwalter - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: 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 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 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. ieee: A. Buchwalter and M. Hetzer, “Nucleolar expansion and elevated protein translation in premature aging,” Nature Communications, vol. 8. Springer Nature, 2017. ista: Buchwalter A, Hetzer M. 2017. Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. 8, 328. 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. short: A. Buchwalter, M. Hetzer, Nature Communications 8 (2017). date_created: 2022-04-07T07:45:50Z date_published: 2017-08-30T00:00:00Z date_updated: 2022-07-18T08:33:03Z day: '30' doi: 10.1038/s41467-017-00322-z extern: '1' external_id: pmid: - '28855503' intvolume: ' 8' keyword: - General Physics and Astronomy - General Biochemistry - Genetics and Molecular Biology - General Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-017-00322-z month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Nucleolar expansion and elevated protein translation in premature aging type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 8 year: '2017' ... --- _id: '11518' 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." 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.' article_number: '145' article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: D. full_name: Sobral, D. last_name: Sobral - first_name: F. full_name: Boone, F. last_name: Boone - first_name: H. full_name: Röttgering, H. last_name: Röttgering - first_name: D. full_name: Schaerer, D. last_name: Schaerer - first_name: M. full_name: Girard, M. last_name: Girard - first_name: A. full_name: Pallottini, A. last_name: Pallottini - first_name: L. full_name: Vallini, L. last_name: Vallini - first_name: A. full_name: Ferrara, A. last_name: Ferrara - first_name: B. full_name: Darvish, B. last_name: Darvish - first_name: B. full_name: Mobasher, B. last_name: Mobasher citation: 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 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 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. 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. 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. 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). date_created: 2022-07-07T08:48:04Z date_published: 2017-12-21T00:00:00Z date_updated: 2022-08-18T10:23:35Z day: '21' doi: 10.3847/1538-4357/aa9931 extern: '1' external_id: arxiv: - '1709.06569' intvolume: ' 851' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - dark ages - reionization - 'first stars – galaxies: formation – galaxies: high-redshift – galaxies: ISM – galaxies: kinematics and dynamics' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.06569 month: '12' oa: 1 oa_version: Preprint publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: ALMA reveals metals yet no dust within multiple components in CR7 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 851 year: '2017' ... --- _id: '11562' abstract: - lang: eng 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. 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.' article_processing_charge: No article_type: original author: - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Philip full_name: Best, Philip last_name: Best - first_name: Andra full_name: Stroe, Andra last_name: Stroe - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Iván full_name: Oteo, Iván last_name: Oteo - first_name: Ian full_name: Smail, Ian last_name: Smail - first_name: Leah full_name: Morabito, Leah last_name: Morabito - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso citation: 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.' 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.' 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.' 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.' 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. date_created: 2022-07-12T12:04:16Z date_published: 2017-04-01T00:00:00Z date_updated: 2022-08-19T07:18:20Z day: '01' doi: 10.1093/mnras/stw3090 extern: '1' external_id: arxiv: - '1609.05897' intvolume: ' 466' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: haloes' - 'galaxies: high-redshift' - 'galaxies: luminosity function' - mass function - 'galaxies: statistics' - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.05897 month: '04' oa: 1 oa_version: Preprint page: 1242-1258 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 466 year: '2017' ... --- _id: '11566' 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. 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 ' article_processing_charge: No article_type: original 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 full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: João full_name: Calhau, João last_name: Calhau - first_name: Ivan full_name: Oteo, Ivan last_name: Oteo citation: 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. 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. 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. 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. short: A. Stroe, D. Sobral, J.J. Matthee, J. Calhau, I. Oteo, Monthly Notices of the Royal Astronomical Society 471 (2017) 2558–2574. date_created: 2022-07-12T12:33:16Z date_published: 2017-11-01T00:00:00Z date_updated: 2022-08-19T07:59:57Z day: '01' doi: 10.1093/mnras/stx1712 extern: '1' external_id: arxiv: - '1703.10169' intvolume: ' 471' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: active' - 'galaxies: high-redshift' - 'quasars: emission lines' - 'galaxies: star formation' - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.10169 month: '11' oa: 1 oa_version: Preprint page: 2558-2574 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public 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 ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2017' ... --- _id: '11564' 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. 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)." article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Philip full_name: Best, Philip last_name: Best - first_name: Ali Ahmad full_name: Khostovan, Ali Ahmad last_name: Khostovan - first_name: Iván full_name: Oteo, Iván last_name: Oteo - first_name: Rychard full_name: Bouwens, Rychard last_name: Bouwens - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering citation: 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 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 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. 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. 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. 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. 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. date_created: 2022-07-12T12:12:14Z date_published: 2017-03-01T00:00:00Z date_updated: 2022-08-19T07:53:04Z day: '01' doi: 10.1093/mnras/stw2973 extern: '1' external_id: arxiv: - '1605.08782' intvolume: ' 465' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: high-redshift' - 'cosmology: observations' - dark ages - reionization - first stars language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1605.08782 month: '03' oa: 1 oa_version: Preprint page: 3637-3655 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 465 year: '2017' ... --- _id: '11567' 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. article_processing_charge: No article_type: original 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 full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: João full_name: Calhau, João last_name: Calhau - first_name: Ivan full_name: Oteo, Ivan last_name: Oteo citation: 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 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. 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. 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. short: A. Stroe, D. Sobral, J.J. Matthee, J. Calhau, I. Oteo, Monthly Notices of the Royal Astronomical Society 471 (2017) 2575–2586. date_created: 2022-07-12T12:54:57Z date_published: 2017-11-01T00:00:00Z date_updated: 2022-08-19T08:02:04Z day: '01' doi: 10.1093/mnras/stx1713 extern: '1' external_id: arxiv: - '1703.10169' intvolume: ' 471' issue: '3' 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' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.10169 month: '11' oa: 1 oa_version: Preprint page: 2575-2586 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public 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 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2017' ... --- _id: '11565' 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. 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). article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Joop full_name: Schaye, Joop last_name: Schaye - first_name: Robert A. full_name: Crain, Robert A. last_name: Crain - first_name: Matthieu full_name: Schaller, Matthieu last_name: Schaller - first_name: Richard full_name: Bower, Richard last_name: Bower - first_name: Tom full_name: Theuns, Tom last_name: Theuns citation: 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 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 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. 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. 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. 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. 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. date_created: 2022-07-12T12:25:08Z date_published: 2017-02-01T00:00:00Z date_updated: 2022-08-19T07:56:07Z day: '01' doi: 10.1093/mnras/stw2884 extern: '1' external_id: arxiv: - '1608.08218' intvolume: ' 465' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: formation' - 'galaxies: haloes' - 'cosmology: theory' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1608.08218 month: '02' oa: 1 oa_version: Preprint page: 2381-2396 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 465 year: '2017' ... --- _id: '11561' 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. article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Philip full_name: Best, Philip last_name: Best - first_name: Ian full_name: Smail, Ian last_name: Smail - first_name: Fuyan full_name: Bian, Fuyan last_name: Bian - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Xiaohui full_name: Fan, Xiaohui last_name: Fan citation: 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' 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' 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.' 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.' 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.' 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.' 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. date_created: 2022-07-12T11:01:35Z date_published: 2017-10-01T00:00:00Z date_updated: 2022-08-19T07:15:14Z day: '01' doi: 10.1093/mnras/stx1569 extern: '1' external_id: arxiv: - '1702.04721' intvolume: ' 471' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics galaxies - active - galaxies - evolution - galaxies - high-redshift - galaxies - luminosity function - mass function - 'galaxies: star formation' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.04721 month: '10' oa: 1 oa_version: Preprint page: 629-649 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2017' ... --- _id: '11572' 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. 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).' article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Sérgio full_name: Santos, Sérgio last_name: Santos - first_name: Bahram full_name: Mobasher, Bahram last_name: Mobasher - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Lara full_name: Alegre, Lara last_name: Alegre citation: 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. 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. 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. 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. 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. date_created: 2022-07-13T09:47:39Z date_published: 2017-11-01T00:00:00Z date_updated: 2022-08-19T08:05:37Z day: '01' doi: 10.1093/mnras/stx2061 extern: '1' external_id: arxiv: - '1706.06591' intvolume: ' 472' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution – galaxies: high-redshift' - dark ages - reionization - first stars - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.06591 month: '11' oa: 1 oa_version: Preprint page: 772-787 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 472 year: '2017' ... --- _id: '11573' abstract: - lang: eng 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. 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).' article_processing_charge: No article_type: original author: - first_name: O. J. full_name: Turner, O. J. last_name: Turner - first_name: M. full_name: Cirasuolo, M. last_name: Cirasuolo - first_name: C. M. full_name: Harrison, C. M. last_name: Harrison - first_name: R. J. full_name: McLure, R. J. last_name: McLure - first_name: J. S. full_name: Dunlop, J. S. last_name: Dunlop - first_name: A. M. full_name: Swinbank, A. M. last_name: Swinbank - first_name: H. L. full_name: Johnson, H. L. last_name: Johnson - first_name: D. full_name: Sobral, D. last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: R. M. full_name: Sharples, R. M. last_name: Sharples citation: 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 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. 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. 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. 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. 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. date_created: 2022-07-13T10:03:01Z date_published: 2017-10-01T00:00:00Z date_updated: 2022-08-19T08:07:31Z day: '01' doi: 10.1093/mnras/stx1366 extern: '1' external_id: arxiv: - '1704.06263' intvolume: ' 471' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: high-redshift' - 'galaxies: kinematics and dynamics' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.06263 month: '10' oa: 1 oa_version: Preprint page: 1280-1320 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2017' ... --- _id: '11633' 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. article_number: '1711.02890' article_processing_charge: No author: - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: R. A. full_name: Garcia, R. A. last_name: Garcia - first_name: G. R. full_name: Davies, G. R. last_name: Davies - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: E. full_name: Corsaro, E. last_name: Corsaro citation: 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' 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' 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.' 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. .' 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.' 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.' short: L.A. Bugnet, R.A. Garcia, G.R. Davies, S. Mathur, E. Corsaro, ArXiv (n.d.). date_created: 2022-07-21T07:13:13Z date_published: 2017-11-08T00:00:00Z date_updated: 2022-08-22T08:45:42Z day: '08' doi: 10.48550/arXiv.1711.02890 extern: '1' external_id: arxiv: - '1711.02890' keyword: - asteroseismology - methods - data analysis - stars - oscillations language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1711.02890 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'FliPer: Checking the reliability of global seismic parameters from automatic pipelines' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '11651' 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. alternative_title: - PMLR article_processing_charge: No author: - first_name: Di full_name: Wang, Di last_name: Wang - first_name: Kimon full_name: Fountoulakis, Kimon last_name: Fountoulakis - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Michael W. full_name: Mahoney, Michael W. last_name: Mahoney - first_name: ' Satish' full_name: Rao , Satish last_name: 'Rao ' citation: 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.' 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.' 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. 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. 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. conference: end_date: 2017-08-11 location: Sydney, Australia name: International Conference on Machine Learning start_date: 2017-08-06 date_created: 2022-07-25T13:59:21Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-09T09:15:31Z day: '01' extern: '1' external_id: arxiv: - '1706.05826' intvolume: ' 70' language: - iso: eng main_file_link: - open_access: '1' url: http://proceedings.mlr.press/v70/wang17b/wang17b.pdf month: '09' oa: 1 oa_version: Published Version page: 3598-3607 publication: Proceedings of the 34th International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: Capacity releasing diffusion for speed and locality type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2017' ... --- _id: '11665' abstract: - lang: eng text: "We study the problem of maintaining a breadth-first spanning tree (BFS tree) in partially dynamic distributed networks modeling a sequence of either failures or additions of communication links (but not both). We present deterministic (1+ϵ)-approximation algorithms whose amortized time (over some number of link changes) is sublinear in D, the maximum diameter of the network.\r\n\r\nOur technique also leads to a deterministic (1+ϵ)-approximate incremental algorithm for single-source shortest paths in the sequential (usual RAM) model. Prior to our work, the state of the art was the classic exact algorithm of Even and Shiloach (1981), which is optimal under some assumptions (Roditty and Zwick 2011; Henzinger et al. 2015). Our result is the first to show that, in the incremental setting, this bound can be beaten in certain cases if some approximation is allowed." acknowledgement: "We thank the reviewers of ICALP 2013 for pointing to related articles and to an error in an example\r\ngiven in a previous version of this article. We also thank one of the reviewers of Transactions on\r\nAlgorithms for very detailed comments." article_number: '51' article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks. ACM Transactions on Algorithms. 2017;13(4). doi:10.1145/3146550 apa: Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2017). Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3146550 chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Maintenance of Breadth-First Spanning Trees in Partially Dynamic Networks.” ACM Transactions on Algorithms. Association for Computing Machinery, 2017. https://doi.org/10.1145/3146550. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks,” ACM Transactions on Algorithms, vol. 13, no. 4. Association for Computing Machinery, 2017. ista: Henzinger MH, Krinninger S, Nanongkai D. 2017. Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks. ACM Transactions on Algorithms. 13(4), 51. mla: Henzinger, Monika H., et al. “Sublinear-Time Maintenance of Breadth-First Spanning Trees in Partially Dynamic Networks.” ACM Transactions on Algorithms, vol. 13, no. 4, 51, Association for Computing Machinery, 2017, doi:10.1145/3146550. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, ACM Transactions on Algorithms 13 (2017). date_created: 2022-07-27T11:37:23Z date_published: 2017-10-01T00:00:00Z date_updated: 2022-09-09T11:57:42Z day: '01' doi: 10.1145/3146550 extern: '1' external_id: arxiv: - '1512.08147' intvolume: ' 13' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1512.08147 month: '10' oa: 1 oa_version: Preprint publication: ACM Transactions on Algorithms publication_identifier: eissn: - 1549-6333 issn: - 1549-6325 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '11676' abstract: - lang: eng text: We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the so-called food web, encoding viability constraints between these species. These food webs usually have constant depth. The goal is to select a subset of k species that satisfies the viability constraints and has maximal phylogenetic diversity. As this problem is known to be NP-hard, we investigate approximation algorithms. We present the first constant factor approximation algorithm if the depth is constant. Its approximation ratio is (1−1e√). This algorithm not only applies to phylogenetic trees with viability constraints but for arbitrary monotone submodular set functions with viability constraints. Second, we show that there is no (1−1/e+ϵ)-approximation algorithm for our problem setting (even for additive functions) and that there is no approximation algorithm for a slight extension of this setting. acknowledgement: "The research leading to these results has received funding from the European Research\r\nCouncil under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement No. 340506." article_processing_charge: No article_type: original author: - first_name: Wolfgang full_name: Dvořák, Wolfgang last_name: Dvořák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: David P. full_name: Williamson, David P. last_name: Williamson citation: ama: Dvořák W, Henzinger MH, Williamson DP. Maximizing a submodular function with viability constraints. Algorithmica. 2017;77(1):152-172. doi:10.1007/s00453-015-0066-y apa: Dvořák, W., Henzinger, M. H., & Williamson, D. P. (2017). Maximizing a submodular function with viability constraints. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-015-0066-y chicago: Dvořák, Wolfgang, Monika H Henzinger, and David P. Williamson. “Maximizing a Submodular Function with Viability Constraints.” Algorithmica. Springer Nature, 2017. https://doi.org/10.1007/s00453-015-0066-y. ieee: W. Dvořák, M. H. Henzinger, and D. P. Williamson, “Maximizing a submodular function with viability constraints,” Algorithmica, vol. 77, no. 1. Springer Nature, pp. 152–172, 2017. ista: Dvořák W, Henzinger MH, Williamson DP. 2017. Maximizing a submodular function with viability constraints. Algorithmica. 77(1), 152–172. mla: Dvořák, Wolfgang, et al. “Maximizing a Submodular Function with Viability Constraints.” Algorithmica, vol. 77, no. 1, Springer Nature, 2017, pp. 152–72, doi:10.1007/s00453-015-0066-y. short: W. Dvořák, M.H. Henzinger, D.P. Williamson, Algorithmica 77 (2017) 152–172. date_created: 2022-07-27T14:37:24Z date_published: 2017-01-01T00:00:00Z date_updated: 2022-09-12T08:58:16Z day: '01' doi: 10.1007/s00453-015-0066-y extern: '1' external_id: arxiv: - '1611.05753' intvolume: ' 77' issue: '1' keyword: - Approximation algorithms - Submodular functions - Phylogenetic diversity - Viability constraints language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.05753 month: '01' oa: 1 oa_version: Preprint page: 152-172 publication: Algorithmica publication_identifier: eissn: - 1432-0541 issn: - 0178-4617 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Maximizing a submodular function with viability constraints type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2017' ... --- _id: '1175' abstract: - lang: eng text: We study space complexity and time-space trade-offs with a focus not on peak memory usage but on overall memory consumption throughout the computation. Such a cumulative space measure was introduced for the computational model of parallel black pebbling by [Alwen and Serbinenko ’15] as a tool for obtaining results in cryptography. We consider instead the non- deterministic black-white pebble game and prove optimal cumulative space lower bounds and trade-offs, where in order to minimize pebbling time the space has to remain large during a significant fraction of the pebbling. We also initiate the study of cumulative space in proof complexity, an area where other space complexity measures have been extensively studied during the last 10–15 years. Using and extending the connection between proof complexity and pebble games in [Ben-Sasson and Nordström ’08, ’11] we obtain several strong cumulative space results for (even parallel versions of) the resolution proof system, and outline some possible future directions of study of this, in our opinion, natural and interesting space measure. alternative_title: - LIPIcs author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Susanna full_name: De Rezende, Susanna last_name: De Rezende - first_name: Jakob full_name: Nordstrom, Jakob last_name: Nordstrom - first_name: Marc full_name: Vinyals, Marc last_name: Vinyals citation: ama: 'Alwen JF, De Rezende S, Nordstrom J, Vinyals M. Cumulative space in black-white pebbling and resolution. In: Papadimitriou C, ed. Vol 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:38:1-38-21. doi:10.4230/LIPIcs.ITCS.2017.38' apa: 'Alwen, J. F., De Rezende, S., Nordstrom, J., & Vinyals, M. (2017). Cumulative space in black-white pebbling and resolution. In C. Papadimitriou (Ed.) (Vol. 67, p. 38:1-38-21). Presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2017.38' chicago: Alwen, Joel F, Susanna De Rezende, Jakob Nordstrom, and Marc Vinyals. “Cumulative Space in Black-White Pebbling and Resolution.” edited by Christos Papadimitriou, 67:38:1-38-21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ITCS.2017.38. ieee: 'J. F. Alwen, S. De Rezende, J. Nordstrom, and M. Vinyals, “Cumulative space in black-white pebbling and resolution,” presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States, 2017, vol. 67, p. 38:1-38-21.' ista: 'Alwen JF, De Rezende S, Nordstrom J, Vinyals M. 2017. Cumulative space in black-white pebbling and resolution. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 67, 38:1-38-21.' mla: Alwen, Joel F., et al. Cumulative Space in Black-White Pebbling and Resolution. Edited by Christos Papadimitriou, vol. 67, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21, doi:10.4230/LIPIcs.ITCS.2017.38. short: J.F. Alwen, S. De Rezende, J. Nordstrom, M. Vinyals, in:, C. Papadimitriou (Ed.), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21. conference: end_date: 2017-01-11 location: Berkeley, CA, United States name: 'ITCS: Innovations in Theoretical Computer Science' start_date: 2017-01-09 date_created: 2018-12-11T11:50:33Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T06:48:51Z day: '01' ddc: - '005' - '600' department: - _id: KrPi doi: 10.4230/LIPIcs.ITCS.2017.38 editor: - first_name: Christos full_name: Papadimitriou, Christos last_name: Papadimitriou file: - access_level: open_access checksum: dbc94810be07c2fb1945d5c2a6130e6c content_type: application/pdf creator: system date_created: 2018-12-12T10:17:11Z date_updated: 2020-07-14T12:44:37Z file_id: '5263' file_name: IST-2018-927-v1+1_LIPIcs-ITCS-2017-38.pdf file_size: 557769 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 67' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 38:1-38-21 publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6179' pubrep_id: '927' quality_controlled: '1' scopus_import: 1 status: public title: Cumulative space in black-white pebbling and resolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 67 year: '2017' ... --- _id: '11829' abstract: - lang: eng text: "In recent years it has become popular to study dynamic problems in a sensitivity setting: Instead of allowing for an arbitrary sequence of updates, the sensitivity model only allows to apply batch updates of small size to the original input data. The sensitivity model is particularly appealing since recent strong conditional lower bounds ruled out fast algorithms for many dynamic problems, such as shortest paths, reachability, or subgraph connectivity.\r\n\r\nIn this paper we prove conditional lower bounds for these and additional problems in a sensitivity setting. For example, we show that under the Boolean Matrix Multiplication (BMM) conjecture combinatorial algorithms cannot compute the (4/3-\\varepsilon)-approximate diameter of an undirected unweighted dense graph with truly subcubic preprocessing time and truly subquadratic update/query time. This result is surprising since in the static setting it is not clear whether a reduction from BMM to diameter is possible. We further show under the BMM conjecture that many problems, such as reachability or approximate shortest paths, cannot be solved faster than by recomputation from scratch even after only one or two edge insertions. We extend our reduction from BMM to Diameter to give a reduction from All Pairs Shortest Paths to Diameter under one deletion in weighted graphs. This is intriguing, as in the static setting it is a big open problem whether Diameter is as hard as APSP. We further get a nearly tight lower bound for shortest paths after two edge deletions based on the APSP conjecture. We give more lower bounds under the Strong Exponential Time Hypothesis. Many of our lower bounds also hold for static oracle data structures where no sensitivity is required.\r\n\r\nFinally, we give the first algorithm for the (1+\\varepsilon)-approximate radius, diameter, and eccentricity problems in directed or undirected unweighted graphs in case of single edges failures. The algorithm has a truly subcubic running time for graphs with a truly subquadratic number of edges; it is tight w.r.t. the conditional lower bounds we obtain." alternative_title: - LIPIcs article_number: '26' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Andrea full_name: Lincoln, Andrea last_name: Lincoln - first_name: Stefan full_name: Neumann, Stefan last_name: Neumann - first_name: Virginia full_name: Vassilevska Williams, Virginia last_name: Vassilevska Williams citation: ama: 'Henzinger MH, Lincoln A, Neumann S, Vassilevska Williams V. Conditional hardness for sensitivity problems. In: 8th Innovations in Theoretical Computer Science Conference. Vol 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ITCS.2017.26' apa: 'Henzinger, M. H., Lincoln, A., Neumann, S., & Vassilevska Williams, V. (2017). Conditional hardness for sensitivity problems. In 8th Innovations in Theoretical Computer Science Conference (Vol. 67). Berkley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2017.26' chicago: Henzinger, Monika H, Andrea Lincoln, Stefan Neumann, and Virginia Vassilevska Williams. “Conditional Hardness for Sensitivity Problems.” In 8th Innovations in Theoretical Computer Science Conference, Vol. 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ITCS.2017.26. ieee: M. H. Henzinger, A. Lincoln, S. Neumann, and V. Vassilevska Williams, “Conditional hardness for sensitivity problems,” in 8th Innovations in Theoretical Computer Science Conference, Berkley, CA, United States, 2017, vol. 67. ista: 'Henzinger MH, Lincoln A, Neumann S, Vassilevska Williams V. 2017. Conditional hardness for sensitivity problems. 8th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science Conference, LIPIcs, vol. 67, 26.' mla: Henzinger, Monika H., et al. “Conditional Hardness for Sensitivity Problems.” 8th Innovations in Theoretical Computer Science Conference, vol. 67, 26, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ITCS.2017.26. short: M.H. Henzinger, A. Lincoln, S. Neumann, V. Vassilevska Williams, in:, 8th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-01-11 location: Berkley, CA, United States name: 'ITCS: Innovations in Theoretical Computer Science Conference' start_date: 2017-01-09 date_created: 2022-08-12T08:55:33Z date_published: 2017-11-28T00:00:00Z date_updated: 2023-02-16T11:49:15Z day: '28' doi: 10.4230/LIPICS.ITCS.2017.26 extern: '1' external_id: arxiv: - '1703.01638' intvolume: ' 67' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.ITCS.2017.26 month: '11' oa: 1 oa_version: Published Version publication: 8th Innovations in Theoretical Computer Science Conference publication_identifier: isbn: - '9783959770293' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Conditional hardness for sensitivity problems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 67 year: '2017' ... --- _id: '11833' abstract: - lang: eng text: "We introduce a new algorithmic framework for designing dynamic graph algorithms in minor-free graphs, by exploiting the structure of such graphs and a tool called vertex sparsification, which is a way to compress large graphs into small ones that well preserve relevant properties among a subset of vertices and has previously mainly been used in the design of approximation algorithms.\r\n\r\nUsing this framework, we obtain a Monte Carlo randomized fully dynamic algorithm for (1 + epsilon)-approximating the energy of electrical flows in n-vertex planar graphs with tilde{O}(r epsilon^{-2}) worst-case update time and tilde{O}((r + n / sqrt{r}) epsilon^{-2}) worst-case query time, for any r larger than some constant. For r=n^{2/3}, this gives tilde{O}(n^{2/3} epsilon^{-2}) update time and tilde{O}(n^{2/3} epsilon^{-2}) query time. We also extend this algorithm to work for minor-free graphs with similar approximation and running time guarantees. Furthermore, we illustrate our framework on the all-pairs max flow and shortest path problems by giving corresponding dynamic algorithms in minor-free graphs with both sublinear update and query times. To the best of our knowledge, our results are the first to systematically establish such a connection between dynamic graph algorithms and vertex sparsification.\r\n\r\nWe also present both upper bound and lower bound for maintaining the energy of electrical flows in the incremental subgraph model, where updates consist of only vertex activations, which might be of independent interest." alternative_title: - LIPIcs article_number: '45' article_processing_charge: No author: - first_name: Gramoz full_name: Goranci, Gramoz last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Pan full_name: Peng, Pan last_name: Peng citation: ama: 'Goranci G, Henzinger MH, Peng P. The power of vertex sparsifiers in dynamic graph algorithms. In: 25th Annual European Symposium on Algorithms. Vol 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ESA.2017.45' apa: 'Goranci, G., Henzinger, M. H., & Peng, P. (2017). The power of vertex sparsifiers in dynamic graph algorithms. In 25th Annual European Symposium on Algorithms (Vol. 87). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2017.45' chicago: Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “The Power of Vertex Sparsifiers in Dynamic Graph Algorithms.” In 25th Annual European Symposium on Algorithms, Vol. 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ESA.2017.45. ieee: G. Goranci, M. H. Henzinger, and P. Peng, “The power of vertex sparsifiers in dynamic graph algorithms,” in 25th Annual European Symposium on Algorithms, Vienna, Austria, 2017, vol. 87. ista: 'Goranci G, Henzinger MH, Peng P. 2017. The power of vertex sparsifiers in dynamic graph algorithms. 25th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 87, 45.' mla: Goranci, Gramoz, et al. “The Power of Vertex Sparsifiers in Dynamic Graph Algorithms.” 25th Annual European Symposium on Algorithms, vol. 87, 45, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ESA.2017.45. short: G. Goranci, M.H. Henzinger, P. Peng, in:, 25th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-06 location: Vienna, Austria name: 'ESA: Annual European Symposium on Algorithms' start_date: 2017-09-04 date_created: 2022-08-12T10:46:26Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-16T11:56:37Z day: '01' doi: 10.4230/LIPICS.ESA.2017.45 extern: '1' external_id: arxiv: - '1712.06473' intvolume: ' 87' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2017.45 month: '09' oa: 1 oa_version: Published Version publication: 25th Annual European Symposium on Algorithms publication_identifier: isbn: - 978-3-95977-049-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: The power of vertex sparsifiers in dynamic graph algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2017' ... --- _id: '11832' abstract: - lang: eng text: "In this paper, we study the problem of opening centers to cluster a set of clients in a metric space so as to minimize the sum of the costs of the centers and of the cluster radii, in a dynamic environment where clients arrive and depart, and the solution must be updated efficiently while remaining competitive with respect to the current optimal solution. We call this dynamic sum-of-radii clustering problem.\r\n\r\nWe present a data structure that maintains a solution whose cost is within a constant factor of the cost of an optimal solution in metric spaces with bounded doubling dimension and whose worst-case update time is logarithmic in the parameters of the problem." alternative_title: - LIPIcs article_number: '48' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Dariusz full_name: Leniowski, Dariusz last_name: Leniowski - first_name: Claire full_name: Mathieu, Claire last_name: Mathieu citation: ama: 'Henzinger MH, Leniowski D, Mathieu C. Dynamic clustering to minimize the sum of radii. In: 25th Annual European Symposium on Algorithms. Vol 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ESA.2017.48' apa: 'Henzinger, M. H., Leniowski, D., & Mathieu, C. (2017). Dynamic clustering to minimize the sum of radii. In 25th Annual European Symposium on Algorithms (Vol. 87). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2017.48' chicago: Henzinger, Monika H, Dariusz Leniowski, and Claire Mathieu. “Dynamic Clustering to Minimize the Sum of Radii.” In 25th Annual European Symposium on Algorithms, Vol. 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ESA.2017.48. ieee: M. H. Henzinger, D. Leniowski, and C. Mathieu, “Dynamic clustering to minimize the sum of radii,” in 25th Annual European Symposium on Algorithms, Vienna, Austria, 2017, vol. 87. ista: 'Henzinger MH, Leniowski D, Mathieu C. 2017. Dynamic clustering to minimize the sum of radii. 25th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 87, 48.' mla: Henzinger, Monika H., et al. “Dynamic Clustering to Minimize the Sum of Radii.” 25th Annual European Symposium on Algorithms, vol. 87, 48, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ESA.2017.48. short: M.H. Henzinger, D. Leniowski, C. Mathieu, in:, 25th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-06 location: Vienna, Austria name: 'ESA: Annual European Symposium on Algorithms' start_date: 2017-09-04 date_created: 2022-08-12T09:58:46Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-16T11:54:12Z day: '01' doi: 10.4230/LIPICS.ESA.2017.48 extern: '1' external_id: arxiv: - '1707.02577' intvolume: ' 87' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.ESA.2017.48 month: '09' oa: 1 oa_version: Published Version publication: 25th Annual European Symposium on Algorithms publication_identifier: isbn: - 978-3-95977-049-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Dynamic clustering to minimize the sum of radii type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2017' ... --- _id: '11874' abstract: - lang: eng text: "We consider the problem of maintaining an approximately maximum (fractional) matching and an approximately minimum vertex cover in a dynamic graph. Starting with the seminal paper by Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. There remains, however, a polynomial gap between the best known worst case update time and the best known amortised update time for this problem, even after allowing for randomisation. Specifically, Bernstein and Stein [ICALP 2015, SODA 2016] have the best known worst case update time. They present a deterministic data structure with approximation ratio (3/2 + ∊) and worst case update time O(m1/4/ ∊2), where m is the number of edges in the graph. In recent past, Gupta and Peng [FOCS 2013] gave a deterministic data structure with approximation ratio (1+ ∊) and worst case update time No known randomised data structure beats the worst case update times of these two results. In contrast, the paper by Onak and Rubinfeld [STOC 2010] gave a randomised data structure with approximation ratio O(1) and amortised update time O(log2 n), where n is the number of nodes in the graph. This was later improved by Baswana, Gupta and Sen [FOCS 2011] and Solomon [FOCS 2016], leading to a randomised date structure with approximation ratio 2 and amortised update time O(1).\r\n\r\nWe bridge the polynomial gap between the worst case and amortised update times for this problem, without using any randomisation. We present a deterministic data structure with approximation ratio (2 + ∊) and worst case update time O(log3 n), for all sufficiently small constants ∊." article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Bhattacharya S, Henzinger MH, Nanongkai D. Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time. In: 28th Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 0. Society for Industrial and Applied Mathematics; 2017:470-489. doi:10.1137/1.9781611974782.30' apa: 'Bhattacharya, S., Henzinger, M. H., & Nanongkai, D. (2017). Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time. In 28th Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 0, pp. 470–489). Barcelona, Spain: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611974782.30' chicago: Bhattacharya, Sayan, Monika H Henzinger, and Danupon Nanongkai. “Fully Dynamic Approximate Maximum Matching and Minimum Vertex Cover in o(Log3 n) Worst Case Update Time.” In 28th Annual ACM-SIAM Symposium on Discrete Algorithms, 0:470–89. Society for Industrial and Applied Mathematics, 2017. https://doi.org/10.1137/1.9781611974782.30. ieee: S. Bhattacharya, M. H. Henzinger, and D. Nanongkai, “Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time,” in 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Barcelona, Spain, 2017, vol. 0, pp. 470–489. ista: 'Bhattacharya S, Henzinger MH, Nanongkai D. 2017. Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time. 28th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 0, 470–489.' mla: Bhattacharya, Sayan, et al. “Fully Dynamic Approximate Maximum Matching and Minimum Vertex Cover in o(Log3 n) Worst Case Update Time.” 28th Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 0, Society for Industrial and Applied Mathematics, 2017, pp. 470–89, doi:10.1137/1.9781611974782.30. short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, in:, 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2017, pp. 470–489. conference: end_date: 2017-01-19 location: Barcelona, Spain name: 'SODA: Symposium on Discrete Algorithms' start_date: 2017-01-16 date_created: 2022-08-16T12:28:27Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-02-17T11:54:22Z day: '01' doi: 10.1137/1.9781611974782.30 extern: '1' external_id: arxiv: - '1704.02844' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.02844 month: '01' oa: 1 oa_version: Preprint page: 470 - 489 publication: 28th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-161197478-2 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: '0' year: '2017' ... --- _id: '11873' abstract: - lang: eng text: "We study the problem of computing a minimum cut in a simple, undirected graph and give a deterministic O(m log2 n log log2 n) time algorithm. This improves both on the best previously known deterministic running time of O(m log12 n) (Kawarabayashi and Thorup [12]) and the best previously known randomized running time of O(mlog3n) (Karger [11]) for this problem, though Karger's algorithm can be further applied to weighted graphs.\r\n\r\nOur approach is using the Kawarabayashi and Tho- rup graph compression technique, which repeatedly finds low-conductance cuts. To find these cuts they use a diffusion-based local algorithm. We use instead a flow- based local algorithm and suitably adjust their framework to work with our flow-based subroutine. Both flow and diffusion based methods have a long history of being applied to finding low conductance cuts. Diffusion algorithms have several variants that are naturally local while it is more complicated to make flow methods local. Some prior work has proven nice properties for local flow based algorithms with respect to improving or cleaning up low conductance cuts. Our flow subroutine, however, is the first that is both local and produces low conductance cuts. Thus, it may be of independent interest." article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Satish full_name: Rao, Satish last_name: Rao - first_name: Di full_name: Wang, Di last_name: Wang citation: ama: 'Henzinger MH, Rao S, Wang D. Local flow partitioning for faster edge connectivity. In: 28th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2017:1919-1938. doi:10.1137/1.9781611974782.125' apa: 'Henzinger, M. H., Rao, S., & Wang, D. (2017). Local flow partitioning for faster edge connectivity. In 28th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1919–1938). Barcelona, Spain: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611974782.125' chicago: Henzinger, Monika H, Satish Rao, and Di Wang. “Local Flow Partitioning for Faster Edge Connectivity.” In 28th Annual ACM-SIAM Symposium on Discrete Algorithms, 1919–38. Society for Industrial and Applied Mathematics, 2017. https://doi.org/10.1137/1.9781611974782.125. ieee: M. H. Henzinger, S. Rao, and D. Wang, “Local flow partitioning for faster edge connectivity,” in 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Barcelona, Spain, 2017, pp. 1919–1938. ista: 'Henzinger MH, Rao S, Wang D. 2017. Local flow partitioning for faster edge connectivity. 28th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1919–1938.' mla: Henzinger, Monika H., et al. “Local Flow Partitioning for Faster Edge Connectivity.” 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2017, pp. 1919–38, doi:10.1137/1.9781611974782.125. short: M.H. Henzinger, S. Rao, D. Wang, in:, 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2017, pp. 1919–1938. conference: end_date: 2017-01-19 location: Barcelona, Spain name: 'SODA: Symposium on Discrete Algorithms' start_date: 2017-01-16 date_created: 2022-08-16T12:20:59Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-02-21T16:32:01Z day: '01' doi: 10.1137/1.9781611974782.125 extern: '1' external_id: arxiv: - '1704.01254' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.01254 month: '01' oa: 1 oa_version: Preprint page: 1919-1938 publication: 28th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-161197478-2 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '11889' relation: earlier_version status: public scopus_import: '1' status: public title: Local flow partitioning for faster edge connectivity type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '11831' abstract: - lang: eng text: "Graph Sparsification aims at compressing large graphs into smaller ones while (approximately) preserving important characteristics of the input graph. In this work we study Vertex Sparsifiers, i.e., sparsifiers whose goal is to reduce the number of vertices. Given a weighted graph G=(V,E), and a terminal set K with |K|=k, a quality-q vertex cut sparsifier of G is a graph H with K contained in V_H that preserves the value of minimum cuts separating any bipartition of K, up to a factor of q. We show that planar graphs with all the k terminals lying on the same face admit quality-1 vertex cut sparsifier of size O(k^2) that are also planar. Our result extends to vertex flow and distance sparsifiers. It improves the previous best known bound of O(k^2 2^(2k)) for cut and flow sparsifiers by an exponential factor, and matches an Omega(k^2) lower-bound for this class of graphs.\r\n\r\nWe also study vertex reachability sparsifiers for directed graphs. Given a digraph G=(V,E) and a terminal set K, a vertex reachability sparsifier of G is a digraph H=(V_H,E_H), K contained in V_H that preserves all reachability information among terminal pairs. We introduce the notion of reachability-preserving minors, i.e., we require H to be a minor of G. Among others, for general planar digraphs, we construct reachability-preserving minors of size O(k^2 log^2 k). We complement our upper-bound by showing that there exists an infinite family of acyclic planar digraphs such that any reachability-preserving minor must have Omega(k^2) vertices." alternative_title: - LIPIcs article_number: '44' article_processing_charge: No author: - first_name: Gramoz full_name: Goranci, Gramoz last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Pan full_name: Peng, Pan last_name: Peng citation: ama: 'Goranci G, Henzinger MH, Peng P. Improved guarantees for vertex sparsification in planar graphs. In: 25th Annual European Symposium on Algorithms. Vol 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ESA.2017.44' apa: 'Goranci, G., Henzinger, M. H., & Peng, P. (2017). Improved guarantees for vertex sparsification in planar graphs. In 25th Annual European Symposium on Algorithms (Vol. 87). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2017.44' chicago: Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “Improved Guarantees for Vertex Sparsification in Planar Graphs.” In 25th Annual European Symposium on Algorithms, Vol. 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ESA.2017.44. ieee: G. Goranci, M. H. Henzinger, and P. Peng, “Improved guarantees for vertex sparsification in planar graphs,” in 25th Annual European Symposium on Algorithms, Vienna, Austria, 2017, vol. 87. ista: 'Goranci G, Henzinger MH, Peng P. 2017. Improved guarantees for vertex sparsification in planar graphs. 25th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 87, 44.' mla: Goranci, Gramoz, et al. “Improved Guarantees for Vertex Sparsification in Planar Graphs.” 25th Annual European Symposium on Algorithms, vol. 87, 44, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ESA.2017.44. short: G. Goranci, M.H. Henzinger, P. Peng, in:, 25th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-06 location: Vienna, Austria name: 'ESA: Annual European Symposium on Algorithms' start_date: 2017-09-04 date_created: 2022-08-12T09:27:11Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-21T16:32:16Z day: '01' doi: 10.4230/LIPICS.ESA.2017.44 extern: '1' external_id: arxiv: - '1702.01136' intvolume: ' 87' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2017.44 month: '09' oa: 1 oa_version: Published Version publication: 25th Annual European Symposium on Algorithms publication_identifier: isbn: - 978-3-95977-049-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '11894' relation: later_version status: public scopus_import: '1' status: public title: Improved guarantees for vertex sparsification in planar graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2017' ... --- _id: '11903' abstract: - lang: eng text: "Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1−1/e). (2) On the positive side we present (i) an \U0001D442(\U0001D45B√)-approximation algorithm for general concave externality functions, (ii) an O(log m)-approximation algorithm for linear externality functions, and (iii) a 518(1−1/\U0001D452)-approximation algorithm for 2-hop step function externalities. We also improve the result from [7] for 1-hop step function externalities by giving a 12(1−1/\U0001D452)-approximation algorithm." article_processing_charge: No article_type: original author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Wolfgang full_name: Dvořák, Wolfgang last_name: Dvořák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: Bhattacharya S, Dvořák W, Henzinger MH, Starnberger M. Welfare maximization with friends-of-friends network externalities. Theory of Computing Systems. 2017;61(4):948-986. doi:10.1007/s00224-017-9759-8 apa: Bhattacharya, S., Dvořák, W., Henzinger, M. H., & Starnberger, M. (2017). Welfare maximization with friends-of-friends network externalities. Theory of Computing Systems. Springer Nature. https://doi.org/10.1007/s00224-017-9759-8 chicago: Bhattacharya, Sayan, Wolfgang Dvořák, Monika H Henzinger, and Martin Starnberger. “Welfare Maximization with Friends-of-Friends Network Externalities.” Theory of Computing Systems. Springer Nature, 2017. https://doi.org/10.1007/s00224-017-9759-8. ieee: S. Bhattacharya, W. Dvořák, M. H. Henzinger, and M. Starnberger, “Welfare maximization with friends-of-friends network externalities,” Theory of Computing Systems, vol. 61, no. 4. Springer Nature, pp. 948–986, 2017. ista: Bhattacharya S, Dvořák W, Henzinger MH, Starnberger M. 2017. Welfare maximization with friends-of-friends network externalities. Theory of Computing Systems. 61(4), 948–986. mla: Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network Externalities.” Theory of Computing Systems, vol. 61, no. 4, Springer Nature, 2017, pp. 948–86, doi:10.1007/s00224-017-9759-8. short: S. Bhattacharya, W. Dvořák, M.H. Henzinger, M. Starnberger, Theory of Computing Systems 61 (2017) 948–986. date_created: 2022-08-17T11:14:12Z date_published: 2017-11-01T00:00:00Z date_updated: 2023-02-21T16:29:58Z day: '01' doi: 10.1007/s00224-017-9759-8 extern: '1' intvolume: ' 61' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00224-017-9759-8 month: '11' oa: 1 oa_version: Published Version page: 948-986 publication: Theory of Computing Systems publication_identifier: eissn: - 1433-0490 issn: - 1432-4350 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '11837' relation: earlier_version status: public scopus_import: '1' status: public title: Welfare maximization with friends-of-friends network externalities type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2017' ... --- _id: '1191' abstract: - lang: eng text: Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed. acknowledgement: "We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project." author: - first_name: Richard full_name: Kollár, Richard last_name: Kollár - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak citation: ama: Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3 apa: Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3 chicago: Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3. ieee: R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017. ista: Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559. mla: Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3. short: R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559. date_created: 2018-12-11T11:50:38Z date_published: 2017-03-01T00:00:00Z date_updated: 2021-01-12T06:48:58Z day: '01' department: - _id: NiBa doi: 10.1007/s11538-016-0244-3 ec_funded: 1 intvolume: ' 79' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.00944 month: '03' oa: 1 oa_version: Preprint page: 525-559 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Bulletin of Mathematical Biology publication_status: published publisher: Springer publist_id: '6160' quality_controlled: '1' scopus_import: 1 status: public title: Existence of traveling waves for the generalized F–KPP equation type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 79 year: '2017' ... --- _id: '11976' abstract: - lang: eng text: The way organic multistep synthesis is performed is changing due to the adoption of flow chemical techniques, which has enabled the development of improved methods to make complex molecules. The modular nature of the technique provides not only access to target molecules via linear flow approaches but also for the targeting of structural cores with single systems. This perspective article summarizes the state of the art of continuous multistep synthesis and discusses the main challenges and opportunities in this area. article_processing_charge: No article_type: original author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Kerry full_name: Gilmore, Kerry last_name: Gilmore - first_name: Peter H. full_name: Seeberger, Peter H. last_name: Seeberger citation: ama: Pieber B, Gilmore K, Seeberger PH. Integrated flow processing - challenges in continuous multistep synthesis. Journal of Flow Chemistry. 2017;7(3-4):129-136. doi:10.1556/1846.2017.00016 apa: Pieber, B., Gilmore, K., & Seeberger, P. H. (2017). Integrated flow processing - challenges in continuous multistep synthesis. Journal of Flow Chemistry. AKJournals. https://doi.org/10.1556/1846.2017.00016 chicago: Pieber, Bartholomäus, Kerry Gilmore, and Peter H. Seeberger. “Integrated Flow Processing - Challenges in Continuous Multistep Synthesis.” Journal of Flow Chemistry. AKJournals, 2017. https://doi.org/10.1556/1846.2017.00016. ieee: B. Pieber, K. Gilmore, and P. H. Seeberger, “Integrated flow processing - challenges in continuous multistep synthesis,” Journal of Flow Chemistry, vol. 7, no. 3–4. AKJournals, pp. 129–136, 2017. ista: Pieber B, Gilmore K, Seeberger PH. 2017. Integrated flow processing - challenges in continuous multistep synthesis. Journal of Flow Chemistry. 7(3–4), 129–136. mla: Pieber, Bartholomäus, et al. “Integrated Flow Processing - Challenges in Continuous Multistep Synthesis.” Journal of Flow Chemistry, vol. 7, no. 3–4, AKJournals, 2017, pp. 129–36, doi:10.1556/1846.2017.00016. short: B. Pieber, K. Gilmore, P.H. Seeberger, Journal of Flow Chemistry 7 (2017) 129–136. date_created: 2022-08-25T10:47:51Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-21T10:10:02Z day: '01' doi: 10.1556/1846.2017.00016 extern: '1' intvolume: ' 7' issue: 3-4 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1556/1846.2017.00016 month: '09' oa: 1 oa_version: Published Version page: 129-136 publication: Journal of Flow Chemistry publication_identifier: eissn: - 2063-0212 issn: - 2062-249X publication_status: published publisher: AKJournals quality_controlled: '1' scopus_import: '1' status: public title: Integrated flow processing - challenges in continuous multistep synthesis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2017' ... --- _id: '1211' abstract: - lang: eng text: Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here. acknowledgement: 'This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ' author: - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Predrag full_name: Cvitanović, Predrag last_name: Cvitanović citation: ama: Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 2017;167(3-4):636-655. doi:10.1007/s10955-016-1672-z apa: Budanur, N. B., & Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1672-z chicago: Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics. Springer, 2017. https://doi.org/10.1007/s10955-016-1672-z. ieee: N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer, pp. 636–655, 2017. ista: Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655. mla: Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:10.1007/s10955-016-1672-z. short: N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655. date_created: 2018-12-11T11:50:44Z date_published: 2017-05-01T00:00:00Z date_updated: 2021-01-12T06:49:07Z day: '01' ddc: - '530' department: - _id: BjHo doi: 10.1007/s10955-016-1672-z file: - access_level: open_access checksum: 3e971d09eb167761aa0888ed415b0056 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:01Z date_updated: 2020-07-14T12:44:39Z file_id: '5319' file_name: IST-2017-782-v1+1_BudCvi15.pdf file_size: 2820207 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 167' issue: 3-4 language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 636-655 publication: Journal of Statistical Physics publication_status: published publisher: Springer publist_id: '6136' pubrep_id: '782' quality_controlled: '1' scopus_import: 1 status: public title: Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 167 year: '2017' ... --- _id: '123' abstract: - lang: eng text: The Leidenfrost effect occurs when an object near a hot surface vaporizes rapidly enough to lift itself up and hover. Although well understood for liquids and stiff sublimable solids, nothing is known about the effect with materials whose stiffness lies between these extremes. Here we introduce a new phenomenon that occurs with vaporizable soft solids - the elastic Leidenfrost effect. By dropping hydrogel spheres onto hot surfaces we find that, rather than hovering, they energetically bounce several times their diameter for minutes at a time. With high-speed video during a single impact, we uncover high-frequency microscopic gap dynamics at the sphere/substrate interface. We show how these otherwise-hidden agitations constitute work cycles that harvest mechanical energy from the vapour and sustain the bouncing. Our findings suggest a new strategy for injecting mechanical energy into a widely used class of soft materials, with potential relevance to fields such as active matter, soft robotics and microfluidics. acknowledgement: A.S. acknowledges funding from the Delta Institute for Theoretical Physics and the hospitality of the IBS Center for Theoretical Physics of Complex Systems, Daejeon, South Korea. We acknowledge funding from the Netherlands Organisation for Scientific Research through grants VICI No. NWO-680-47-609 (M.v.H. and S.R.W.), VENI No. NWO-680-47-445 (C.C.) and VENI No. NWO-680-47-453 (S.R.W.). author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Antal full_name: Zuiderwijk, Antal last_name: Zuiderwijk - first_name: Anton full_name: Souslov, Anton last_name: Souslov - first_name: Corentin full_name: Coulais, Corentin last_name: Coulais - first_name: Martin full_name: Van Hecke, Martin last_name: Van Hecke citation: ama: Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. 2017;13(11):1095-1099. doi:10.1038/nphys4194 apa: Waitukaitis, S. R., Zuiderwijk, A., Souslov, A., Coulais, C., & Van Hecke, M. (2017). Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys4194 chicago: Waitukaitis, Scott R, Antal Zuiderwijk, Anton Souslov, Corentin Coulais, and Martin Van Hecke. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” Nature Physics. Nature Publishing Group, 2017. https://doi.org/10.1038/nphys4194. ieee: S. R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, and M. Van Hecke, “Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing,” Nature Physics, vol. 13, no. 11. Nature Publishing Group, pp. 1095–1099, 2017. ista: Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. 2017. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. 13(11), 1095–1099. mla: Waitukaitis, Scott R., et al. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” Nature Physics, vol. 13, no. 11, Nature Publishing Group, 2017, pp. 1095–99, doi:10.1038/nphys4194. short: S.R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, M. Van Hecke, Nature Physics 13 (2017) 1095–1099. date_created: 2018-12-11T11:44:45Z date_published: 2017-07-24T00:00:00Z date_updated: 2021-01-12T06:49:14Z day: '24' doi: 10.1038/nphys4194 extern: '1' external_id: arxiv: - '1705.03530' intvolume: ' 13' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.03530 month: '07' oa: 1 oa_version: Preprint page: 1095 - 1099 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7931' quality_controlled: '1' status: public title: Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '12571' abstract: - lang: eng text: We consider the problems of maintaining approximate maximum matching and minimum vertex cover in a dynamic graph. Starting with the seminal work of Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. Very recently, extending the framework of Baswana, Gupta and Sen [FOCS 2011], Solomon [FOCS 2016] gave a randomized 2-approximation dynamic algorithm for this problem that has amortized update time of O(1) with high probability. We consider the natural open question of derandomizing this result. We present a new deterministic fully dynamic algorithm that maintains a O(1)-approximate minimum vertex cover and maximum fractional matching, with an amortized update time of O(1). Previously, the best deterministic algorithm for this problem was due to Bhattacharya, Henzinger and Italiano [SODA 2015]; it had an approximation ratio of (2+ϵ) and an amortized update time of O(logn/ϵ2). Our result can be generalized to give a fully dynamic O(f3)-approximation algorithm with O(f2) amortized update time for the hypergraph vertex cover and fractional matching problems, where every hyperedge has at most f vertices. alternative_title: - LNCS article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Deeparnab full_name: Chakrabarty, Deeparnab last_name: Chakrabarty - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: 'Bhattacharya S, Chakrabarty D, Henzinger MH. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In: 19th International Conference on Integer Programming and Combinatorial Optimization. Vol 10328. Springer Nature; 2017:86-98. doi:10.1007/978-3-319-59250-3_8' apa: 'Bhattacharya, S., Chakrabarty, D., & Henzinger, M. H. (2017). Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In 19th International Conference on Integer Programming and Combinatorial Optimization (Vol. 10328, pp. 86–98). Waterloo, ON, Canada: Springer Nature. https://doi.org/10.1007/978-3-319-59250-3_8' chicago: Bhattacharya, Sayan, Deeparnab Chakrabarty, and Monika H Henzinger. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” In 19th International Conference on Integer Programming and Combinatorial Optimization, 10328:86–98. Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59250-3_8. ieee: S. Bhattacharya, D. Chakrabarty, and M. H. Henzinger, “Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time,” in 19th International Conference on Integer Programming and Combinatorial Optimization, Waterloo, ON, Canada, 2017, vol. 10328, pp. 86–98. ista: 'Bhattacharya S, Chakrabarty D, Henzinger MH. 2017. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. 19th International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 10328, 86–98.' mla: Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” 19th International Conference on Integer Programming and Combinatorial Optimization, vol. 10328, Springer Nature, 2017, pp. 86–98, doi:10.1007/978-3-319-59250-3_8. short: S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, in:, 19th International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2017, pp. 86–98. conference: end_date: 2017-06-28 location: Waterloo, ON, Canada name: 'IPCO: Integer Programming and Combinatorial Optimization' start_date: 2017-06-26 date_created: 2023-02-20T07:52:31Z date_published: 2017-05-24T00:00:00Z date_updated: 2023-02-20T07:57:24Z day: '24' doi: 10.1007/978-3-319-59250-3_8 extern: '1' external_id: arxiv: - '1611.00198' intvolume: ' 10328' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.00198 month: '05' oa: 1 oa_version: Preprint page: 86-98 publication: 19th International Conference on Integer Programming and Combinatorial Optimization publication_identifier: eisbn: - '9783319592503' isbn: - '9783319592497' issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10328 year: '2017' ... --- _id: '1113' abstract: - lang: eng text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric circles C 1 , . . . , C k with common center c , and edges are drawn radially : every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Toth.' article_processing_charge: No article_type: original author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Michael full_name: Pelsmajer, Michael last_name: Pelsmajer - first_name: Marcus full_name: Schaefer, Marcus last_name: Schaefer citation: ama: Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 2017;21(1):135-154. doi:10.7155/jgaa.00408 apa: Fulek, R., Pelsmajer, M., & Schaefer, M. (2017). Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00408 chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications. Brown University, 2017. https://doi.org/10.7155/jgaa.00408. ieee: R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” Journal of Graph Algorithms and Applications, vol. 21, no. 1. Brown University, pp. 135–154, 2017. ista: Fulek R, Pelsmajer M, Schaefer M. 2017. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 21(1), 135–154. mla: Fulek, Radoslav, et al. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications, vol. 21, no. 1, Brown University, 2017, pp. 135–54, doi:10.7155/jgaa.00408. short: R. Fulek, M. Pelsmajer, M. Schaefer, Journal of Graph Algorithms and Applications 21 (2017) 135–154. date_created: 2018-12-11T11:50:13Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-02-23T10:05:57Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.7155/jgaa.00408 ec_funded: 1 external_id: arxiv: - '1608.08662' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-10-24T10:54:37Z date_updated: 2019-10-24T10:54:37Z file_id: '6967' file_name: 2017_JournalGraphAlgorithms_Fulek.pdf file_size: 573623 relation: main_file success: 1 file_date_updated: 2019-10-24T10:54:37Z has_accepted_license: '1' intvolume: ' 21' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 135 - 154 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Graph Algorithms and Applications publication_status: published publisher: Brown University publist_id: '6254' quality_controlled: '1' related_material: record: - id: '1164' relation: earlier_version status: public - id: '1595' relation: earlier_version status: public scopus_import: 1 status: public title: Hanani-Tutte for radial planarity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2017' ... --- _id: '169' abstract: - lang: eng text: We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman sums leads to an optimal covering exponent for S3. article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Vinay full_name: Kumaraswamy, Vinay last_name: Kumaraswamy - first_name: Rapael full_name: Steiner, Rapael last_name: Steiner citation: ama: Browning TD, Kumaraswamy V, Steiner R. Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx116 apa: Browning, T. D., Kumaraswamy, V., & Steiner, R. (2017). Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnx116 chicago: Browning, Timothy D, Vinay Kumaraswamy, and Rapael Steiner. “Twisted Linnik Implies Optimal Covering Exponent for S3.” International Mathematics Research Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx116. ieee: T. D. Browning, V. Kumaraswamy, and R. Steiner, “Twisted Linnik implies optimal covering exponent for S3,” International Mathematics Research Notices. Oxford University Press, 2017. ista: Browning TD, Kumaraswamy V, Steiner R. 2017. Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices. mla: Browning, Timothy D., et al. “Twisted Linnik Implies Optimal Covering Exponent for S3.” International Mathematics Research Notices, Oxford University Press, 2017, doi:10.1093/imrn/rnx116. short: T.D. Browning, V. Kumaraswamy, R. Steiner, International Mathematics Research Notices (2017). date_created: 2018-12-11T11:44:59Z date_published: 2017-06-19T00:00:00Z date_updated: 2021-01-12T06:52:32Z day: '19' doi: 10.1093/imrn/rnx116 extern: '1' external_id: arxiv: - '1609.06097' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.06097 month: '06' oa: 1 oa_version: None publication: International Mathematics Research Notices publication_status: published publisher: Oxford University Press publist_id: '7752' quality_controlled: '1' status: public title: Twisted Linnik implies optimal covering exponent for S3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '172' abstract: - lang: eng text: We study strong approximation for some algebraic varieties over ℚ which are defined using norm forms. This allows us to confirm a special case of a conjecture due to Harpaz and Wittenberg. article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Damaris full_name: Schindler, Damaris last_name: Schindler citation: ama: Browning TD, Schindler D. Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx252 apa: Browning, T. D., & Schindler, D. (2017). Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnx252 chicago: Browning, Timothy D, and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” International Mathematics Research Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx252. ieee: T. D. Browning and D. Schindler, “Strong approximation and a conjecture of Harpaz and Wittenberg,” International Mathematics Research Notices. Oxford University Press, 2017. ista: Browning TD, Schindler D. 2017. Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices. mla: Browning, Timothy D., and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” International Mathematics Research Notices, Oxford University Press, 2017, doi:10.1093/imrn/rnx252. short: T.D. Browning, D. Schindler, International Mathematics Research Notices (2017). date_created: 2018-12-11T11:45:00Z date_published: 2017-10-30T00:00:00Z date_updated: 2021-01-12T06:52:45Z day: '30' doi: 10.1093/imrn/rnx252 extern: '1' external_id: arxiv: - '1509.07744' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1509.07744 month: '10' oa: 1 oa_version: None publication: International Mathematics Research Notices publication_status: published publisher: Oxford University Press publist_id: '7749' quality_controlled: '1' status: public title: Strong approximation and a conjecture of Harpaz and Wittenberg type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '393' abstract: - lang: eng text: 'We use a three-pulse ultrafast optical spectroscopy to study the relaxation processes in a frustrated Mott insulator Na2IrO3. By being able to independently produce the out-of-equilibrium bound states (excitons) of doublons and holons with the first pulse and suppress the underlying antiferromagnetic order with the second one, we were able to elucidate the relaxation mechanism of quasiparticles in this system. By observing the difference in the exciton dynamics in the magnetically ordered and disordered phases we found that the mass of this quasiparticle is mostly determined by its interaction with the surrounding spins. ' acknowledgement: "Z.A. gratefully acknowledges discussions with P. A. Lee and A. Kemper. A conversation with J. Zaanen was instrumental in clarifying the physical picture described in this paper. We would also like to thank A. Kogar for thoroughly reading the manuscript and making valuable comments. This work was supported by Army Research Office Grant No. W911NF-15-1-0128 and Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4540 (time resolved optical spectroscopy), Skoltech, as part of the Skoltech NGP program (theory) and National Science Foundation Grant No. DMR-1265162 (material growth).\r\n\r\n" author: - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Edbert full_name: Sie, Edbert last_name: Sie - first_name: Fahad full_name: Mahmood, Fahad last_name: Mahmood - first_name: Gang full_name: Cao, Gang last_name: Cao - first_name: Nuh full_name: Gedik, Nuh last_name: Gedik citation: ama: Alpichshev Z, Sie E, Mahmood F, Cao G, Gedik N. Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. 2017;96(23). doi:10.1103/PhysRevB.96.235141 apa: Alpichshev, Z., Sie, E., Mahmood, F., Cao, G., & Gedik, N. (2017). Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.235141 chicago: Alpichshev, Zhanybek, Edbert Sie, Fahad Mahmood, Gang Cao, and Nuh Gedik. “Origin of the Exciton Mass in the Frustrated Mott Insulator Na2IrO3.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.235141. ieee: Z. Alpichshev, E. Sie, F. Mahmood, G. Cao, and N. Gedik, “Origin of the exciton mass in the frustrated Mott insulator Na2IrO3,” Physical Review B, vol. 96, no. 23. American Physical Society, 2017. ista: Alpichshev Z, Sie E, Mahmood F, Cao G, Gedik N. 2017. Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. 96(23). mla: Alpichshev, Zhanybek, et al. “Origin of the Exciton Mass in the Frustrated Mott Insulator Na2IrO3.” Physical Review B, vol. 96, no. 23, American Physical Society, 2017, doi:10.1103/PhysRevB.96.235141. short: Z. Alpichshev, E. Sie, F. Mahmood, G. Cao, N. Gedik, Physical Review B 96 (2017). date_created: 2018-12-11T11:46:13Z date_published: 2017-12-26T00:00:00Z date_updated: 2021-01-12T07:53:16Z day: '26' doi: 10.1103/PhysRevB.96.235141 extern: '1' intvolume: ' 96' issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: http://dspace.mit.edu/handle/1721.1/114259 month: '12' oa: 1 oa_version: None publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '7436' status: public title: Origin of the exciton mass in the frustrated Mott insulator Na2IrO3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 96 year: '2017' ... --- _id: '392' abstract: - lang: eng text: We used femtosecond optical pump-probe spectroscopy to study the photoinduced change in reflectivity of thin films of the electron-doped cuprate La2-xCexCuO4 (LCCO) with dopings of x=0.08 (underdoped) and x=0.11 (optimally doped). Above Tc, we observe fluence-dependent relaxation rates that begin at a temperature similar to the one where transport measurements first show signatures of antiferromagnetic correlations. Upon suppressing superconductivity with a magnetic field, it is found that the fluence and temperature dependence of relaxation rates are consistent with bimolecular recombination of electrons and holes across a gap (2ΔAF) originating from antiferromagnetic correlations which comprise the pseudogap in electron-doped cuprates. This can be used to learn about coupling between electrons and high-energy (ω>2ΔAF) excitations in these compounds and set limits on the time scales on which antiferromagnetic correlations are static. acknowledgement: Optical pump-probe work was supported by the Gordon and Betty Moore Foundation's EPiQS initiative through Grant No. GBMF4540. Materials growth and characterization was supported by AFOSR FA95501410332 and NSF DMR1410665. author: - first_name: Inna full_name: Vishik, Inna last_name: Vishik - first_name: Fahad full_name: Mahmood, Fahad last_name: Mahmood - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Nuh full_name: Gedik, Nuh last_name: Gedik - first_name: Joshu full_name: Higgins, Joshu last_name: Higgins - first_name: Richard full_name: Greene, Richard last_name: Greene citation: ama: Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 2017;95(11). doi:10.1103/PhysRevB.95.115125 apa: Vishik, I., Mahmood, F., Alpichshev, Z., Gedik, N., Higgins, J., & Greene, R. (2017). Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.95.115125 chicago: Vishik, Inna, Fahad Mahmood, Zhanybek Alpichshev, Nuh Gedik, Joshu Higgins, and Richard Greene. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.115125. ieee: I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, and R. Greene, “Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ,” Physical Review B, vol. 95, no. 11. American Physical Society, 2017. ista: Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. 2017. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 95(11). mla: Vishik, Inna, et al. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B, vol. 95, no. 11, American Physical Society, 2017, doi:10.1103/PhysRevB.95.115125. short: I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, R. Greene, Physical Review B 95 (2017). date_created: 2018-12-11T11:46:13Z date_published: 2017-03-13T00:00:00Z date_updated: 2021-01-12T07:53:12Z day: '13' doi: 10.1103/PhysRevB.95.115125 extern: '1' intvolume: ' 95' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: http://dspace.mit.edu/handle/1721.1/109835 month: '03' oa: 1 oa_version: None publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '7437' status: public title: Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 95 year: '2017' ... --- _id: '443' abstract: - lang: eng text: Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited. author: - first_name: Rae full_name: Hardie, Rae last_name: Hardie - first_name: Ellen full_name: Van Dam, Ellen last_name: Van Dam - first_name: Mark full_name: Cowley, Mark last_name: Cowley - first_name: Ting full_name: Han, Ting last_name: Han - first_name: Seher full_name: Balaban, Seher last_name: Balaban - first_name: Marina full_name: Pajic, Marina last_name: Pajic - first_name: Mark full_name: Pinese, Mark last_name: Pinese - first_name: Mary full_name: Iconomou, Mary last_name: Iconomou - first_name: Robert full_name: Shearer, Robert last_name: Shearer - first_name: Jessie full_name: Mckenna, Jessie last_name: Mckenna - first_name: David full_name: Miller, David last_name: Miller - first_name: Nicola full_name: Waddell, Nicola last_name: Waddell - first_name: John full_name: Pearson, John last_name: Pearson - first_name: Sean full_name: Grimmond, Sean last_name: Grimmond - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Andrew full_name: Biankin, Andrew last_name: Biankin - first_name: Silas full_name: Villas Boas, Silas last_name: Villas Boas - first_name: Andrew full_name: Hoy, Andrew last_name: Hoy - first_name: Nigel full_name: Turner, Nigel last_name: Turner - first_name: Darren full_name: Saunders, Darren last_name: Saunders citation: ama: Hardie R, Van Dam E, Cowley M, et al. Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. 2017;5(2). doi:10.1186/s40170-017-0164-1 apa: Hardie, R., Van Dam, E., Cowley, M., Han, T., Balaban, S., Pajic, M., … Saunders, D. (2017). Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. BioMed Central. https://doi.org/10.1186/s40170-017-0164-1 chicago: Hardie, Rae, Ellen Van Dam, Mark Cowley, Ting Han, Seher Balaban, Marina Pajic, Mark Pinese, et al. “Mitochondrial Mutations and Metabolic Adaptation in Pancreatic Cancer.” Cancer & Metabolism. BioMed Central, 2017. https://doi.org/10.1186/s40170-017-0164-1. ieee: R. Hardie et al., “Mitochondrial mutations and metabolic adaptation in pancreatic cancer,” Cancer & Metabolism, vol. 5, no. 2. BioMed Central, 2017. ista: Hardie R, Van Dam E, Cowley M, Han T, Balaban S, Pajic M, Pinese M, Iconomou M, Shearer R, Mckenna J, Miller D, Waddell N, Pearson J, Grimmond S, Sazanov LA, Biankin A, Villas Boas S, Hoy A, Turner N, Saunders D. 2017. Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. 5(2). mla: Hardie, Rae, et al. “Mitochondrial Mutations and Metabolic Adaptation in Pancreatic Cancer.” Cancer & Metabolism, vol. 5, no. 2, BioMed Central, 2017, doi:10.1186/s40170-017-0164-1. short: R. Hardie, E. Van Dam, M. Cowley, T. Han, S. Balaban, M. Pajic, M. Pinese, M. Iconomou, R. Shearer, J. Mckenna, D. Miller, N. Waddell, J. Pearson, S. Grimmond, L.A. Sazanov, A. Biankin, S. Villas Boas, A. Hoy, N. Turner, D. Saunders, Cancer & Metabolism 5 (2017). date_created: 2018-12-11T11:46:30Z date_published: 2017-01-30T00:00:00Z date_updated: 2021-01-12T07:56:55Z day: '30' ddc: - '570' doi: 10.1186/s40170-017-0164-1 extern: '1' file: - access_level: open_access checksum: 337a65786875f64a1fe9fc0ac24767dc content_type: application/pdf creator: dernst date_created: 2019-01-22T08:17:56Z date_updated: 2020-07-14T12:46:29Z file_id: '5868' file_name: 2017_Cancer_Hardie.pdf file_size: 1609174 relation: main_file file_date_updated: 2020-07-14T12:46:29Z has_accepted_license: '1' intvolume: ' 5' issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Cancer & Metabolism publication_status: published publisher: BioMed Central publist_id: '7380' quality_controlled: '1' status: public title: Mitochondrial mutations and metabolic adaptation in pancreatic cancer tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2017' ... --- _id: '445' abstract: - lang: eng text: The Loschmidt echo, defined as the overlap between quantum wave function evolved with different Hamiltonians, quantifies the sensitivity of quantum dynamics to perturbations and is often used as a probe of quantum chaos. In this work we consider the behavior of the Loschmidt echo in the many-body localized phase, which is characterized by emergent local integrals of motion and provides a generic example of nonergodic dynamics. We demonstrate that the fluctuations of the Loschmidt echo decay as a power law in time in the many-body localized phase, in contrast to the exponential decay in few-body ergodic systems. We consider the spin-echo generalization of the Loschmidt echo and argue that the corresponding correlation function saturates to a finite value in localized systems. Slow, power-law decay of fluctuations of such spin-echo-type overlap is related to the operator spreading and is present only in the many-body localized phase, but not in a noninteracting Anderson insulator. While most of the previously considered probes of dephasing dynamics could be understood by approximating physical spin operators with local integrals of motion, the Loschmidt echo and its generalizations crucially depend on the full expansion of the physical operators via local integrals of motion operators, as well as operators which flip local integrals of motion. Hence these probes allow one to get insights into the relation between physical operators and local integrals of motion and access the operator spreading in the many-body localized phase. acknowledgement: |- This research was supported in part by the National Science Foundation under Grant No. NSF PHY11-25915. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant No. GBMF4307. D.A. also acknowledges support by Swiss National Science Foundation. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Dimitry full_name: Abanin, Dimitry A last_name: Abanin citation: ama: Serbyn M, Abanin D. Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. 2017;96(1). doi:10.1103/PhysRevB.96.014202 apa: Serbyn, M., & Abanin, D. (2017). Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.014202 chicago: Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized Phases.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.014202. ieee: M. Serbyn and D. Abanin, “Loschmidt echo in many body localized phases,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 1. American Physical Society, 2017. ista: Serbyn M, Abanin D. 2017. Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. 96(1). mla: Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized Phases.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 1, American Physical Society, 2017, doi:10.1103/PhysRevB.96.014202. short: M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017). date_created: 2018-12-11T11:46:31Z date_published: 2017-07-12T00:00:00Z date_updated: 2021-01-12T07:57:03Z day: '12' doi: 10.1103/PhysRevB.96.014202 extern: 1 intvolume: ' 96' issue: '1' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1701.07772 month: '07' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '7378' quality_controlled: 0 status: public title: Loschmidt echo in many body localized phases type: journal_article volume: 96 year: '2017' ... --- _id: '453' abstract: - lang: eng text: Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor. acknowledgement: 'The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). ' article_processing_charge: No article_type: original author: - first_name: Todd full_name: Fallesen, Todd last_name: Fallesen - first_name: Johanna full_name: Roostalu, Johanna last_name: Roostalu - first_name: Christian F full_name: Düllberg, Christian F id: 459064DC-F248-11E8-B48F-1D18A9856A87 last_name: Düllberg orcid: 0000-0001-6335-9748 - first_name: Gunnar full_name: Pruessner, Gunnar last_name: Pruessner - first_name: Thomas full_name: Surrey, Thomas last_name: Surrey citation: ama: Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 2017;113(9):2055-2067. doi:10.1016/j.bpj.2017.09.006 apa: Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., & Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.09.006 chicago: Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal. Biophysical Society, 2017. https://doi.org/10.1016/j.bpj.2017.09.006. ieee: T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” Biophysical Journal, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017. ista: Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 113(9), 2055–2067. mla: Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:10.1016/j.bpj.2017.09.006. short: T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067. date_created: 2018-12-11T11:46:33Z date_published: 2017-11-07T00:00:00Z date_updated: 2021-01-12T07:59:28Z day: '07' ddc: - '570' department: - _id: MaLo doi: 10.1016/j.bpj.2017.09.006 file: - access_level: open_access checksum: 99a2474088e20ac74b1882c4fbbb45b1 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:03Z date_updated: 2020-07-14T12:46:31Z file_id: '5052' file_name: IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf file_size: 977192 relation: main_file file_date_updated: 2020-07-14T12:46:31Z has_accepted_license: '1' intvolume: ' 113' issue: '9' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 2055 - 2067 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '7369' pubrep_id: '965' quality_controlled: '1' status: public title: Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2017' ... --- _id: '464' abstract: - lang: eng text: The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years. article_number: '26' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:26)2017 apa: Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:26)2017 chicago: Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017. ieee: K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for parity and Streett objectives,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017. ista: Chatterjee K, Henzinger MH, Loitzenbauer V. 2017. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26. mla: Chatterjee, Krishnendu, et al. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science, vol. 13, no. 3, 26, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:26)2017. short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer Science 13 (2017). date_created: 2018-12-11T11:46:37Z date_published: 2017-09-26T00:00:00Z date_updated: 2023-02-23T10:08:55Z day: '26' ddc: - '004' department: - _id: KrCh doi: 10.23638/LMCS-13(3:26)2017 ec_funded: 1 external_id: arxiv: - '1410.0833' file: - access_level: open_access checksum: 12d469ae69b80361333d7dead965cf5d content_type: application/pdf creator: system date_created: 2018-12-12T10:13:27Z date_updated: 2020-07-14T12:46:32Z file_id: '5010' file_name: IST-2018-956-v1+1_2017_Chatterjee_Improved_algorithms.pdf file_size: 582940 relation: main_file file_date_updated: 2020-07-14T12:46:32Z has_accepted_license: '1' intvolume: ' 13' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '09' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Logical Methods in Computer Science publication_identifier: issn: - 1860-5974 publication_status: published publisher: International Federation of Computational Logic publist_id: '7357' pubrep_id: '956' quality_controlled: '1' related_material: record: - id: '1661' relation: earlier_version status: public scopus_import: '1' status: public title: Improved algorithms for parity and Streett objectives tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '470' abstract: - lang: eng text: This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios. acknowledged_ssus: - _id: ScienComp article_number: '103' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics. 2017;36(4). doi:10.1145/3072959.3073678 apa: Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3072959.3073678 chicago: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3072959.3073678. ieee: S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics, vol. 36, no. 4. ACM, 2017. ista: Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103. mla: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678. short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017). date_created: 2018-12-11T11:46:39Z date_published: 2017-07-01T00:00:00Z date_updated: 2023-02-23T12:20:26Z day: '01' ddc: - '006' department: - _id: ChWo doi: 10.1145/3072959.3073678 ec_funded: 1 file: - access_level: open_access checksum: 82a3b2bfeee4ddef16ecc21675d1a48a content_type: application/pdf creator: wojtan date_created: 2020-01-24T09:32:35Z date_updated: 2020-07-14T12:46:34Z file_id: '7359' file_name: wavepackets_final.pdf file_size: 13131683 relation: main_file file_date_updated: 2020-07-14T12:46:34Z has_accepted_license: '1' intvolume: ' 36' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: ACM Transactions on Graphics publication_identifier: issn: - '07300301' publication_status: published publisher: ACM publist_id: '7350' quality_controlled: '1' scopus_import: 1 status: public title: Water wave packets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2017' ...