[{"department":[{"_id":"MaIb"}],"publication_identifier":{"eissn":["2574-0962"]},"isi":1,"intvolume":"         3","date_published":"2020-03-01T00:00:00Z","page":"2120-2129","year":"2020","type":"journal_article","issue":"3","title":"Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials","publication":"ACS Applied Energy Materials","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","date_created":"2022-08-23T08:34:17Z","date_updated":"2022-08-23T08:34:17Z","file_name":"2020_ACSAppliedEnergyMat_Cadavid.pdf","checksum":"f23be731a766a480c77c962c1380315c","relation":"main_file","file_size":6423548,"creator":"dernst","success":1,"file_id":"11942","access_level":"open_access"}],"scopus_import":"1","quality_controlled":"1","date_created":"2020-02-09T23:00:52Z","volume":3,"status":"public","citation":{"chicago":"Cadavid, Doris, Silvia Ortega, Sergio Illera, Yu Liu, Maria Ibáñez, Alexey Shavel, Yu Zhang, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>.","apa":"Cadavid, D., Ortega, S., Illera, S., Liu, Y., Ibáñez, M., Shavel, A., … Cabot, A. (2020). Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>","ieee":"D. Cadavid <i>et al.</i>, “Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials,” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3. American Chemical Society, pp. 2120–2129, 2020.","mla":"Cadavid, Doris, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3, American Chemical Society, 2020, pp. 2120–29, doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>.","ama":"Cadavid D, Ortega S, Illera S, et al. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. 2020;3(3):2120-2129. doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>","short":"D. Cadavid, S. Ortega, S. Illera, Y. Liu, M. Ibáñez, A. Shavel, Y. Zhang, M. Li, A.M. López, G. Noriega, O.J. Durá, M.A. López De La Torre, J.D. Prades, A. Cabot, ACS Applied Energy Materials 3 (2020) 2120–2129.","ista":"Cadavid D, Ortega S, Illera S, Liu Y, Ibáñez M, Shavel A, Zhang Y, Li M, López AM, Noriega G, Durá OJ, López De La Torre MA, Prades JD, Cabot A. 2020. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. 3(3), 2120–2129."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"article_type":"original","oa_version":"Submitted Version","file_date_updated":"2022-08-23T08:34:17Z","month":"03","date_updated":"2025-04-14T07:44:03Z","has_accepted_license":"1","acknowledgement":"This work was supported by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R) and the Generalitat de Catalunya through the project 2017SGR1246. D.C. acknowledges support from Universidad Nacional de Colombia. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 754411. M.I. acknowledges financial support from IST Austria.","ddc":["540"],"ec_funded":1,"day":"01","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"publication_status":"published","_id":"7467","external_id":{"isi":["000526598300012"]},"author":[{"last_name":"Cadavid","full_name":"Cadavid, Doris","first_name":"Doris"},{"last_name":"Ortega","first_name":"Silvia","full_name":"Ortega, Silvia"},{"last_name":"Illera","full_name":"Illera, Sergio","first_name":"Sergio"},{"orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria"},{"full_name":"Shavel, Alexey","first_name":"Alexey","last_name":"Shavel"},{"last_name":"Zhang","full_name":"Zhang, Yu","first_name":"Yu"},{"full_name":"Li, Mengyao","first_name":"Mengyao","last_name":"Li"},{"full_name":"López, Antonio M.","first_name":"Antonio M.","last_name":"López"},{"last_name":"Noriega","first_name":"Germán","full_name":"Noriega, Germán"},{"last_name":"Durá","full_name":"Durá, Oscar Juan","first_name":"Oscar Juan"},{"first_name":"M. A.","full_name":"López De La Torre, M. A.","last_name":"López De La Torre"},{"full_name":"Prades, Joan Daniel","first_name":"Joan Daniel","last_name":"Prades"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"publisher":"American Chemical Society","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Nanomaterials produced from the bottom-up assembly of nanocrystals may incorporate ∼1020–1021 cm–3 not fully coordinated surface atoms, i.e., ∼1020–1021 cm–3 potential donor or acceptor states that can strongly affect transport properties. Therefore, to exploit the full potential of nanocrystal building blocks to produce functional nanomaterials and thin films, a proper control of their surface chemistry is required. Here, we analyze how the ligand stripping procedure influences the charge and heat transport properties of sintered PbSe nanomaterials produced from the bottom-up assembly of colloidal PbSe nanocrystals. First, we show that the removal of the native organic ligands by thermal decomposition in an inert atmosphere leaves relatively large amounts of carbon at the crystal interfaces. This carbon blocks crystal growth during consolidation and at the same time hampers charge and heat transport through the final nanomaterial. Second, we demonstrate that, by stripping ligands from the nanocrystal surface before consolidation, nanomaterials with larger crystal domains, lower porosity, and higher charge carrier concentrations are obtained, thus resulting in nanomaterials with higher electrical and thermal conductivities. In addition, the ligand displacement leaves the nanocrystal surface unprotected, facilitating oxidation and chalcogen evaporation. The influence of the ligand displacement on the nanomaterial charge transport properties is rationalized here using a two-band model based on the standard Boltzmann transport equation with the relaxation time approximation. Finally, we present an application of the produced functional nanomaterials by modeling, fabricating, and testing a simple PbSe-based thermoelectric device with a ring geometry."}],"doi":"10.1021/acsaem.9b02137"},{"day":"19","conference":{"name":"AHPC: Austrian High-Performance-Computing Meeting","start_date":"2020-02-19","location":"Klosterneuburg, Austria","end_date":"2020-02-21"},"publisher":"IST Austria","_id":"7474","publication_status":"published","doi":"10.15479/AT:ISTA:7474","article_processing_charge":"No","abstract":[{"text":"This booklet is a collection of abstracts presented at the AHPC conference.","lang":"eng"}],"place":"Klosterneuburg, Austria","ddc":["000"],"month":"02","has_accepted_license":"1","date_updated":"2023-05-16T07:48:28Z","oa":1,"editor":[{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kiss, Janos","first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss"},{"last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano","first_name":"Stefano"}],"file_date_updated":"2020-07-14T12:47:59Z","oa_version":"Published Version","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2020-02-11T07:59:04Z","status":"public","citation":{"apa":"Schlögl, A., Kiss, J., &#38; Elefante, S. (Eds.). (2020). <i>Austrian High-Performance-Computing meeting (AHPC2020)</i>. Presented at the AHPC: Austrian High-Performance-Computing Meeting, Klosterneuburg, Austria: IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7474\">https://doi.org/10.15479/AT:ISTA:7474</a>","ieee":"A. Schlögl, J. Kiss, and S. Elefante, Eds., <i>Austrian High-Performance-Computing meeting (AHPC2020)</i>. Klosterneuburg, Austria: IST Austria, 2020.","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante, eds. <i>Austrian High-Performance-Computing Meeting (AHPC2020)</i>. Klosterneuburg, Austria: IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7474\">https://doi.org/10.15479/AT:ISTA:7474</a>.","short":"A. Schlögl, J. Kiss, S. Elefante, eds., Austrian High-Performance-Computing Meeting (AHPC2020), IST Austria, Klosterneuburg, Austria, 2020.","ista":"Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p.","mla":"Schlögl, Alois, et al., editors. <i>Austrian High-Performance-Computing Meeting (AHPC2020)</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7474\">10.15479/AT:ISTA:7474</a>.","ama":"Schlögl A, Kiss J, Elefante S, eds. <i>Austrian High-Performance-Computing Meeting (AHPC2020)</i>. Klosterneuburg, Austria: IST Austria; 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7474\">10.15479/AT:ISTA:7474</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_editor","year":"2020","title":"Austrian High-Performance-Computing meeting (AHPC2020)","file":[{"file_name":"BOOKLET_AHPC2020.final.pdf","checksum":"49798edb9e57bbd6be18362d1d7b18a9","relation":"main_file","file_size":90899507,"content_type":"application/pdf","date_created":"2020-02-19T06:53:38Z","date_updated":"2020-07-14T12:47:59Z","file_id":"7504","access_level":"open_access","creator":"schloegl"}],"language":[{"iso":"eng"}],"date_published":"2020-02-19T00:00:00Z","page":"72","publication_identifier":{"isbn":["978-3-99078-004-6"]},"department":[{"_id":"ScienComp"}]},{"oa":1,"article_type":"original","oa_version":"Published Version","date_updated":"2026-06-18T19:22:29Z","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.12905"}],"acknowledgement":"We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for providing generous support with the IAA and JA measurements. We thank Professor Guohua Xu (Nanjing Agricultural University) for generously providing the Nipponbare rice expressing DR5::GUS. We thank Professor Muyuan Zhu (Zhejiang University) for generously providing a rice line expressing 35S::miR393b. We thank Professor Yinong Yang (Pennsylvania State University) for generously providing the rice line coi1-18. This work was supported by grants from the National Natural Science Foundation of China (31660501, 31460453, 31860064 and 31470382), the Major Special Program for Scientific Research, Education Department of Yunnan Province (ZD2015005), the Project sponsored by SRF for ROCS, SEM ([2013] 1792), the Major Science and Technique Programs in Yunnan Province (2016ZF001), the Key Projects of the Applied Basic Research Plan of Yunnan Province (2017FA018), the National Key R&D Program of China (2018YFD0201100) and the China Agriculture Research System (CARS-21).","ddc":["580"],"publisher":"Wiley","_id":"7497","external_id":{"isi":["000515803000001"],"pmid":["31912615"]},"publication_status":"published","author":[{"last_name":"Han","full_name":"Han, L","first_name":"L"},{"last_name":"Zhou","full_name":"Zhou, X","first_name":"X"},{"last_name":"Zhao","first_name":"Y","full_name":"Zhao, Y"},{"last_name":"Zhu","full_name":"Zhu, S","first_name":"S"},{"first_name":"L","full_name":"Wu, L","last_name":"Wu"},{"first_name":"Y","full_name":"He, Y","last_name":"He"},{"first_name":"X","full_name":"Ping, X","last_name":"Ping"},{"last_name":"Lu","full_name":"Lu, X","first_name":"X"},{"last_name":"Huang","first_name":"W","full_name":"Huang, W"},{"first_name":"J","full_name":"Qian, J","last_name":"Qian"},{"last_name":"Zhang","full_name":"Zhang, L","first_name":"L"},{"first_name":"X","full_name":"Jiang, X","last_name":"Jiang"},{"last_name":"Zhu","full_name":"Zhu, D","first_name":"D"},{"full_name":"Luo, C","first_name":"C","last_name":"Luo"},{"last_name":"Li","full_name":"Li, S","first_name":"S"},{"last_name":"Dong","first_name":"Q","full_name":"Dong, Q"},{"last_name":"Fu","full_name":"Fu, Q","first_name":"Q"},{"last_name":"Deng","first_name":"K","full_name":"Deng, K"},{"last_name":"Wang","first_name":"X","full_name":"Wang, X"},{"last_name":"Wang","full_name":"Wang, L","first_name":"L"},{"last_name":"Peng","full_name":"Peng, S","first_name":"S"},{"full_name":"Wu, J","first_name":"J","last_name":"Wu"},{"first_name":"W","full_name":"Li, W","last_name":"Li"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhu","first_name":"Y","full_name":"Zhu, Y"},{"last_name":"He","full_name":"He, X","first_name":"X"},{"last_name":"Du","first_name":"Y","full_name":"Du, Y"}],"day":"01","abstract":[{"text":"Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover, the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross‐talk between JA signalling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1111/jipb.12905","department":[{"_id":"JiFr"}],"publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"isi":1,"intvolume":"        62","page":"1433-1451","date_published":"2020-09-01T00:00:00Z","issue":"9","type":"journal_article","year":"2020","pmid":1,"language":[{"iso":"eng"}],"title":"Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid","publication":"Journal of Integrative Plant Biology","date_created":"2020-02-18T10:02:25Z","quality_controlled":"1","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"L. Han, X. Zhou, Y. Zhao, S. Zhu, L. Wu, Y. He, X. Ping, X. Lu, W. Huang, J. Qian, L. Zhang, X. Jiang, D. Zhu, C. Luo, S. Li, Q. Dong, Q. Fu, K. Deng, X. Wang, L. Wang, S. Peng, J. Wu, W. Li, J. Friml, Y. Zhu, X. He, Y. Du, Journal of Integrative Plant Biology 62 (2020) 1433–1451.","ista":"Han L, Zhou X, Zhao Y, Zhu S, Wu L, He Y, Ping X, Lu X, Huang W, Qian J, Zhang L, Jiang X, Zhu D, Luo C, Li S, Dong Q, Fu Q, Deng K, Wang X, Wang L, Peng S, Wu J, Li W, Friml J, Zhu Y, He X, Du Y. 2020. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. Journal of Integrative Plant Biology. 62(9), 1433–1451.","mla":"Han, L., et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9, Wiley, 2020, pp. 1433–51, doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>.","ama":"Han L, Zhou X, Zhao Y, et al. Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. <i>Journal of Integrative Plant Biology</i>. 2020;62(9):1433-1451. doi:<a href=\"https://doi.org/10.1111/jipb.12905\">10.1111/jipb.12905</a>","apa":"Han, L., Zhou, X., Zhao, Y., Zhu, S., Wu, L., He, Y., … Du, Y. (2020). Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>","ieee":"L. Han <i>et al.</i>, “Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid,” <i>Journal of Integrative Plant Biology</i>, vol. 62, no. 9. Wiley, pp. 1433–1451, 2020.","chicago":"Han, L, X Zhou, Y Zhao, S Zhu, L Wu, Y He, X Ping, et al. “Colonization of Endophyte Acremonium Sp. D212 in Panax Notoginseng and Rice Mediated by Auxin and Jasmonic Acid.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/jipb.12905\">https://doi.org/10.1111/jipb.12905</a>."},"volume":62,"status":"public"},{"oa_version":"Submitted Version","oa":1,"article_type":"original","acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","OA_type":"green","main_file_link":[{"open_access":"1","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7610641/"}],"month":"10","date_updated":"2026-07-02T22:30:23Z","doi":"10.1038/s41588-020-00712-y","article_processing_charge":"No","abstract":[{"text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.","lang":"eng"}],"day":"19","_id":"8707","publisher":"Springer Nature","publication_status":"published","external_id":{"pmid":["33077914"],"isi":["000579693500004"]},"author":[{"full_name":" Galan, Silvia","first_name":"Silvia","last_name":" Galan"},{"first_name":"Nick N","full_name":"Machnik, Nick N","orcid":"0000-0001-6617-9742","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","last_name":"Machnik"},{"last_name":"Kruse","full_name":"Kruse, Kai","first_name":"Kai"},{"full_name":"Díaz, Noelia","first_name":"Noelia","last_name":"Díaz"},{"last_name":"Marti-Renom","first_name":"Marc A","full_name":"Marti-Renom, Marc A"},{"full_name":"Vaquerizas, Juan M","first_name":"Juan M","last_name":"Vaquerizas"}],"OA_place":"repository","isi":1,"department":[{"_id":"FyKo"}],"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"date_published":"2020-10-19T00:00:00Z","page":"1247-1255","intvolume":"        52","publication":"Nature Genetics","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","language":[{"iso":"eng"}],"pmid":1,"year":"2020","type":"journal_article","status":"public","volume":52,"citation":{"ieee":"S.  Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” <i>Nature Genetics</i>, vol. 52. Springer Nature, pp. 1247–1255, 2020.","apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., &#38; Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-020-00712-y\">https://doi.org/10.1038/s41588-020-00712-y</a>","chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” <i>Nature Genetics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41588-020-00712-y\">https://doi.org/10.1038/s41588-020-00712-y</a>.","ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","short":"S.  Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. <i>Nature Genetics</i>. 2020;52:1247-1255. doi:<a href=\"https://doi.org/10.1038/s41588-020-00712-y\">10.1038/s41588-020-00712-y</a>","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” <i>Nature Genetics</i>, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:<a href=\"https://doi.org/10.1038/s41588-020-00712-y\">10.1038/s41588-020-00712-y</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"id":"18642","status":"public","relation":"dissertation_contains"}]},"date_created":"2020-10-25T23:01:20Z"},{"acknowledgement":"I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","month":"09","has_accepted_license":"1","date_updated":"2026-04-08T07:43:58Z","oa_version":"None","file_date_updated":"2021-09-11T22:30:04Z","oa":1,"doi":"10.15479/AT:ISTA:8340","article_processing_charge":"No","abstract":[{"text":"Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies.","lang":"eng"}],"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"day":"09","author":[{"full_name":"Kampjut, Domen","orcid":"0000-0002-6018-3422","first_name":"Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut"}],"_id":"8340","publication_status":"published","publisher":"Institute of Science and Technology Austria","ec_funded":1,"ddc":["572"],"alternative_title":["ISTA Thesis"],"date_published":"2020-09-09T00:00:00Z","page":"242","OA_place":"publisher","publication_identifier":{"isbn":["978-3-99078-008-4"],"issn":["2663-337X"]},"department":[{"_id":"LeSa"}],"supervisor":[{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Kampjut, Domen. <i>Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8340\">10.15479/AT:ISTA:8340</a>.","ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8340\">10.15479/AT:ISTA:8340</a>","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","chicago":"Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8340\">https://doi.org/10.15479/AT:ISTA:8340</a>.","apa":"Kampjut, D. (2020). <i>Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8340\">https://doi.org/10.15479/AT:ISTA:8340</a>","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020."},"degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"6848","status":"public"}]},"date_created":"2020-09-07T18:42:23Z","corr_author":"1","title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","file":[{"relation":"source_file","file_size":166146359,"file_name":"ThesisFull20200908.docx","checksum":"dd270baf82121eb4472ad19d77bf227c","date_created":"2020-09-08T13:32:06Z","date_updated":"2021-09-11T22:30:04Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"8345","creator":"dkampjut"},{"content_type":"application/pdf","embargo":"2021-09-10","date_updated":"2021-09-11T22:30:04Z","date_created":"2020-09-14T15:02:20Z","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c","file_name":"2020_Thesis_Kampjut.pdf","file_size":13873769,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"8393"}],"language":[{"iso":"eng"}],"type":"dissertation","year":"2020"},{"ddc":["610"],"project":[{"name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and epilepsy","grant_number":"F7807"}],"day":"12","_id":"8620","publisher":"Institute of Science and Technology Austria","publication_status":"published","author":[{"full_name":"Morandell, Jasmin","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell"}],"doi":"10.15479/AT:ISTA:8620","abstract":[{"text":"The development of the human brain occurs through a tightly regulated series of dynamic and adaptive processes during prenatal and postnatal life. A disruption of this strictly orchestrated series of events can lead to a number of neurodevelopmental conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common, etiologically and phenotypically heterogeneous group of disorders sharing the core symptoms of social interaction and communication deficits and restrictive and repetitive interests and behaviors. They are estimated to affect one in 59 individuals in the U.S. and, over the last three decades, mutations in more than a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet, for the vast majority of these ASD-risk genes their role during brain development and precise molecular function still remain elusive.\r\nDe novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In the study described here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display cortical lamination abnormalities due to defective migration of post-mitotic excitatory neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal cortical organization, Cul3 heterozygous deletion is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neural cells results in atypical organization of the actin mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult mice does not induce the majority of the behavioral defects observed in constitutive Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn conclusion, our data indicate that Cul3 plays a critical role in the regulation of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral abnormalities are primarily due to dosage sensitive Cul3 functions at early brain developmental stages.","lang":"eng"}],"article_processing_charge":"No","oa":1,"file_date_updated":"2021-10-16T22:30:04Z","oa_version":"Published Version","month":"10","has_accepted_license":"1","date_updated":"2026-04-14T09:07:16Z","acknowledgement":"I would like to especially thank Armel Nicolas from the Proteomics and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka, Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line maintenance and their great support.","year":"2020","type":"dissertation","corr_author":"1","title":"Illuminating the role of Cul3 in autism spectrum disorder pathogenesis","file":[{"access_level":"open_access","file_id":"8621","creator":"jmorande","file_size":16155786,"relation":"main_file","file_name":"Jasmin_Morandell_Thesis-2020_final.pdf","checksum":"7ee83e42de3e5ce2fedb44dff472f75f","date_created":"2020-10-07T14:41:49Z","date_updated":"2021-10-16T22:30:04Z","embargo":"2021-10-15","content_type":"application/pdf"},{"file_id":"8622","access_level":"closed","creator":"jmorande","checksum":"5e0464af453734210ce7aab7b4a92e3a","file_name":"Jasmin_Morandell_Thesis-2020_final.zip","file_size":24344152,"relation":"source_file","embargo_to":"open_access","content_type":"application/x-zip-compressed","date_updated":"2021-10-16T22:30:04Z","date_created":"2020-10-07T14:45:07Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"7800","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8131","status":"public"}]},"degree_awarded":"PhD","date_created":"2020-10-07T14:53:13Z","status":"public","citation":{"chicago":"Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8620\">https://doi.org/10.15479/AT:ISTA:8620</a>.","apa":"Morandell, J. (2020). <i>Illuminating the role of Cul3 in autism spectrum disorder pathogenesis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8620\">https://doi.org/10.15479/AT:ISTA:8620</a>","ieee":"J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020.","mla":"Morandell, Jasmin. <i>Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8620\">10.15479/AT:ISTA:8620</a>.","ama":"Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8620\">10.15479/AT:ISTA:8620</a>","short":"J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis, Institute of Science and Technology Austria, 2020.","ista":"Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"department":[{"_id":"GaNo"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"date_published":"2020-10-12T00:00:00Z","page":"138"},{"file_date_updated":"2020-10-11T22:30:02Z","oa_version":"Published Version","keyword":["Cell Biology"],"article_type":"original","oa":1,"acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","date_updated":"2025-04-15T07:52:13Z","has_accepted_license":"1","month":"04","ddc":["570"],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. "}],"doi":"10.1242/jcs.239020","_id":"8434","author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","first_name":"Georgi A"},{"last_name":"Amiri","full_name":"Amiri, Behnam","first_name":"Behnam"},{"last_name":"Humphries","full_name":"Humphries, Ashley C.","first_name":"Ashley C."},{"full_name":"Schaks, Matthias","first_name":"Matthias","last_name":"Schaks"},{"first_name":"Vanessa","full_name":"Dimchev, Vanessa","last_name":"Dimchev"},{"last_name":"Stradal","first_name":"Theresia E. B.","full_name":"Stradal, Theresia E. B."},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"first_name":"Matthias","full_name":"Krause, Matthias","last_name":"Krause"},{"full_name":"Way, Michael","first_name":"Michael","last_name":"Way"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"}],"external_id":{"isi":["000534387800005"],"pmid":[" 32094266"]},"publication_status":"published","publisher":"The Company of Biologists","day":"09","project":[{"name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02495"}],"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"department":[{"_id":"FlSc"}],"isi":1,"article_number":"jcs239020","date_published":"2020-04-09T00:00:00Z","intvolume":"       133","language":[{"iso":"eng"}],"file":[{"embargo":"2020-10-10","content_type":"application/pdf","date_updated":"2020-10-11T22:30:02Z","date_created":"2020-09-17T14:07:51Z","checksum":"ba917e551acc4ece2884b751434df9ae","file_name":"2020_JournalCellScience_Dimchev.pdf","relation":"main_file","file_size":13493302,"creator":"dernst","access_level":"open_access","file_id":"8435"}],"title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","publication":"Journal of Cell Science","issue":"7","type":"journal_article","year":"2020","pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>.","ieee":"G. A. Dimchev <i>et al.</i>, “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” <i>Journal of Cell Science</i>, vol. 133, no. 7. The Company of Biologists, 2020.","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.239020\">https://doi.org/10.1242/jcs.239020</a>","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. <i>Journal of Cell Science</i>. 2020;133(7). doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.239020\">10.1242/jcs.239020</a>.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020."},"volume":133,"status":"public","date_created":"2020-09-17T14:00:33Z","scopus_import":"1","quality_controlled":"1"},{"type":"dissertation","year":"2020","language":[{"iso":"eng"}],"file":[{"creator":"bkavcic","access_level":"open_access","file_id":"8663","date_created":"2020-10-15T06:41:20Z","date_updated":"2021-10-07T22:30:03Z","embargo":"2021-10-06","content_type":"application/pdf","relation":"main_file","file_size":52636162,"file_name":"kavcicB_thesis202009.pdf","checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb"},{"file_name":"2020b.zip","checksum":"bb35f2352a04db19164da609f00501f3","file_size":321681247,"relation":"source_file","content_type":"application/zip","embargo_to":"open_access","date_created":"2020-10-15T06:41:53Z","date_updated":"2021-10-07T22:30:03Z","access_level":"closed","file_id":"8664","creator":"bkavcic"}],"title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","corr_author":"1","date_created":"2020-10-13T16:46:14Z","related_material":{"record":[{"status":"public","id":"7673","relation":"part_of_dissertation"},{"status":"public","id":"8250","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"chicago":"Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8657\">https://doi.org/10.15479/AT:ISTA:8657</a>.","ieee":"B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.","apa":"Kavcic, B. (2020). <i>Perturbations of protein synthesis: from antibiotics to genetics and physiology</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8657\">https://doi.org/10.15479/AT:ISTA:8657</a>","ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8657\">10.15479/AT:ISTA:8657</a>","mla":"Kavcic, Bor. <i>Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8657\">10.15479/AT:ISTA:8657</a>.","ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria.","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020."},"status":"public","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-011-4"]},"supervisor":[{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"}],"department":[{"_id":"GaTk"}],"OA_place":"publisher","page":"271","date_published":"2020-10-14T00:00:00Z","alternative_title":["ISTA Thesis"],"ddc":["571","530","570"],"publication_status":"published","_id":"8657","publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Bor","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"}],"day":"14","abstract":[{"text":"Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation.","lang":"eng"}],"article_processing_charge":"No","doi":"10.15479/AT:ISTA:8657","oa":1,"oa_version":"Published Version","file_date_updated":"2021-10-07T22:30:03Z","date_updated":"2026-04-08T07:27:48Z","has_accepted_license":"1","month":"10","acknowledgement":"I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop."},{"article_type":"original","oa":1,"oa_version":"Published Version","file_date_updated":"2020-09-21T14:08:58Z","month":"09","has_accepted_license":"1","date_updated":"2026-07-02T22:31:03Z","acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","ddc":["570"],"ec_funded":1,"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020"},{"name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus","_id":"25D32BC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"785907","call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 2","_id":"26436750-B435-11E9-9278-68D0E5697425"}],"day":"14","publisher":"MDPI","_id":"8532","author":[{"last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","first_name":"David"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber"},{"orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","first_name":"Pradeep","last_name":"Bhandari","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthew J","full_name":"Case, Matthew J","last_name":"Case","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"}],"publication_status":"published","external_id":{"isi":["000579945300001"]},"doi":"10.3390/ijms21186737","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography."}],"isi":1,"publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"department":[{"_id":"RySh"}],"intvolume":"        21","article_number":"6737","date_published":"2020-09-14T00:00:00Z","issue":"18","type":"journal_article","year":"2020","corr_author":"1","publication":"International Journal of Molecular Sciences","title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","file":[{"success":1,"access_level":"open_access","file_id":"8551","creator":"dernst","file_name":"2020_JournMolecSciences_Kleindienst.pdf","checksum":"2e4f62f3cfe945b7391fc3070e5a289f","relation":"main_file","file_size":5748456,"content_type":"application/pdf","date_created":"2020-09-21T14:08:58Z","date_updated":"2020-09-21T14:08:58Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","quality_controlled":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"9562","status":"public"}]},"date_created":"2020-09-20T22:01:35Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","volume":21,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18, 6737, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>.","ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. 2020;21(18). doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>","apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., &#38; Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>","ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18. MDPI, 2020.","chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>."}},{"quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"date_created":"2020-11-06T07:30:05Z","status":"public","volume":12302,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Asadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Kiarash Mohammadi, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” In <i>Automated Technology for Verification and Analysis</i>, 12302:253–70. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-59152-6_14\">https://doi.org/10.1007/978-3-030-59152-6_14</a>.","ieee":"A. Asadi, K. Chatterjee, A. K. Goharshady, K. Mohammadi, and A. Pavlogiannis, “Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth,” in <i>Automated Technology for Verification and Analysis</i>, Hanoi, Vietnam, 2020, vol. 12302, pp. 253–270.","apa":"Asadi, A., Chatterjee, K., Goharshady, A. K., Mohammadi, K., &#38; Pavlogiannis, A. (2020). Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In <i>Automated Technology for Verification and Analysis</i> (Vol. 12302, pp. 253–270). Hanoi, Vietnam: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-59152-6_14\">https://doi.org/10.1007/978-3-030-59152-6_14</a>","ama":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In: <i>Automated Technology for Verification and Analysis</i>. Vol 12302. Springer Nature; 2020:253-270. doi:<a href=\"https://doi.org/10.1007/978-3-030-59152-6_14\">10.1007/978-3-030-59152-6_14</a>","mla":"Asadi, Ali, et al. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” <i>Automated Technology for Verification and Analysis</i>, vol. 12302, Springer Nature, 2020, pp. 253–70, doi:<a href=\"https://doi.org/10.1007/978-3-030-59152-6_14\">10.1007/978-3-030-59152-6_14</a>.","short":"A. Asadi, K. Chatterjee, A.K. Goharshady, K. Mohammadi, A. Pavlogiannis, in:, Automated Technology for Verification and Analysis, Springer Nature, 2020, pp. 253–270.","ista":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. 2020. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 12302, 253–270."},"year":"2020","type":"conference","publication":"Automated Technology for Verification and Analysis","title":"Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth","file":[{"creator":"dernst","success":1,"access_level":"open_access","file_id":"8729","content_type":"application/pdf","date_created":"2020-11-06T07:41:03Z","date_updated":"2020-11-06T07:41:03Z","file_name":"2020_LNCS_ATVA_Asadi_accepted.pdf","checksum":"ae83f27e5b189d5abc2e7514f1b7e1b5","file_size":726648,"relation":"main_file"}],"language":[{"iso":"eng"}],"intvolume":"     12302","alternative_title":["LNCS"],"date_published":"2020-10-12T00:00:00Z","page":"253-270","isi":1,"publication_identifier":{"isbn":["9783030591519"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783030591526"]},"department":[{"_id":"KrCh"}],"project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2020-10-19","location":"Hanoi, Vietnam","end_date":"2020-10-23"},"day":"12","publication_status":"published","_id":"8728","publisher":"Springer Nature","author":[{"first_name":"Ali","full_name":"Asadi, Ali","last_name":"Asadi"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mohammadi","full_name":"Mohammadi, Kiarash","first_name":"Kiarash"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","first_name":"Andreas"}],"external_id":{"isi":["000723555700014"]},"doi":"10.1007/978-3-030-59152-6_14","article_processing_charge":"No","abstract":[{"text":"Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improvements. In this work, we show that treewidth can also be used to obtain faster algorithms for the quantitative problems. For an MC with n states and m transitions, we show that each of the classical quantitative objectives can be computed in   O((n+m)⋅t2)  time, given a tree decomposition of the MC with width t. Our results also imply a bound of   O(κ⋅(n+m)⋅t2)  for each objective on MDPs, where   κ  is the number of strategy-iteration refinements required for the given input and objective. Finally, we make an experimental evaluation of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms outperform existing well-established methods by one or more orders of magnitude.","lang":"eng"}],"ddc":["000"],"month":"10","has_accepted_license":"1","date_updated":"2026-07-02T22:31:07Z","oa":1,"file_date_updated":"2020-11-06T07:41:03Z","oa_version":"Submitted Version"},{"date_created":"2020-05-10T22:00:50Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"quality_controlled":"1","scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In: <i>European Symposium on Programming</i>. Vol 12075. Springer Nature; 2020:112-140. doi:<a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">10.1007/978-3-030-44914-8_5</a>","mla":"Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” <i>European Symposium on Programming</i>, vol. 12075, Springer Nature, 2020, pp. 112–40, doi:<a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">10.1007/978-3-030-44914-8_5</a>.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European Symposium on Programming, Springer Nature, 2020, pp. 112–140.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” In <i>European Symposium on Programming</i>, 12075:112–40. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">https://doi.org/10.1007/978-3-030-44914-8_5</a>.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal and perfectly parallel algorithms for on-demand data-flow analysis,” in <i>European Symposium on Programming</i>, Dublin, Ireland, 2020, vol. 12075, pp. 112–140.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In <i>European Symposium on Programming</i> (Vol. 12075, pp. 112–140). Dublin, Ireland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">https://doi.org/10.1007/978-3-030-44914-8_5</a>"},"volume":12075,"status":"public","year":"2020","type":"conference","language":[{"iso":"eng"}],"file":[{"checksum":"8618b80f4cf7b39a60e61a6445ad9807","file_name":"2020_LNCS_Chatterjee.pdf","file_size":651250,"relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-26T13:34:48Z","file_id":"7895","access_level":"open_access","creator":"dernst"}],"title":"Optimal and perfectly parallel algorithms for on-demand data-flow analysis","publication":"European Symposium on Programming","corr_author":"1","intvolume":"     12075","page":"112-140","date_published":"2020-04-18T00:00:00Z","alternative_title":["LNCS"],"department":[{"_id":"KrCh"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783030449131"],"eissn":["1611-3349"]},"isi":1,"_id":"7810","publication_status":"published","external_id":{"isi":["000681656800005"]},"publisher":"Springer Nature","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389"},{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"conference":{"end_date":"2020-04-30","name":"ESOP: Programming Languages and Systems","location":"Dublin, Ireland","start_date":"2020-04-25"},"day":"18","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","abstract":[{"text":"Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries.\r\nIn this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques.","lang":"eng"}],"doi":"10.1007/978-3-030-44914-8_5","ddc":["000"],"date_updated":"2026-07-02T22:31:08Z","has_accepted_license":"1","month":"04","oa":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:03Z"},{"ec_funded":1,"ddc":["570"],"doi":"10.3389/fcell.2020.574382","abstract":[{"lang":"eng","text":"Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future."}],"article_processing_charge":"Yes (via OA deal)","project":[{"grant_number":"24812","name":"Molecular mechanisms of radial neuronal migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618444"}],"day":"25","_id":"8569","external_id":{"isi":["000577915900001"],"pmid":["33102480"]},"publication_status":"published","publisher":"Frontiers","author":[{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","file_date_updated":"2020-09-28T13:11:17Z","oa":1,"article_type":"original","acknowledgement":"AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.","month":"09","has_accepted_license":"1","date_updated":"2026-07-02T22:31:15Z","publication":"Frontiers in Cell and Developmental Biology","corr_author":"1","title":"Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex","file":[{"file_size":5527139,"relation":"main_file","checksum":"01f731824194c94c81a5da360d997073","file_name":"2020_Frontiers_Hansen.pdf","date_updated":"2020-09-28T13:11:17Z","date_created":"2020-09-28T13:11:17Z","content_type":"application/pdf","access_level":"open_access","file_id":"8584","success":1,"creator":"dernst"}],"language":[{"iso":"eng"}],"pmid":1,"type":"journal_article","issue":"9","year":"2020","status":"public","volume":8,"citation":{"ista":"Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 8(9), 574382.","short":"A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology 8 (2020).","ama":"Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. <i>Frontiers in Cell and Developmental Biology</i>. 2020;8(9). doi:<a href=\"https://doi.org/10.3389/fcell.2020.574382\">10.3389/fcell.2020.574382</a>","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 8, no. 9, 574382, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fcell.2020.574382\">10.3389/fcell.2020.574382</a>.","ieee":"A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 8, no. 9. Frontiers, 2020.","apa":"Hansen, A. H., &#38; Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fcell.2020.574382\">https://doi.org/10.3389/fcell.2020.574382</a>","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fcell.2020.574382\">https://doi.org/10.3389/fcell.2020.574382</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"9962","relation":"dissertation_contains"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2020-09-26T06:11:07Z","isi":1,"department":[{"_id":"SiHi"}],"publication_identifier":{"issn":["2296-634X"]},"article_number":"574382","date_published":"2020-09-25T00:00:00Z","intvolume":"         8"},{"author":[{"last_name":"Ionica","first_name":"Sorina","full_name":"Ionica, Sorina"},{"last_name":"Kılıçer","first_name":"Pınar","full_name":"Kılıçer, Pınar"},{"last_name":"Lauter","first_name":"Kristin","full_name":"Lauter, Kristin"},{"last_name":"Lorenzo García","full_name":"Lorenzo García, Elisa","first_name":"Elisa"},{"last_name":"Manzateanu","id":"be8d652e-a908-11ec-82a4-e2867729459c","full_name":"Manzateanu, Maria-Adelina","first_name":"Maria-Adelina"},{"last_name":"Massierer","first_name":"Maike","full_name":"Massierer, Maike"},{"full_name":"Vincent, Christelle","first_name":"Christelle","last_name":"Vincent"}],"_id":"10874","external_id":{"arxiv":["1807.08986"]},"publisher":"Springer Nature","publication_status":"published","day":"02","doi":"10.1007/s40993-018-0146-6","abstract":[{"text":"In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM.","lang":"eng"}],"article_processing_charge":"No","date_updated":"2023-09-05T15:39:31Z","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1807.08986","open_access":"1"}],"acknowledgement":"The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. ","oa":1,"article_type":"original","oa_version":"Preprint","keyword":["Algebra and Number Theory"],"date_created":"2022-03-18T12:09:48Z","quality_controlled":"1","scopus_import":"1","citation":{"chicago":"Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” <i>Research in Number Theory</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s40993-018-0146-6\">https://doi.org/10.1007/s40993-018-0146-6</a>.","apa":"Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., &#38; Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. <i>Research in Number Theory</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40993-018-0146-6\">https://doi.org/10.1007/s40993-018-0146-6</a>","ieee":"S. Ionica <i>et al.</i>, “Modular invariants for genus 3 hyperelliptic curves,” <i>Research in Number Theory</i>, vol. 5. Springer Nature, 2019.","mla":"Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” <i>Research in Number Theory</i>, vol. 5, 9, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1007/s40993-018-0146-6\">10.1007/s40993-018-0146-6</a>.","ama":"Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. <i>Research in Number Theory</i>. 2019;5. doi:<a href=\"https://doi.org/10.1007/s40993-018-0146-6\">10.1007/s40993-018-0146-6</a>","ista":"Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9.","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","volume":5,"type":"journal_article","year":"2019","language":[{"iso":"eng"}],"publication":"Research in Number Theory","title":"Modular invariants for genus 3 hyperelliptic curves","intvolume":"         5","arxiv":1,"article_number":"9","date_published":"2019-01-02T00:00:00Z","department":[{"_id":"TiBr"}],"publication_identifier":{"issn":["2522-0160"],"eissn":["2363-9555"]}},{"oa_version":"Published Version","keyword":["Space and Planetary Science","Astronomy and Astrophysics","gravitational lensing: strong / galaxies: high-redshift / dark ages","reionization","first stars / galaxies: clusters: general / galaxies: luminosity function","mass function"],"article_type":"original","oa":1,"acknowledgement":"We thank the anonymous referee for their critical review and useful suggestions. This work has been carried out thanks to the support of the OCEVU Labex (ANR-11-LABX-0060) and the A*MIDEX project (ANR-11-IDEX-0001-02) funded by the “Investissements d’Avenir” French government programme managed by the ANR. Partially funded by the ERC starting grant CALENDS (JR, VP, BC, JM), the Agence Nationale de la recherche bearing the reference ANR-13-BS05-0010-02 (FOGHAR), and the “Programme National de Cosmologie and Galaxies” (PNCG) of CNRS/INSU, France. GdV, RP, JR, GM, JM, BC, and VP also acknowledge support by the Programa de Cooperacion Cientifica – ECOS SUD Program C16U02. NL acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 669253), ABD acknowledges support from the ERC advanced grant “Cosmic Gas”. LW acknowledges support by the Competitive Fund of the Leibniz Association through grant SAW-2015-AIP-2, and TG acknowledges support from the European Research Council under grant agreement ERC-stg-757258 (TRIPLE).. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 060.A-9345, 094.A-0115, 095.A-0181, 096.A-0710, 097.A0269, 100.A-0249, and 294.A-5032. Also based on observations obtained with the NASA/ESA Hubble Space Telescope, retrieved from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute (STScI). STScI is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS 5-26555. This research made use of Astropy, a community-developed core Python package for Astronomy (Astropy Collaboration 2013). All plots in this paper were created using Matplotlib (Hunter 2007).","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.13696"}],"month":"07","date_updated":"2022-07-19T09:36:31Z","doi":"10.1051/0004-6361/201834471","abstract":[{"lang":"eng","text":"Contact. This paper presents the results obtained with the Multi-Unit Spectroscopic Explorer (MUSE) at the ESO Very Large Telescope on the faint end of the Lyman-alpha luminosity function (LF) based on deep observations of four lensing clusters. The goal of our project is to set strong constraints on the relative contribution of the Lyman-alpha emitter (LAE) population to cosmic reionization.\r\n\r\nAims. The precise aim of the present study is to further constrain the abundance of LAEs by taking advantage of the magnification provided by lensing clusters to build a blindly selected sample of galaxies which is less biased than current blank field samples in redshift and luminosity. By construction, this sample of LAEs is complementary to those built from deep blank fields, whether observed by MUSE or by other facilities, and makes it possible to determine the shape of the LF at fainter levels, as well as its evolution with redshift.\r\n\r\nMethods. We selected a sample of 156 LAEs with redshifts between 2.9 ≤ z ≤ 6.7 and magnification-corrected luminosities in the range 39 ≲ log LLyα [erg s−1] ≲43. To properly take into account the individual differences in detection conditions between the LAEs when computing the LF, including lensing configurations, and spatial and spectral morphologies, the non-parametric 1/Vmax method was adopted. The price to pay to benefit from magnification is a reduction of the effective volume of the survey, together with a more complex analysis procedure to properly determine the effective volume Vmax for each galaxy. In this paper we present a complete procedure for the determination of the LF based on IFU detections in lensing clusters. This procedure, including some new methods for masking, effective volume integration and (individual) completeness determinations, has been fully automated when possible, and it can be easily generalized to the analysis of IFU observations in blank fields.\r\n\r\nResults. As a result of this analysis, the Lyman-alpha LF has been obtained in four different redshift bins: 2.9 <  z <  6, 7, 2.9 <  z <  4.0, 4.0 <  z <  5.0, and 5.0 <  z <  6.7 with constraints down to log LLyα = 40.5. From our data only, no significant evolution of LF mean slope can be found. When performing a Schechter analysis also including data from the literature to complete the present sample towards the brightest luminosities, a steep faint end slope was measured varying from α = −1.69−0.08+0.08 to α = −1.87−0.12+0.12 between the lowest and the highest redshift bins.\r\n\r\nConclusions. The contribution of the LAE population to the star formation rate density at z ∼ 6 is ≲50% depending on the luminosity limit considered, which is of the same order as the Lyman-break galaxy (LBG) contribution. The evolution of the LAE contribution with redshift depends on the assumed escape fraction of Lyman-alpha photons, and appears to slightly increase with increasing redshift when this fraction is conservatively set to one. Depending on the intersection between the LAE/LBG populations, the contribution of the observed galaxies to the ionizing flux may suffice to keep the universe ionized at z ∼ 6."}],"article_processing_charge":"No","day":"25","external_id":{"arxiv":["1905.13696"]},"_id":"11505","publication_status":"published","publisher":"EDP Sciences","author":[{"full_name":"de La Vieuville, G.","first_name":"G.","last_name":"de La Vieuville"},{"first_name":"D.","full_name":"Bina, D.","last_name":"Bina"},{"last_name":"Pello","full_name":"Pello, R.","first_name":"R."},{"last_name":"Mahler","full_name":"Mahler, G.","first_name":"G."},{"first_name":"J.","full_name":"Richard, J.","last_name":"Richard"},{"full_name":"Drake, A. B.","first_name":"A. B.","last_name":"Drake"},{"last_name":"Herenz","full_name":"Herenz, E. C.","first_name":"E. C."},{"last_name":"Bauer","full_name":"Bauer, F. E.","first_name":"F. E."},{"last_name":"Clément","first_name":"B.","full_name":"Clément, B."},{"full_name":"Lagattuta, D.","first_name":"D.","last_name":"Lagattuta"},{"full_name":"Laporte, N.","first_name":"N.","last_name":"Laporte"},{"first_name":"J.","full_name":"Martinez, J.","last_name":"Martinez"},{"full_name":"Patrício, V.","first_name":"V.","last_name":"Patrício"},{"first_name":"L.","full_name":"Wisotzki, L.","last_name":"Wisotzki"},{"last_name":"Zabl","full_name":"Zabl, J.","first_name":"J."},{"last_name":"Bouwens","first_name":"R. J.","full_name":"Bouwens, R. J."},{"first_name":"T.","full_name":"Contini, T.","last_name":"Contini"},{"last_name":"Garel","full_name":"Garel, T.","first_name":"T."},{"first_name":"B.","full_name":"Guiderdoni, B.","last_name":"Guiderdoni"},{"first_name":"R. A.","full_name":"Marino, R. A.","last_name":"Marino"},{"last_name":"Maseda","first_name":"M. V.","full_name":"Maseda, M. V."},{"last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"},{"first_name":"J.","full_name":"Schaye, J.","last_name":"Schaye"},{"last_name":"Soucail","full_name":"Soucail, G.","first_name":"G."}],"extern":"1","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"date_published":"2019-07-25T00:00:00Z","article_number":"A3","arxiv":1,"intvolume":"       628","publication":"Astronomy & Astrophysics","title":"Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE","language":[{"iso":"eng"}],"year":"2019","type":"journal_article","status":"public","volume":628,"citation":{"chicago":"La Vieuville, G. de, D. Bina, R. Pello, G. Mahler, J. Richard, A. B. Drake, E. C. Herenz, et al. “Faint End of the z ∼ 3–7 Luminosity Function of Lyman-Alpha Emitters behind Lensing Clusters Observed with MUSE.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2019. <a href=\"https://doi.org/10.1051/0004-6361/201834471\">https://doi.org/10.1051/0004-6361/201834471</a>.","apa":"de La Vieuville, G., Bina, D., Pello, R., Mahler, G., Richard, J., Drake, A. B., … Soucail, G. (2019). Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/201834471\">https://doi.org/10.1051/0004-6361/201834471</a>","ieee":"G. de La Vieuville <i>et al.</i>, “Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE,” <i>Astronomy &#38; Astrophysics</i>, vol. 628. EDP Sciences, 2019.","mla":"de La Vieuville, G., et al. “Faint End of the z ∼ 3–7 Luminosity Function of Lyman-Alpha Emitters behind Lensing Clusters Observed with MUSE.” <i>Astronomy &#38; Astrophysics</i>, vol. 628, A3, EDP Sciences, 2019, doi:<a href=\"https://doi.org/10.1051/0004-6361/201834471\">10.1051/0004-6361/201834471</a>.","ama":"de La Vieuville G, Bina D, Pello R, et al. Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE. <i>Astronomy &#38; Astrophysics</i>. 2019;628. doi:<a href=\"https://doi.org/10.1051/0004-6361/201834471\">10.1051/0004-6361/201834471</a>","ista":"de La Vieuville G, Bina D, Pello R, Mahler G, Richard J, Drake AB, Herenz EC, Bauer FE, Clément B, Lagattuta D, Laporte N, Martinez J, Patrício V, Wisotzki L, Zabl J, Bouwens RJ, Contini T, Garel T, Guiderdoni B, Marino RA, Maseda MV, Matthee JJ, Schaye J, Soucail G. 2019. Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE. Astronomy &#38; Astrophysics. 628, A3.","short":"G. de La Vieuville, D. Bina, R. Pello, G. Mahler, J. Richard, A.B. Drake, E.C. Herenz, F.E. Bauer, B. Clément, D. Lagattuta, N. Laporte, J. Martinez, V. Patrício, L. Wisotzki, J. Zabl, R.J. Bouwens, T. Contini, T. Garel, B. Guiderdoni, R.A. Marino, M.V. Maseda, J.J. Matthee, J. Schaye, G. Soucail, Astronomy &#38; Astrophysics 628 (2019)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","quality_controlled":"1","date_created":"2022-07-06T10:09:36Z"},{"title":"The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy","publication":"The Astrophysical Journal","language":[{"iso":"eng"}],"type":"journal_article","year":"2019","issue":"2","volume":882,"status":"public","citation":{"apa":"Boogaard, L. A., Decarli, R., González-López, J., van der Werf, P., Walter, F., Bouwens, R., … Wagg, J. (2019). The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ab3102\">https://doi.org/10.3847/1538-4357/ab3102</a>","ieee":"L. A. Boogaard <i>et al.</i>, “The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy,” <i>The Astrophysical Journal</i>, vol. 882, no. 2. IOP Publishing, 2019.","chicago":"Boogaard, Leindert A., Roberto Decarli, Jorge González-López, Paul van der Werf, Fabian Walter, Rychard Bouwens, Manuel Aravena, et al. “The ALMA Spectroscopic Survey in the HUDF: Nature and Physical Properties of Gas-Mass Selected Galaxies Using MUSE Spectroscopy.” <i>The Astrophysical Journal</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.3847/1538-4357/ab3102\">https://doi.org/10.3847/1538-4357/ab3102</a>.","short":"L.A. Boogaard, R. Decarli, J. González-López, P. van der Werf, F. Walter, R. Bouwens, M. Aravena, C. Carilli, F.E. Bauer, J. Brinchmann, T. Contini, P. Cox, E. da Cunha, E. Daddi, T. Díaz-Santos, J. Hodge, H. Inami, R. Ivison, M. Maseda, J.J. Matthee, P. Oesch, G. Popping, D. Riechers, J. Schaye, S. Schouws, I. Smail, A. Weiss, L. Wisotzki, R. Bacon, P.C. Cortes, H.-W. Rix, R.S. Somerville, M. Swinbank, J. Wagg, The Astrophysical Journal 882 (2019).","ista":"Boogaard LA, Decarli R, González-López J, van der Werf P, Walter F, Bouwens R, Aravena M, Carilli C, Bauer FE, Brinchmann J, Contini T, Cox P, da Cunha E, Daddi E, Díaz-Santos T, Hodge J, Inami H, Ivison R, Maseda M, Matthee JJ, Oesch P, Popping G, Riechers D, Schaye J, Schouws S, Smail I, Weiss A, Wisotzki L, Bacon R, Cortes PC, Rix H-W, Somerville RS, Swinbank M, Wagg J. 2019. The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy. The Astrophysical Journal. 882(2), 140.","mla":"Boogaard, Leindert A., et al. “The ALMA Spectroscopic Survey in the HUDF: Nature and Physical Properties of Gas-Mass Selected Galaxies Using MUSE Spectroscopy.” <i>The Astrophysical Journal</i>, vol. 882, no. 2, 140, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.3847/1538-4357/ab3102\">10.3847/1538-4357/ab3102</a>.","ama":"Boogaard LA, Decarli R, González-López J, et al. The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy. <i>The Astrophysical Journal</i>. 2019;882(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ab3102\">10.3847/1538-4357/ab3102</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":"1","date_created":"2022-07-06T13:31:35Z","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"article_number":"140","date_published":"2019-09-11T00:00:00Z","arxiv":1,"intvolume":"       882","article_processing_charge":"No","abstract":[{"text":"We discuss the nature and physical properties of gas-mass selected galaxies in the ALMA spectroscopic survey (ASPECS) of the Hubble Ultra Deep Field (HUDF). We capitalize on the deep optical integral-field spectroscopy from the Multi Unit Spectroscopic Explorer (MUSE) HUDF Survey and multiwavelength data to uniquely associate all 16 line emitters, detected in the ALMA data without preselection, with rotational transitions of carbon monoxide (CO). We identify 10 as CO(2–1) at 1 < z < 2, 5 as CO(3–2) at 2 < z < 3, and 1 as CO(4–3) at z = 3.6. Using the MUSE data as a prior, we identify two additional CO(2–1) emitters, increasing the total sample size to 18. We infer metallicities consistent with (super-)solar for the CO-detected galaxies at z ≤ 1.5, motivating our choice of a Galactic conversion factor between CO luminosity and molecular gas mass for these galaxies. Using deep Chandra imaging of the HUDF, we determine an X-ray AGN fraction of 20% and 60% among the CO emitters at z ∼ 1.4 and z ∼ 2.6, respectively. Being a CO-flux-limited survey, ASPECS-LP detects molecular gas in galaxies on, above, and below the main sequence (MS) at z ∼ 1.4. For stellar masses ≥1010 (1010.5) ${M}_{\\odot }$, we detect about 40% (50%) of all galaxies in the HUDF at 1 < z < 2 (2 < z < 3). The combination of ALMA and MUSE integral-field spectroscopy thus enables an unprecedented view of MS galaxies during the peak of galaxy formation.","lang":"eng"}],"doi":"10.3847/1538-4357/ab3102","day":"11","extern":"1","external_id":{"arxiv":["1903.09167"]},"_id":"11514","publisher":"IOP Publishing","publication_status":"published","author":[{"last_name":"Boogaard","full_name":"Boogaard, Leindert A.","first_name":"Leindert A."},{"last_name":"Decarli","first_name":"Roberto","full_name":"Decarli, Roberto"},{"last_name":"González-López","first_name":"Jorge","full_name":"González-López, Jorge"},{"last_name":"van der Werf","first_name":"Paul","full_name":"van der Werf, Paul"},{"full_name":"Walter, Fabian","first_name":"Fabian","last_name":"Walter"},{"first_name":"Rychard","full_name":"Bouwens, Rychard","last_name":"Bouwens"},{"last_name":"Aravena","first_name":"Manuel","full_name":"Aravena, Manuel"},{"last_name":"Carilli","first_name":"Chris","full_name":"Carilli, Chris"},{"first_name":"Franz Erik","full_name":"Bauer, Franz Erik","last_name":"Bauer"},{"first_name":"Jarle","full_name":"Brinchmann, Jarle","last_name":"Brinchmann"},{"last_name":"Contini","first_name":"Thierry","full_name":"Contini, Thierry"},{"full_name":"Cox, Pierre","first_name":"Pierre","last_name":"Cox"},{"full_name":"da Cunha, Elisabete","first_name":"Elisabete","last_name":"da Cunha"},{"last_name":"Daddi","first_name":"Emanuele","full_name":"Daddi, Emanuele"},{"last_name":"Díaz-Santos","full_name":"Díaz-Santos, Tanio","first_name":"Tanio"},{"first_name":"Jacqueline","full_name":"Hodge, Jacqueline","last_name":"Hodge"},{"last_name":"Inami","first_name":"Hanae","full_name":"Inami, Hanae"},{"last_name":"Ivison","first_name":"Rob","full_name":"Ivison, Rob"},{"first_name":"Michael","full_name":"Maseda, Michael","last_name":"Maseda"},{"first_name":"Jorryt J","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee"},{"last_name":"Oesch","first_name":"Pascal","full_name":"Oesch, Pascal"},{"full_name":"Popping, Gergö","first_name":"Gergö","last_name":"Popping"},{"last_name":"Riechers","full_name":"Riechers, Dominik","first_name":"Dominik"},{"last_name":"Schaye","full_name":"Schaye, Joop","first_name":"Joop"},{"last_name":"Schouws","full_name":"Schouws, Sander","first_name":"Sander"},{"first_name":"Ian","full_name":"Smail, Ian","last_name":"Smail"},{"last_name":"Weiss","full_name":"Weiss, Axel","first_name":"Axel"},{"last_name":"Wisotzki","first_name":"Lutz","full_name":"Wisotzki, Lutz"},{"full_name":"Bacon, Roland","first_name":"Roland","last_name":"Bacon"},{"first_name":"Paulo C.","full_name":"Cortes, Paulo C.","last_name":"Cortes"},{"last_name":"Rix","first_name":"Hans-Walter","full_name":"Rix, Hans-Walter"},{"full_name":"Somerville, Rachel S.","first_name":"Rachel S.","last_name":"Somerville"},{"full_name":"Swinbank, Mark","first_name":"Mark","last_name":"Swinbank"},{"last_name":"Wagg","full_name":"Wagg, Jeff","first_name":"Jeff"}],"oa_version":"Preprint","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"oa":1,"article_type":"original","acknowledgement":"We are grateful to the referee for providing a constructive report. L.A.B. wants to thank Madusha L.P. Gunawardhana for her help with platefit. Based on observations collected at the European Southern Observatory under ESO programme(s): 094.A-2089(B), 095.A-0010(A), 096.A-0045(A), and 096.A-0045(B). This paper makes use of the following ALMA data: ADS/JAO.ALMA#2016.1.00324.L. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), 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. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc.\r\n\r\n\"Este trabajo contó con el apoyo de CONICYT+Programa de Astronomía+ Fondo CHINA-CONICYT\" J.G-L. acknowledges partial support from ALMA-CONICYT project 31160033. F.E.B. acknowledges support from CONICYT grant Basal AFB-170002 (FEB), and the Ministry of Economy, Development, and Tourism's Millennium Science Initiative through grant IC120009, awarded to The Millennium Institute of Astrophysics, MAS (FEB). J.B. acknowledges support by Fundação para a Ciência e a Tecnologia (FCT) through national funds (UID/FIS/04434/2013) and Investigador FCT contract IF/01654/2014/CP1215/CT0003., and by FEDER through COMPETE2020 (POCI-01-0145-FEDER-007672). T.D-S. acknowledges support from ALMA-CONYCIT project 31130005 and FONDECYT project 1151239. J.H. acknowledges support of the VIDI research programme with project number 639.042.611, which is (partly) financed by the Netherlands Organization for Scientific Research (NWO). D.R. acknowledges support from the National Science Foundation under grant No. AST-1614213. I.R.S. acknowledges support from the ERC Advanced Grant DUSTYGAL (321334) and STFC (ST/P000541/1)\r\n\r\nWork on Gnuastro has been funded by the Japanese MEXT scholarship and its Grant-in-Aid for Scientific Research (21244012, 24253003), the ERC advanced grant 339659-MUSICOS, European Union's Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement No. 721463 to the SUNDIAL ITN, and from the Spanish MINECO under grant No. AYA2016-76219-P.","main_file_link":[{"url":"https://arxiv.org/abs/1903.09167","open_access":"1"}],"month":"09","date_updated":"2022-07-19T09:50:55Z"},{"_id":"11535","publication_status":"published","author":[{"first_name":"A A","full_name":"Khostovan, A A","last_name":"Khostovan"},{"first_name":"D","full_name":"Sobral, D","last_name":"Sobral"},{"first_name":"B","full_name":"Mobasher, B","last_name":"Mobasher"},{"last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"},{"first_name":"R K","full_name":"Cochrane, R K","last_name":"Cochrane"},{"full_name":"Chartab, N","first_name":"N","last_name":"Chartab"},{"last_name":"Jafariyazani","first_name":"M","full_name":"Jafariyazani, M"},{"first_name":"A","full_name":"Paulino-Afonso, A","last_name":"Paulino-Afonso"},{"last_name":"Santos","full_name":"Santos, S","first_name":"S"},{"last_name":"Calhau","full_name":"Calhau, J","first_name":"J"}],"external_id":{"arxiv":["1811.00556"]},"publisher":"Oxford University Press","extern":"1","day":"01","doi":"10.1093/mnras/stz2149","abstract":[{"lang":"eng","text":"We investigate the clustering and halo properties of ∼5000 Ly α-selected emission-line galaxies (LAEs) from the Slicing COSMOS 4K (SC4K) and from archival NB497 imaging of SA22 split in 15 discrete redshift slices between z ∼ 2.5 and 6. We measure clustering lengths of r0 ∼ 3–6 h−1 Mpc and typical halo masses of ∼1011 M⊙ for our narrowband-selected LAEs with typical LLy α ∼ 1042–43 erg s−1. The intermediate-band-selected LAEs are observed to have r0 ∼ 3.5–15 h−1 Mpc with typical halo masses of ∼1011–12 M⊙ and typical LLy α ∼ 1043–43.6 erg s−1. We find a strong, redshift-independent correlation between halo mass and Ly α luminosity normalized by the characteristic Ly α luminosity, L⋆(z). The faintest LAEs (L ∼ 0.1 L⋆(z)) typically identified by deep narrowband surveys are found in 1010 M⊙ haloes and the brightest LAEs (L ∼ 7 L⋆(z)) are found in ∼5 × 1012 M⊙ haloes. A dependency on the rest-frame 1500 Å UV luminosity, MUV, is also observed where the halo masses increase from 1011 to 1013 M⊙ for MUV ∼ −19 to −23.5 mag. Halo mass is also observed to increase from 109.8 to 1012 M⊙ for dust-corrected UV star formation rates from ∼0.6 to 10 M⊙ yr−1 and continues to increase up to 1013 M⊙ in halo mass, where the majority of those sources are active galactic nuclei. All the trends we observe are found to be redshift independent. Our results reveal that LAEs are the likely progenitors of a wide range of galaxies depending on their luminosity, from dwarf-like, to Milky Way-type, to bright cluster galaxies. LAEs therefore provide unique insight into the early formation and evolution of the galaxies we observe in the local Universe."}],"article_processing_charge":"No","oa":1,"article_type":"original","oa_version":"Preprint","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: haloes","galaxies: high-redshift","galaxies: star formation","cosmology: observations","large-scale structure of Universe"],"date_updated":"2022-08-19T06:38:42Z","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1811.00556","open_access":"1"}],"acknowledgement":"We thank the anonymous referee for their useful comments and suggestions that helped improve this study. AAK acknowledges that this work was supported by NASA Headquarters under the NASA Earth and Space Science Fellowship Program – Grant NNX16AO92H. JM acknowledges support from the ETH Zwicky fellowship. RKC acknowledges funding from STFC via a studentship. APA acknowledges support from the Fundac¸ao para a Ci ˜ encia e a Tecnologia FCT through the fellowship PD/BD/52706/2014 and the research grant UID/FIS/04434/2013. JC and SS both acknowledge their support from the Lancaster University PhD Fellowship. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY, SCIPY, MATPLOTLIB, SCIKIT-LEARN, and ASTROPY packages, as well as the TOPCAT analysis program. The SC4K samples used in this paper are all publicly available for use by the community (Sobral et al. 2018a). The catalogue is also available on the COSMOS IPAC website (https://irsa.ipac.caltech.edu/data/COSMOS/overview.html).","year":"2019","issue":"1","type":"journal_article","language":[{"iso":"eng"}],"publication":"Monthly Notices of the Royal Astronomical Society","title":"The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities","date_created":"2022-07-07T13:01:03Z","scopus_import":"1","quality_controlled":"1","citation":{"chicago":"Khostovan, A A, D Sobral, B Mobasher, Jorryt J Matthee, R K Cochrane, N Chartab, M Jafariyazani, A Paulino-Afonso, S Santos, and J Calhau. “The Clustering of Typical Ly α Emitters from z ∼ 2.5–6: Host Halo Masses Depend on Ly α and UV Luminosities.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/mnras/stz2149\">https://doi.org/10.1093/mnras/stz2149</a>.","apa":"Khostovan, A. A., Sobral, D., Mobasher, B., Matthee, J. J., Cochrane, R. K., Chartab, N., … Calhau, J. (2019). The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stz2149\">https://doi.org/10.1093/mnras/stz2149</a>","ieee":"A. A. Khostovan <i>et al.</i>, “The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 489, no. 1. Oxford University Press, pp. 555–573, 2019.","mla":"Khostovan, A. A., et al. “The Clustering of Typical Ly α Emitters from z ∼ 2.5–6: Host Halo Masses Depend on Ly α and UV Luminosities.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 489, no. 1, Oxford University Press, 2019, pp. 555–73, doi:<a href=\"https://doi.org/10.1093/mnras/stz2149\">10.1093/mnras/stz2149</a>.","ama":"Khostovan AA, Sobral D, Mobasher B, et al. The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities. <i>Monthly Notices of the Royal Astronomical Society</i>. 2019;489(1):555-573. doi:<a href=\"https://doi.org/10.1093/mnras/stz2149\">10.1093/mnras/stz2149</a>","ista":"Khostovan AA, Sobral D, Mobasher B, Matthee JJ, Cochrane RK, Chartab N, Jafariyazani M, Paulino-Afonso A, Santos S, Calhau J. 2019. The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities. Monthly Notices of the Royal Astronomical Society. 489(1), 555–573.","short":"A.A. Khostovan, D. Sobral, B. Mobasher, J.J. Matthee, R.K. Cochrane, N. Chartab, M. Jafariyazani, A. Paulino-Afonso, S. Santos, J. Calhau, Monthly Notices of the Royal Astronomical Society 489 (2019) 555–573."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":489,"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"intvolume":"       489","arxiv":1,"page":"555-573","date_published":"2019-10-01T00:00:00Z"},{"article_processing_charge":"No","abstract":[{"lang":"eng","text":"We present the discovery of HD 221416 b, the first transiting planet identified by the Transiting Exoplanet Survey Satellite (TESS) for which asteroseismology of the host star is possible. HD 221416 b (HIP 116158, TOI-197) is a bright (V = 8.2 mag), spectroscopically classified subgiant that oscillates with an average frequency of about 430 μHz and displays a clear signature of mixed modes. The oscillation amplitude confirms that the redder TESS bandpass compared to Kepler has a small effect on the oscillations, supporting the expected yield of thousands of solar-like oscillators with TESS 2 minute cadence observations. Asteroseismic modeling yields a robust determination of the host star radius (R⋆ = 2.943 ± 0.064 R⊙), mass (M⋆ = 1.212 ± 0.074 M⊙), and age (4.9 ± 1.1 Gyr), and demonstrates that it has just started ascending the red-giant branch. Combining asteroseismology with transit modeling and radial-velocity observations, we show that the planet is a \"hot Saturn\" (Rp = 9.17 ± 0.33 R⊕) with an orbital period of ∼14.3 days, irradiance of F = 343 ± 24 F⊕, and moderate mass (Mp = 60.5 ± 5.7 M⊕) and density (ρp = 0.431 ± 0.062 g cm−3). The properties of HD 221416 b show that the host-star metallicity–planet mass correlation found in sub-Saturns (4–8 R⊕) does not extend to larger radii, indicating that planets in the transition between sub-Saturns and Jupiters follow a relatively narrow range of densities. With a density measured to ∼15%, HD 221416 b is one of the best characterized Saturn-size planets to date, augmenting the small number of known transiting planets around evolved stars and demonstrating the power of TESS to characterize exoplanets and their host stars using asteroseismology."}],"doi":"10.3847/1538-3881/ab1488","day":"30","extern":"1","external_id":{"arxiv":["1901.01643"]},"_id":"11616","publisher":"IOP Publishing","author":[{"last_name":"Huber","full_name":"Huber, Daniel","first_name":"Daniel"},{"full_name":"Chaplin, William J.","first_name":"William J.","last_name":"Chaplin"},{"last_name":"Chontos","full_name":"Chontos, Ashley","first_name":"Ashley"},{"last_name":"Kjeldsen","full_name":"Kjeldsen, Hans","first_name":"Hans"},{"last_name":"Christensen-Dalsgaard","first_name":"Jørgen","full_name":"Christensen-Dalsgaard, Jørgen"},{"full_name":"Bedding, Timothy R.","first_name":"Timothy R.","last_name":"Bedding"},{"last_name":"Ball","full_name":"Ball, Warrick","first_name":"Warrick"},{"first_name":"Rafael","full_name":"Brahm, Rafael","last_name":"Brahm"},{"last_name":"Espinoza","first_name":"Nestor","full_name":"Espinoza, Nestor"},{"last_name":"Henning","first_name":"Thomas","full_name":"Henning, Thomas"},{"first_name":"Andrés","full_name":"Jordán, Andrés","last_name":"Jordán"},{"full_name":"Sarkis, Paula","first_name":"Paula","last_name":"Sarkis"},{"first_name":"Emil","full_name":"Knudstrup, Emil","last_name":"Knudstrup"},{"last_name":"Albrecht","first_name":"Simon","full_name":"Albrecht, Simon"},{"last_name":"Grundahl","full_name":"Grundahl, Frank","first_name":"Frank"},{"last_name":"Andersen","first_name":"Mads Fredslund","full_name":"Andersen, Mads Fredslund"},{"last_name":"Pallé","first_name":"Pere L.","full_name":"Pallé, Pere L."},{"first_name":"Ian","full_name":"Crossfield, Ian","last_name":"Crossfield"},{"first_name":"Benjamin","full_name":"Fulton, Benjamin","last_name":"Fulton"},{"last_name":"Howard","first_name":"Andrew W.","full_name":"Howard, Andrew W."},{"last_name":"Isaacson","full_name":"Isaacson, Howard T.","first_name":"Howard T."},{"last_name":"Weiss","full_name":"Weiss, Lauren M.","first_name":"Lauren M."},{"full_name":"Handberg, Rasmus","first_name":"Rasmus","last_name":"Handberg"},{"first_name":"Mikkel N.","full_name":"Lund, Mikkel N.","last_name":"Lund"},{"last_name":"Serenelli","first_name":"Aldo M.","full_name":"Serenelli, Aldo M."},{"first_name":"Jakob","full_name":"Rørsted Mosumgaard, Jakob","last_name":"Rørsted Mosumgaard"},{"last_name":"Stokholm","first_name":"Amalie","full_name":"Stokholm, Amalie"},{"first_name":"Allyson","full_name":"Bieryla, Allyson","last_name":"Bieryla"},{"last_name":"Buchhave","first_name":"Lars A.","full_name":"Buchhave, Lars A."},{"last_name":"Latham","first_name":"David W.","full_name":"Latham, David W."},{"last_name":"Quinn","first_name":"Samuel N.","full_name":"Quinn, Samuel N."},{"last_name":"Gaidos","first_name":"Eric","full_name":"Gaidos, Eric"},{"full_name":"Hirano, Teruyuki","first_name":"Teruyuki","last_name":"Hirano"},{"full_name":"Ricker, George R.","first_name":"George R.","last_name":"Ricker"},{"full_name":"Vanderspek, Roland K.","first_name":"Roland K.","last_name":"Vanderspek"},{"first_name":"Sara","full_name":"Seager, Sara","last_name":"Seager"},{"last_name":"Jenkins","full_name":"Jenkins, Jon M.","first_name":"Jon M."},{"full_name":"Winn, Joshua N.","first_name":"Joshua N.","last_name":"Winn"},{"last_name":"Antia","first_name":"H. M.","full_name":"Antia, H. M."},{"first_name":"Thierry","full_name":"Appourchaux, Thierry","last_name":"Appourchaux"},{"first_name":"Sarbani","full_name":"Basu, Sarbani","last_name":"Basu"},{"first_name":"Keaton J.","full_name":"Bell, Keaton J.","last_name":"Bell"},{"full_name":"Benomar, Othman","first_name":"Othman","last_name":"Benomar"},{"last_name":"Bonanno","first_name":"Alfio","full_name":"Bonanno, Alfio"},{"last_name":"Buzasi","first_name":"Derek L.","full_name":"Buzasi, Derek L."},{"full_name":"Campante, Tiago L.","first_name":"Tiago L.","last_name":"Campante"},{"last_name":"Çelik Orhan","first_name":"Z.","full_name":"Çelik Orhan, Z."},{"full_name":"Corsaro, Enrico","first_name":"Enrico","last_name":"Corsaro"},{"last_name":"Cunha","full_name":"Cunha, Margarida S.","first_name":"Margarida S."},{"full_name":"Davies, Guy R.","first_name":"Guy R.","last_name":"Davies"},{"last_name":"Deheuvels","full_name":"Deheuvels, Sebastien","first_name":"Sebastien"},{"last_name":"Grunblatt","full_name":"Grunblatt, Samuel K.","first_name":"Samuel K."},{"first_name":"Amir","full_name":"Hasanzadeh, Amir","last_name":"Hasanzadeh"},{"last_name":"Di Mauro","full_name":"Di Mauro, Maria Pia","first_name":"Maria Pia"},{"full_name":"A. García, Rafael","first_name":"Rafael","last_name":"A. García"},{"last_name":"Gaulme","full_name":"Gaulme, Patrick","first_name":"Patrick"},{"first_name":"Léo","full_name":"Girardi, Léo","last_name":"Girardi"},{"last_name":"Guzik","full_name":"Guzik, Joyce A.","first_name":"Joyce A."},{"last_name":"Hon","first_name":"Marc","full_name":"Hon, Marc"},{"full_name":"Jiang, Chen","first_name":"Chen","last_name":"Jiang"},{"first_name":"Thomas","full_name":"Kallinger, Thomas","last_name":"Kallinger"},{"full_name":"Kawaler, Steven D.","first_name":"Steven D.","last_name":"Kawaler"},{"first_name":"James S.","full_name":"Kuszlewicz, James S.","last_name":"Kuszlewicz"},{"full_name":"Lebreton, Yveline","first_name":"Yveline","last_name":"Lebreton"},{"last_name":"Li","full_name":"Li, Tanda","first_name":"Tanda"},{"first_name":"Miles","full_name":"Lucas, Miles","last_name":"Lucas"},{"last_name":"Lundkvist","full_name":"Lundkvist, Mia S.","first_name":"Mia S."},{"last_name":"Mann","first_name":"Andrew W.","full_name":"Mann, Andrew W."},{"first_name":"Stéphane","full_name":"Mathis, Stéphane","last_name":"Mathis"},{"last_name":"Mathur","first_name":"Savita","full_name":"Mathur, Savita"},{"first_name":"Anwesh","full_name":"Mazumdar, Anwesh","last_name":"Mazumdar"},{"last_name":"Metcalfe","full_name":"Metcalfe, Travis S.","first_name":"Travis S."},{"full_name":"Miglio, Andrea","first_name":"Andrea","last_name":"Miglio"},{"last_name":"F. G. Monteiro","first_name":"Mário J. P.","full_name":"F. G. Monteiro, Mário J. P."},{"last_name":"Mosser","full_name":"Mosser, Benoit","first_name":"Benoit"},{"last_name":"Noll","full_name":"Noll, Anthony","first_name":"Anthony"},{"last_name":"Nsamba","full_name":"Nsamba, Benard","first_name":"Benard"},{"full_name":"Joel Ong, Jia Mian","first_name":"Jia Mian","last_name":"Joel Ong"},{"last_name":"Örtel","full_name":"Örtel, S.","first_name":"S."},{"full_name":"Pereira, Filipe","first_name":"Filipe","last_name":"Pereira"},{"last_name":"Ranadive","full_name":"Ranadive, Pritesh","first_name":"Pritesh"},{"first_name":"Clara","full_name":"Régulo, Clara","last_name":"Régulo"},{"last_name":"Rodrigues","first_name":"Thaíse S.","full_name":"Rodrigues, Thaíse S."},{"full_name":"Roxburgh, Ian W.","first_name":"Ian W.","last_name":"Roxburgh"},{"last_name":"Aguirre","first_name":"Victor Silva","full_name":"Aguirre, Victor Silva"},{"last_name":"Smalley","full_name":"Smalley, Barry","first_name":"Barry"},{"last_name":"Schofield","first_name":"Mathew","full_name":"Schofield, Mathew"},{"last_name":"Sousa","first_name":"Sérgio G.","full_name":"Sousa, Sérgio G."},{"last_name":"Stassun","first_name":"Keivan G.","full_name":"Stassun, Keivan G."},{"last_name":"Stello","full_name":"Stello, Dennis","first_name":"Dennis"},{"last_name":"Tayar","first_name":"Jamie","full_name":"Tayar, Jamie"},{"last_name":"White","first_name":"Timothy R.","full_name":"White, Timothy R."},{"first_name":"Kuldeep","full_name":"Verma, Kuldeep","last_name":"Verma"},{"last_name":"Vrard","full_name":"Vrard, Mathieu","first_name":"Mathieu"},{"first_name":"M.","full_name":"Yıldız, M.","last_name":"Yıldız"},{"last_name":"Baker","full_name":"Baker, David","first_name":"David"},{"last_name":"Bazot","first_name":"Michaël","full_name":"Bazot, Michaël"},{"last_name":"Beichmann","first_name":"Charles","full_name":"Beichmann, Charles"},{"first_name":"Christoph","full_name":"Bergmann, Christoph","last_name":"Bergmann"},{"id":"d9edb345-f866-11ec-9b37-d119b5234501","last_name":"Bugnet","first_name":"Lisa Annabelle","full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000"},{"last_name":"Cale","full_name":"Cale, Bryson","first_name":"Bryson"},{"last_name":"Carlino","full_name":"Carlino, Roberto","first_name":"Roberto"},{"last_name":"Cartwright","full_name":"Cartwright, Scott M.","first_name":"Scott M."},{"last_name":"Christiansen","first_name":"Jessie L.","full_name":"Christiansen, Jessie L."},{"first_name":"David R.","full_name":"Ciardi, David R.","last_name":"Ciardi"},{"first_name":"Orlagh","full_name":"Creevey, Orlagh","last_name":"Creevey"},{"full_name":"Dittmann, Jason A.","first_name":"Jason A.","last_name":"Dittmann"},{"last_name":"Nascimento","full_name":"Nascimento, Jose-Dias Do","first_name":"Jose-Dias Do"},{"last_name":"Eylen","full_name":"Eylen, Vincent Van","first_name":"Vincent Van"},{"full_name":"Fürész, Gabor","first_name":"Gabor","last_name":"Fürész"},{"last_name":"Gagné","full_name":"Gagné, Jonathan","first_name":"Jonathan"},{"full_name":"Gao, Peter","first_name":"Peter","last_name":"Gao"},{"first_name":"Kosmas","full_name":"Gazeas, Kosmas","last_name":"Gazeas"},{"first_name":"Frank","full_name":"Giddens, Frank","last_name":"Giddens"},{"full_name":"Hall, Oliver J.","first_name":"Oliver J.","last_name":"Hall"},{"first_name":"Saskia","full_name":"Hekker, Saskia","last_name":"Hekker"},{"full_name":"Ireland, Michael J.","first_name":"Michael J.","last_name":"Ireland"},{"last_name":"Latouf","full_name":"Latouf, Natasha","first_name":"Natasha"},{"last_name":"LeBrun","full_name":"LeBrun, Danny","first_name":"Danny"},{"last_name":"Levine","full_name":"Levine, Alan M.","first_name":"Alan M."},{"last_name":"Matzko","full_name":"Matzko, William","first_name":"William"},{"first_name":"Eva","full_name":"Natinsky, Eva","last_name":"Natinsky"},{"full_name":"Page, Emma","first_name":"Emma","last_name":"Page"},{"last_name":"Plavchan","full_name":"Plavchan, Peter","first_name":"Peter"},{"last_name":"Mansouri-Samani","full_name":"Mansouri-Samani, Masoud","first_name":"Masoud"},{"last_name":"McCauliff","full_name":"McCauliff, Sean","first_name":"Sean"},{"full_name":"Mullally, Susan E.","first_name":"Susan E.","last_name":"Mullally"},{"first_name":"Brendan","full_name":"Orenstein, Brendan","last_name":"Orenstein"},{"last_name":"Soto","first_name":"Aylin Garcia","full_name":"Soto, Aylin Garcia"},{"last_name":"Paegert","full_name":"Paegert, Martin","first_name":"Martin"},{"full_name":"van Saders, Jennifer L.","first_name":"Jennifer L.","last_name":"van Saders"},{"full_name":"Schnaible, Chloe","first_name":"Chloe","last_name":"Schnaible"},{"first_name":"David R.","full_name":"Soderblom, David R.","last_name":"Soderblom"},{"last_name":"Szabó","full_name":"Szabó, Róbert","first_name":"Róbert"},{"first_name":"Angelle","full_name":"Tanner, Angelle","last_name":"Tanner"},{"full_name":"Tinney, C. G.","first_name":"C. G.","last_name":"Tinney"},{"last_name":"Teske","first_name":"Johanna","full_name":"Teske, Johanna"},{"last_name":"Thomas","first_name":"Alexandra","full_name":"Thomas, Alexandra"},{"last_name":"Trampedach","first_name":"Regner","full_name":"Trampedach, Regner"},{"last_name":"Wright","full_name":"Wright, Duncan","first_name":"Duncan"},{"last_name":"Yuan","full_name":"Yuan, Thomas T.","first_name":"Thomas T."},{"last_name":"Zohrabi","full_name":"Zohrabi, Farzaneh","first_name":"Farzaneh"}],"publication_status":"published","acknowledgement":"The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Maunakea has always had within the indigenous Hawai'ian community. We are most fortunate to have the opportunity to conduct observations from this mountain. We thank Andrei Tokovinin for helpful information on the Speckle observations obtained with SOAR. D.H. acknowledges support by the National Aeronautics and Space Administration through the TESS Guest Investigator Program (80NSSC18K1585) and by the National Science Foundation (AST-1717000). A.C. acknowledges support by the National Science Foundation under the Graduate Research Fellowship Program. W.J.C., W.H.B., A.M., O.J.H., and G.R.D. acknowledge support from the Science and Technology Facilities Council and UK Space Agency. H.K. and F.G. acknowledge support from the European Social Fund via the Lithuanian Science Council grant No. 09.3.3-LMT-K-712-01-0103. Funding for the Stellar Astrophysics Centre is provided by The Danish National Research Foundation (grant DNRF106). A.J. acknowledges support from FONDECYT project 1171208, CONICYT project BASAL AFB-170002, and by the Ministry for the Economy, Development, and Tourism's Programa Iniciativa Científica Milenio through grant IC 120009, awarded to the Millennium Institute of Astrophysics (MAS). R.B. acknowledges support from FONDECYT Post-doctoral Fellowship Project 3180246, and from the Millennium Institute of Astrophysics (MAS). A.M.S. is supported by grants ESP2017-82674-R (MINECO) and SGR2017-1131 (AGAUR). R.A.G. and L.B. acknowledge the support of the PLATO grant from the CNES. The research leading to the presented results has received funding from the European Research Council under the European Community's Seventh Framework Programme (FP72007-2013)ERC grant agreement No. 338251 (StellarAges). S.M. acknowledges support from the European Research Council through the SPIRE grant 647383. This work was also supported by FCT (Portugal) through national funds and by FEDER through COMPETE2020 by these grants: UID/FIS/04434/2013 and POCI-01-0145-FEDER-007672, PTDC/FIS-AST/30389/2017, and POCI-01-0145-FEDER-030389. T.L.C. acknowledges support from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 792848 (PULSATION). E.C. is funded by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 664931. V.S.A. acknowledges support from the Independent Research Fund Denmark (Research grant 7027-00096B). D.S. acknowledges support from the Australian Research Council. S.B. acknowledges NASA grant NNX16AI09G and NSF grant AST-1514676. T.R.W. acknowledges support from the Australian Research Council through grant DP150100250. A.M. acknowledges support from the ERC Consolidator Grant funding scheme (project ASTEROCHRONOMETRY, G.A. n. 772293). S.M. acknowledges support from the Ramon y Cajal fellowship number RYC-2015-17697. M.S.L. is supported by the Carlsberg Foundation (grant agreement No. CF17-0760). A.M. and P.R. acknowledge support from the HBCSE-NIUS programme. J.K.T. and J.T. acknowledge that support for this work was provided by NASA through Hubble Fellowship grants HST-HF2-51399.001 and HST-HF2-51424.001 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. T.S.R. acknowledges financial support from Premiale 2015 MITiC (PI B. Garilli). This project has been supported by the NKFIH K-115709 grant and the Lendület Program of the Hungarian Academy of Sciences, project No. LP2018-7/2018.\r\n\r\nBased on observations made with the Hertzsprung SONG telescope operated on the Spanish Observatorio del Teide on the island of Tenerife by the Aarhus and Copenhagen Universities and by the Instituto de Astrofísica de Canarias. Funding for the TESS mission is provided by NASA's Science Mission directorate. We acknowledge the use of public TESS Alert data from pipelines at the TESS Science Office and at the TESS Science Processing Operations Center. This research has made use of the Exoplanet Follow-up Observation Program website, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program. This paper includes data collected by the TESS mission, which are publicly available from the Mikulski Archive for Space Telescopes (MAST).\r\n\r\nSoftware: Astropy (Astropy Collaboration et al. 2018), Matplotlib (Hunter 2007), DIAMONDS (Corsaro & De Ridder 2014), isoclassify (Huber et al. 2017), EXOFASTv2 (Eastman 2017), ktransit (Barclay 2018).","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.01643"}],"month":"05","date_updated":"2022-08-22T07:38:34Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"oa_version":"Preprint","oa":1,"article_type":"original","volume":157,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Huber, D., Chaplin, W. J., Chontos, A., Kjeldsen, H., Christensen-Dalsgaard, J., Bedding, T. R., … Zohrabi, F. (2019). A hot Saturn orbiting an oscillating late subgiant discovered by TESS. <i>The Astronomical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-3881/ab1488\">https://doi.org/10.3847/1538-3881/ab1488</a>","ieee":"D. Huber <i>et al.</i>, “A hot Saturn orbiting an oscillating late subgiant discovered by TESS,” <i>The Astronomical Journal</i>, vol. 157, no. 6. IOP Publishing, 2019.","chicago":"Huber, Daniel, William J. Chaplin, Ashley Chontos, Hans Kjeldsen, Jørgen Christensen-Dalsgaard, Timothy R. Bedding, Warrick Ball, et al. “A Hot Saturn Orbiting an Oscillating Late Subgiant Discovered by TESS.” <i>The Astronomical Journal</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.3847/1538-3881/ab1488\">https://doi.org/10.3847/1538-3881/ab1488</a>.","short":"D. Huber, W.J. Chaplin, A. Chontos, H. Kjeldsen, J. Christensen-Dalsgaard, T.R. Bedding, W. Ball, R. Brahm, N. Espinoza, T. Henning, A. Jordán, P. Sarkis, E. Knudstrup, S. Albrecht, F. Grundahl, M.F. Andersen, P.L. Pallé, I. Crossfield, B. Fulton, A.W. Howard, H.T. Isaacson, L.M. Weiss, R. Handberg, M.N. Lund, A.M. Serenelli, J. Rørsted Mosumgaard, A. Stokholm, A. Bieryla, L.A. Buchhave, D.W. Latham, S.N. Quinn, E. Gaidos, T. Hirano, G.R. Ricker, R.K. Vanderspek, S. Seager, J.M. Jenkins, J.N. Winn, H.M. Antia, T. Appourchaux, S. Basu, K.J. Bell, O. Benomar, A. Bonanno, D.L. Buzasi, T.L. Campante, Z. Çelik Orhan, E. Corsaro, M.S. Cunha, G.R. Davies, S. Deheuvels, S.K. Grunblatt, A. Hasanzadeh, M.P. Di Mauro, R. A. García, P. Gaulme, L. Girardi, J.A. Guzik, M. Hon, C. Jiang, T. Kallinger, S.D. Kawaler, J.S. Kuszlewicz, Y. Lebreton, T. Li, M. Lucas, M.S. Lundkvist, A.W. Mann, S. Mathis, S. Mathur, A. Mazumdar, T.S. Metcalfe, A. Miglio, M.J.P. F. G. Monteiro, B. Mosser, A. Noll, B. Nsamba, J.M. Joel Ong, S. Örtel, F. Pereira, P. Ranadive, C. Régulo, T.S. Rodrigues, I.W. Roxburgh, V.S. Aguirre, B. Smalley, M. Schofield, S.G. Sousa, K.G. Stassun, D. Stello, J. Tayar, T.R. White, K. Verma, M. Vrard, M. Yıldız, D. Baker, M. Bazot, C. Beichmann, C. Bergmann, L.A. Bugnet, B. Cale, R. Carlino, S.M. Cartwright, J.L. Christiansen, D.R. Ciardi, O. Creevey, J.A. Dittmann, J.-D.D. Nascimento, V.V. Eylen, G. Fürész, J. Gagné, P. Gao, K. Gazeas, F. Giddens, O.J. Hall, S. Hekker, M.J. Ireland, N. Latouf, D. LeBrun, A.M. Levine, W. Matzko, E. Natinsky, E. Page, P. Plavchan, M. Mansouri-Samani, S. McCauliff, S.E. Mullally, B. Orenstein, A.G. Soto, M. Paegert, J.L. van Saders, C. Schnaible, D.R. Soderblom, R. Szabó, A. Tanner, C.G. Tinney, J. Teske, A. Thomas, R. Trampedach, D. Wright, T.T. Yuan, F. Zohrabi, The Astronomical Journal 157 (2019).","ista":"Huber D et al. 2019. A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. 157(6), 245.","mla":"Huber, Daniel, et al. “A Hot Saturn Orbiting an Oscillating Late Subgiant Discovered by TESS.” <i>The Astronomical Journal</i>, vol. 157, no. 6, 245, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.3847/1538-3881/ab1488\">10.3847/1538-3881/ab1488</a>.","ama":"Huber D, Chaplin WJ, Chontos A, et al. A hot Saturn orbiting an oscillating late subgiant discovered by TESS. <i>The Astronomical Journal</i>. 2019;157(6). doi:<a href=\"https://doi.org/10.3847/1538-3881/ab1488\">10.3847/1538-3881/ab1488</a>"},"scopus_import":"1","quality_controlled":"1","date_created":"2022-07-18T14:29:07Z","title":"A hot Saturn orbiting an oscillating late subgiant discovered by TESS","publication":"The Astronomical Journal","language":[{"iso":"eng"}],"issue":"6","type":"journal_article","year":"2019","article_number":"245","date_published":"2019-05-30T00:00:00Z","arxiv":1,"intvolume":"       157","publication_identifier":{"issn":["0004-6256"]}},{"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.ICALP.2019.13"}],"date_updated":"2024-11-06T11:56:23Z","month":"07","abstract":[{"lang":"eng","text":"The diameter, radius and eccentricities are natural graph parameters. While these problems have been studied extensively, there are no known dynamic algorithms for them beyond the ones that follow from trivial recomputation after each update or from solving dynamic All-Pairs Shortest Paths (APSP), which is very computationally intensive. This is the situation for dynamic approximation algorithms as well, and even if only edge insertions or edge deletions need to be supported.\r\nThis paper provides a comprehensive study of the dynamic approximation of Diameter, Radius and Eccentricities, providing both conditional lower bounds, and new algorithms whose bounds are optimal under popular hypotheses in fine-grained complexity. Some of the highlights include:\r\n- Under popular hardness hypotheses, there can be no significantly better fully dynamic approximation algorithms than recomputing the answer after each update, or maintaining full APSP.\r\n- Nearly optimal partially dynamic (incremental/decremental) algorithms can be achieved via efficient reductions to (incremental/decremental) maintenance of Single-Source Shortest Paths. For instance, a nearly (3/2+epsilon)-approximation to Diameter in directed or undirected n-vertex, m-edge graphs can be maintained decrementally in total time m^{1+o(1)}sqrt{n}/epsilon^2. This nearly matches the static 3/2-approximation algorithm for the problem that is known to be conditionally optimal."}],"article_processing_charge":"No","doi":"10.4230/LIPICS.ICALP.2019.13","extern":"1","_id":"11826","author":[{"full_name":"Ancona, Bertie","first_name":"Bertie","last_name":"Ancona"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"last_name":"Roditty","full_name":"Roditty, Liam","first_name":"Liam"},{"first_name":"Virginia Vassilevska","full_name":"Williams, Virginia Vassilevska","last_name":"Williams"},{"last_name":"Wein","first_name":"Nicole","full_name":"Wein, Nicole"}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","external_id":{"arxiv":["811.12527"]},"conference":{"end_date":"2019-07-12","start_date":"2019-07-09","location":"Patras, Greece","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"day":"04","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-109-2"]},"arxiv":1,"date_published":"2019-07-04T00:00:00Z","article_number":"13","alternative_title":["LIPIcs"],"intvolume":"       132","language":[{"iso":"eng"}],"title":"Algorithms and hardness for diameter in dynamic graphs","publication":"46th International Colloquium on Automata, Languages, and Programming","type":"conference","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Ancona B, Henzinger M, Roditty L, Williams VV, Wein N. Algorithms and hardness for diameter in dynamic graphs. In: <i>46th International Colloquium on Automata, Languages, and Programming</i>. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.ICALP.2019.13\">10.4230/LIPICS.ICALP.2019.13</a>","mla":"Ancona, Bertie, et al. “Algorithms and Hardness for Diameter in Dynamic Graphs.” <i>46th International Colloquium on Automata, Languages, and Programming</i>, vol. 132, 13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.ICALP.2019.13\">10.4230/LIPICS.ICALP.2019.13</a>.","short":"B. Ancona, M. Henzinger, L. Roditty, V.V. Williams, N. Wein, in:, 46th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","ista":"Ancona B, Henzinger M, Roditty L, Williams VV, Wein N. 2019. Algorithms and hardness for diameter in dynamic graphs. 46th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 132, 13.","chicago":"Ancona, Bertie, Monika Henzinger, Liam Roditty, Virginia Vassilevska Williams, and Nicole Wein. “Algorithms and Hardness for Diameter in Dynamic Graphs.” In <i>46th International Colloquium on Automata, Languages, and Programming</i>, Vol. 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.ICALP.2019.13\">https://doi.org/10.4230/LIPICS.ICALP.2019.13</a>.","ieee":"B. Ancona, M. Henzinger, L. Roditty, V. V. Williams, and N. Wein, “Algorithms and hardness for diameter in dynamic graphs,” in <i>46th International Colloquium on Automata, Languages, and Programming</i>, Patras, Greece, 2019, vol. 132.","apa":"Ancona, B., Henzinger, M., Roditty, L., Williams, V. V., &#38; Wein, N. (2019). Algorithms and hardness for diameter in dynamic graphs. In <i>46th International Colloquium on Automata, Languages, and Programming</i> (Vol. 132). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ICALP.2019.13\">https://doi.org/10.4230/LIPICS.ICALP.2019.13</a>"},"volume":132,"status":"public","date_created":"2022-08-12T08:14:51Z","quality_controlled":"1","scopus_import":"1"},{"oa_version":"Preprint","month":"05","date_updated":"2024-11-06T12:17:43Z","main_file_link":[{"url":"https://arxiv.org/abs/1808.05458"}],"day":"01","conference":{"end_date":"2019-05-24","start_date":"2019-05-20","location":"Rio de Janeiro, Brazil","name":"IPDPS: International Parallel and Distributed Processing Symposium"},"extern":"1","publication_status":"published","author":[{"first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"first_name":"Alexander","full_name":"Noe, Alexander","last_name":"Noe"},{"full_name":"Schulz, Christian","first_name":"Christian","last_name":"Schulz"}],"publisher":"Institute of Electrical and Electronics Engineers","_id":"11851","external_id":{"arxiv":["1808.05458"]},"abstract":[{"text":"The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weighted sum of the cut edges. In this paper, we engineer the fastest known exact algorithm for the problem. State-of-the-art algorithms like the algorithm of Padberg and Rinaldi or the algorithm of Nagamochi, Ono and Ibaraki identify edges that can be contracted to reduce the graph size such that at least one minimum cut is maintained in the contracted graph. Our algorithm achieves improvements in running time over these algorithms by a multitude of techniques. First, we use a recently developed fast and parallel inexact minimum cut algorithm to obtain a better bound for the problem. Afterwards, we use reductions that depend on this bound to reduce the size of the graph much faster than previously possible. We use improved data structures to further lower the running time of our algorithm. Additionally, we parallelize the contraction routines of Nagamochi et al. . Overall, we arrive at a system that significantly outperforms the fastest state-of-the-art solvers for the exact minimum cut problem.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1109/ipdps.2019.00013","publication_identifier":{"isbn":["978-1-7281-1247-3"],"eisbn":["978-1-7281-1246-6"],"eissn":["1530-2075"]},"date_published":"2019-05-01T00:00:00Z","article_number":"8820968","arxiv":1,"year":"2019","type":"conference","title":"Shared-memory exact minimum cuts","publication":"33rd International Parallel and Distributed Processing Symposium","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"11851"}]},"quality_controlled":"1","scopus_import":"1","date_created":"2022-08-16T07:25:23Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Henzinger, Monika, Alexander Noe, and Christian Schulz. “Shared-Memory Exact Minimum Cuts.” In <i>33rd International Parallel and Distributed Processing Symposium</i>. Institute of Electrical and Electronics Engineers, 2019. <a href=\"https://doi.org/10.1109/ipdps.2019.00013\">https://doi.org/10.1109/ipdps.2019.00013</a>.","ieee":"M. Henzinger, A. Noe, and C. Schulz, “Shared-memory exact minimum cuts,” in <i>33rd International Parallel and Distributed Processing Symposium</i>, Rio de Janeiro, Brazil, 2019.","apa":"Henzinger, M., Noe, A., &#38; Schulz, C. (2019). Shared-memory exact minimum cuts. In <i>33rd International Parallel and Distributed Processing Symposium</i>. Rio de Janeiro, Brazil: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/ipdps.2019.00013\">https://doi.org/10.1109/ipdps.2019.00013</a>","ama":"Henzinger M, Noe A, Schulz C. Shared-memory exact minimum cuts. In: <i>33rd International Parallel and Distributed Processing Symposium</i>. Institute of Electrical and Electronics Engineers; 2019. doi:<a href=\"https://doi.org/10.1109/ipdps.2019.00013\">10.1109/ipdps.2019.00013</a>","mla":"Henzinger, Monika, et al. “Shared-Memory Exact Minimum Cuts.” <i>33rd International Parallel and Distributed Processing Symposium</i>, 8820968, Institute of Electrical and Electronics Engineers, 2019, doi:<a href=\"https://doi.org/10.1109/ipdps.2019.00013\">10.1109/ipdps.2019.00013</a>.","ista":"Henzinger M, Noe A, Schulz C. 2019. Shared-memory exact minimum cuts. 33rd International Parallel and Distributed Processing Symposium. IPDPS: International Parallel and Distributed Processing Symposium, 8820968.","short":"M. Henzinger, A. Noe, C. Schulz, in:, 33rd International Parallel and Distributed Processing Symposium, Institute of Electrical and Electronics Engineers, 2019."}},{"article_processing_charge":"No","abstract":[{"text":"We present a deterministic dynamic algorithm for maintaining a (1+ε)f-approximate minimum cost set cover with O(f log(Cn)/ε^2) amortized update time, when the input set system is undergoing element insertions and deletions. Here, n denotes the number of elements, each element appears in at most f sets, and the cost of each set lies in the range [1/C, 1]. Our result, together with that of Gupta~et~al.~[STOC'17], implies that there is a deterministic algorithm for this problem with O(f log(Cn)) amortized update time and O(min(log n, f)) -approximation ratio, which nearly matches the polynomial-time hardness of approximation for minimum set cover in the static setting. Our update time is only O(log (Cn)) away from a trivial lower bound. Prior to our work, the previous best approximation ratio guaranteed by deterministic algorithms was O(f^2), which was due to Bhattacharya~et~al.~[ICALP`15]. In contrast, the only result that guaranteed O(f) -approximation was obtained very recently by Abboud~et~al.~[STOC`19], who designed a dynamic algorithm with (1+ε)f-approximation ratio and O(f^2 log n/ε) amortized update time. Besides the extra O(f) factor in the update time compared to our and Gupta~et~al.'s results, the Abboud~et~al.~algorithm is randomized, and works only when the adversary is oblivious and the sets are unweighted (each set has the same cost). We achieve our result via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. This approach was pursued previously by Bhattacharya~et~al.~and Gupta~et~al., but not in the recent paper by Abboud~et~al. Unlike previous primal-dual algorithms that try to satisfy some local constraints for individual sets at all time, our algorithm basically waits until the dual solution changes significantly globally, and fixes the solution only where the fix is needed.","lang":"eng"}],"doi":"10.1109/focs.2019.00033","extern":"1","publisher":"Institute of Electrical and Electronics Engineers","external_id":{"arxiv":["1909.11600"]},"author":[{"first_name":"Sayan","full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"full_name":"Nanongkai, Danupon","first_name":"Danupon","last_name":"Nanongkai"}],"publication_status":"published","_id":"11853","conference":{"end_date":"2019-11-12","name":"FOCS: Annual Symposium on Foundations of Computer Science","start_date":"2019-11-09","location":"Baltimore, MD, United States"},"day":"01","oa_version":"Preprint","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1909.11600","open_access":"1"}],"date_updated":"2024-11-06T12:18:05Z","month":"11","language":[{"iso":"eng"}],"title":"A new deterministic algorithm for dynamic set cover","publication":"60th Annual Symposium on Foundations of Computer Science","type":"conference","year":"2019","citation":{"ama":"Bhattacharya S, Henzinger M, Nanongkai D. A new deterministic algorithm for dynamic set cover. In: <i>60th Annual Symposium on Foundations of Computer Science</i>. Institute of Electrical and Electronics Engineers; 2019:406-423. doi:<a href=\"https://doi.org/10.1109/focs.2019.00033\">10.1109/focs.2019.00033</a>","mla":"Bhattacharya, Sayan, et al. “A New Deterministic Algorithm for Dynamic Set Cover.” <i>60th Annual Symposium on Foundations of Computer Science</i>, Institute of Electrical and Electronics Engineers, 2019, pp. 406–23, doi:<a href=\"https://doi.org/10.1109/focs.2019.00033\">10.1109/focs.2019.00033</a>.","ista":"Bhattacharya S, Henzinger M, Nanongkai D. 2019. A new deterministic algorithm for dynamic set cover. 60th Annual Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations of Computer Science, 406–423.","short":"S. Bhattacharya, M. Henzinger, D. Nanongkai, in:, 60th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2019, pp. 406–423.","chicago":"Bhattacharya, Sayan, Monika Henzinger, and Danupon Nanongkai. “A New Deterministic Algorithm for Dynamic Set Cover.” In <i>60th Annual Symposium on Foundations of Computer Science</i>, 406–23. Institute of Electrical and Electronics Engineers, 2019. <a href=\"https://doi.org/10.1109/focs.2019.00033\">https://doi.org/10.1109/focs.2019.00033</a>.","ieee":"S. Bhattacharya, M. Henzinger, and D. Nanongkai, “A new deterministic algorithm for dynamic set cover,” in <i>60th Annual Symposium on Foundations of Computer Science</i>, Baltimore, MD, United States, 2019, pp. 406–423.","apa":"Bhattacharya, S., Henzinger, M., &#38; Nanongkai, D. (2019). A new deterministic algorithm for dynamic set cover. In <i>60th Annual Symposium on Foundations of Computer Science</i> (pp. 406–423). Baltimore, MD, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/focs.2019.00033\">https://doi.org/10.1109/focs.2019.00033</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_created":"2022-08-16T08:00:00Z","quality_controlled":"1","scopus_import":"1","publication_identifier":{"eisbn":["978-1-7281-4952-3"],"issn":["2575-8454"],"isbn":["978-1-7281-4953-0"]},"page":"406-423","arxiv":1,"date_published":"2019-11-01T00:00:00Z"}]