[{"quality_controlled":"1","publisher":"Springer Nature","oa_version":"Preprint","date_updated":"2025-09-10T09:35:56Z","language":[{"iso":"eng"}],"arxiv":1,"_id":"11185","abstract":[{"lang":"eng","text":"Bundling crossings is a strategy which can enhance the readability of graph drawings. In this paper we consider bundlings for families of pseudosegments, i.e., simple curves such that any two have share at most one point at which they cross. Our main result is that there is a polynomial-time algorithm to compute an 8-approximation of the bundled crossing number of such instances (up to adding a term depending on the facial structure). This 8-approximation also holds for bundlings of good drawings of graphs. In the special case of circular drawings the approximation factor is 8 (no extra term), this improves upon the 10-approximation of Fink et al. [6]. We also show how to compute a 92-approximation when the intersection graph of the pseudosegments is bipartite."}],"oa":1,"conference":{"start_date":"2022-03-24","name":"WALCOM: Algorithms and Computation","end_date":"2022-03-26","location":"Jember, Indonesia"},"page":"383-395","related_material":{"record":[{"relation":"later_version","id":"13969","status":"public"}]},"type":"conference","citation":{"apa":"Arroyo Guevara, A. M., &#38; Felsner, S. (2022). Approximating the bundled crossing number. In <i>WALCOM 2022: Algorithms and Computation</i> (Vol. 13174, pp. 383–395). Jember, Indonesia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">https://doi.org/10.1007/978-3-030-96731-4_31</a>","short":"A.M. Arroyo Guevara, S. Felsner, in:, WALCOM 2022: Algorithms and Computation, Springer Nature, 2022, pp. 383–395.","ista":"Arroyo Guevara AM, Felsner S. 2022. Approximating the bundled crossing number. WALCOM 2022: Algorithms and Computation. WALCOM: Algorithms and ComputationLNCS vol. 13174, 383–395.","chicago":"Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled Crossing Number.” In <i>WALCOM 2022: Algorithms and Computation</i>, 13174:383–95. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">https://doi.org/10.1007/978-3-030-96731-4_31</a>.","ama":"Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. In: <i>WALCOM 2022: Algorithms and Computation</i>. Vol 13174. LNCS. Springer Nature; 2022:383-395. doi:<a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">10.1007/978-3-030-96731-4_31</a>","mla":"Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing Number.” <i>WALCOM 2022: Algorithms and Computation</i>, vol. 13174, Springer Nature, 2022, pp. 383–95, doi:<a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">10.1007/978-3-030-96731-4_31</a>.","ieee":"A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,” in <i>WALCOM 2022: Algorithms and Computation</i>, Jember, Indonesia, 2022, vol. 13174, pp. 383–395."},"month":"03","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783030967307"]},"day":"16","isi":1,"status":"public","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.14892"}],"external_id":{"isi":["001435074700031"],"arxiv":["2109.14892"]},"series_title":"LNCS","publication_status":"published","article_processing_charge":"No","department":[{"_id":"UlWa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1007/978-3-030-96731-4_31","acknowledgement":"This work was initiated during the Workshop on Geometric Graphs in November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during the workshop. The first author has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie grant agreement No 754411. The second author has been supported by the German Research Foundation DFG Project FE 340/12-1.","intvolume":"     13174","publication":"WALCOM 2022: Algorithms and Computation","year":"2022","scopus_import":"1","volume":13174,"date_published":"2022-03-16T00:00:00Z","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"ec_funded":1,"date_created":"2022-04-17T22:01:47Z","title":"Approximating the bundled crossing number","author":[{"first_name":"Alan M","full_name":"Arroyo Guevara, Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","last_name":"Arroyo Guevara","orcid":"0000-0003-2401-8670"},{"last_name":"Felsner","full_name":"Felsner, Stefan","first_name":"Stefan"}]},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2023-08-03T06:45:26Z","language":[{"iso":"eng"}],"publisher":"Springer Nature","quality_controlled":"1","oa_version":"Published Version","oa":1,"type":"journal_article","citation":{"short":"G. Glover, M. Voliotis, U. Łapińska, B.M. Invergo, D. Soanes, P. O’Neill, K. Moore, N. Nikolic, P. Petrov, D.S. Milner, S. Roy, K. Heesom, T.A. Richards, K. Tsaneva-Atanasova, S. Pagliara, Communications Biology 5 (2022).","apa":"Glover, G., Voliotis, M., Łapińska, U., Invergo, B. M., Soanes, D., O’Neill, P., … Pagliara, S. (2022). Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03336-6\">https://doi.org/10.1038/s42003-022-03336-6</a>","ama":"Glover G, Voliotis M, Łapińska U, et al. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. <i>Communications Biology</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42003-022-03336-6\">10.1038/s42003-022-03336-6</a>","ista":"Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O’Neill P, Moore K, Nikolic N, Petrov P, Milner DS, Roy S, Heesom K, Richards TA, Tsaneva-Atanasova K, Pagliara S. 2022. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Communications Biology. 5, 385.","chicago":"Glover, Georgina, Margaritis Voliotis, Urszula Łapińska, Brandon M. Invergo, Darren Soanes, Paul O’Neill, Karen Moore, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03336-6\">https://doi.org/10.1038/s42003-022-03336-6</a>.","mla":"Glover, Georgina, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.” <i>Communications Biology</i>, vol. 5, 385, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03336-6\">10.1038/s42003-022-03336-6</a>.","ieee":"G. Glover <i>et al.</i>, “Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells,” <i>Communications Biology</i>, vol. 5. Springer Nature, 2022."},"month":"04","_id":"11339","abstract":[{"lang":"eng","text":"The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role."}],"license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","external_id":{"pmid":["35444215"],"isi":["000784143400001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CaGu"}],"publication_identifier":{"eissn":["2399-3642"]},"day":"20","isi":1,"has_accepted_license":"1","status":"public","file_date_updated":"2022-05-02T06:26:26Z","date_created":"2022-05-01T22:01:41Z","article_number":"385","author":[{"first_name":"Georgina","full_name":"Glover, Georgina","last_name":"Glover"},{"full_name":"Voliotis, Margaritis","first_name":"Margaritis","last_name":"Voliotis"},{"full_name":"Łapińska, Urszula","first_name":"Urszula","last_name":"Łapińska"},{"last_name":"Invergo","full_name":"Invergo, Brandon M.","first_name":"Brandon M."},{"first_name":"Darren","full_name":"Soanes, Darren","last_name":"Soanes"},{"last_name":"O’Neill","first_name":"Paul","full_name":"O’Neill, Paul"},{"last_name":"Moore","first_name":"Karen","full_name":"Moore, Karen"},{"full_name":"Nikolic, Nela","first_name":"Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","full_name":"Petrov, Peter","last_name":"Petrov"},{"first_name":"David S.","full_name":"Milner, David S.","last_name":"Milner"},{"full_name":"Roy, Sumita","first_name":"Sumita","last_name":"Roy"},{"last_name":"Heesom","first_name":"Kate","full_name":"Heesom, Kate"},{"full_name":"Richards, Thomas A.","first_name":"Thomas A.","last_name":"Richards"},{"full_name":"Tsaneva-Atanasova, Krasimira","first_name":"Krasimira","last_name":"Tsaneva-Atanasova"},{"last_name":"Pagliara","full_name":"Pagliara, Stefano","first_name":"Stefano"}],"title":"Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells","file":[{"creator":"dernst","date_created":"2022-05-02T06:26:26Z","file_size":2827723,"relation":"main_file","date_updated":"2022-05-02T06:26:26Z","checksum":"7c6f76ab17393d650825cc240edc84b3","content_type":"application/pdf","file_id":"11342","success":1,"access_level":"open_access","file_name":"2022_CommBiology_Glover.pdf"}],"date_published":"2022-04-20T00:00:00Z","article_type":"original","pmid":1,"scopus_import":"1","year":"2022","publication":"Communications Biology","volume":5,"acknowledgement":"G.G. was supported by an EPSRC DTP PhD studentship (EP/M506527/1). M.V. and K.T.A. gratefully acknowledge financial support from the EPSRC (EP/N014391/1). U.L. was supported through a BBSRC grant (BB/V008021/1) and an MRC Proximity to Discovery EXCITEME2 grant (MCPC17189). This work was further supported by a Royal Society Research Grant (RG180007) awarded to S.P. and a QUEX Initiator grant awarded to S.P. and K.T.A.. D.S.M., T.A.R. and S.P.’s work in this area is also supported by a Marie Skłodowska-Curie project SINGEK (H2020-MSCA-ITN-2015-675752) and the Gordon and Betty Moore Foundation Marine Microbiology Initiative (GBMF5514). B.M.I. acknowledges support from a Wellcome Trust Institutional Strategic Support Award to the University of Exeter (204909/Z/16/Z). This project utilised equipment funded by the Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome Trust Multi User Equipment Award (WT101650MA) and BBSRC LOLA award (BB/K003240/1).","doi":"10.1038/s42003-022-03336-6","ddc":["570"],"intvolume":"         5"},{"oa_version":"None","corr_author":"1","publisher":"Springer Nature","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:02:30Z","alternative_title":["LNCS"],"status":"public","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783031062452"],"isbn":["9783031062445"]},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"HeEd"}],"publication_status":"published","intvolume":"     13238","doi":"10.1007/978-3-031-06245-2","volume":13238,"year":"2022","edition":"1","abstract":[{"text":"This book constitutes the refereed proceedings of the 18th International Symposium on Web and Wireless Geographical Information Systems, W2GIS 2022, held in Konstanz, Germany, in April 2022.\r\nThe 7 full papers presented together with 6 short papers in the volume were carefully reviewed and selected from 16 submissions.  The papers cover topics that range from mobile GIS and Location-Based Services to Spatial Information Retrieval and Wireless Sensor Networks.","lang":"eng"}],"_id":"11429","date_published":"2022-05-01T00:00:00Z","month":"05","citation":{"chicago":"Karimipour, Farid, and Sabine Storandt, eds. <i>Web and Wireless Geographical Information Systems</i>. 1st ed. Vol. 13238. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>.","ista":"Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information Systems 1st ed., Cham: Springer Nature, 153p.","ama":"Karimipour F, Storandt S, eds. <i>Web and Wireless Geographical Information Systems</i>. Vol 13238. 1st ed. Cham: Springer Nature; 2022. doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>","apa":"Karimipour, F., &#38; Storandt, S. (Eds.). (2022). <i>Web and Wireless Geographical Information Systems</i> (1st ed., Vol. 13238). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>","short":"F. Karimipour, S. Storandt, eds., Web and Wireless Geographical Information Systems, 1st ed., Springer Nature, Cham, 2022.","ieee":"F. Karimipour and S. Storandt, Eds., <i>Web and Wireless Geographical Information Systems</i>, 1st ed., vol. 13238. Cham: Springer Nature, 2022.","mla":"Karimipour, Farid, and Sabine Storandt, editors. <i>Web and Wireless Geographical Information Systems</i>. 1st ed., vol. 13238, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>."},"type":"book_editor","place":"Cham","date_created":"2022-06-02T05:40:53Z","title":"Web and Wireless Geographical Information Systems","page":"153","editor":[{"first_name":"Farid","full_name":"Karimipour, Farid","last_name":"Karimipour","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","orcid":"0000-0001-6746-4174"},{"last_name":"Storandt","full_name":"Storandt, Sabine","first_name":"Sabine"}]},{"oa_version":"Preprint","publisher":"Cold Spring Harbor Laboratory","language":[{"iso":"eng"}],"date_updated":"2024-06-04T06:58:41Z","main_file_link":[{"url":"https://doi.org/10.1101/2022.06.13.496011","open_access":"1"}],"status":"public","day":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","extern":"1","publication_status":"submitted","doi":"10.1101/2022.06.13.496011","publication":"bioRxiv","year":"2022","abstract":[{"lang":"eng","text":"CRISPR (Clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems are a type of adaptive immune response in bacteria and archaea that utilize crRNA (CRISPR RNA)-guided effector complexes to target complementary RNA or DNA for destruction. The prototypical type III-A and III-B CRISPR-Cas systems utilize multi-subunit effector complexes composed of individual proteins to cleave ssRNA targets at 6-nt intervals, as well as non-specifically degrading ssDNA and activating cyclic oligoadenylate (cOA) synthesis. Recent studies have shown that type III systems can contain subunit fusions yet maintain canonical type III RNA-targeting capabilities. To understand how a multi-subunit fusion effector functions, we determine structures of a variant type III-D effector and biochemically characterize how it cleaves RNA targets. These findings provide insights into how multi-subunit fusion proteins are tethered together and assemble into an active and programmable RNA endonuclease, how the effector utilizes a novel mechanism for target RNA seeding, and the structural basis for the evolution of type III effector complexes. Furthermore, our results provide a blueprint for fusing subunits in class 1 effectors for design of user-defined effector complexes with disparate activities.</jats:p><jats:sec><jats:title>Important note</jats:title><jats:p>While this manuscript was in preparation, a manuscript describing the structure of the type III-E effector was published<jats:sup>1</jats:sup>. We reference these important findings; however, a careful comparison of the structures will follow once the coordinates have been released by the PDB."}],"_id":"17116","date_published":"2022-06-14T00:00:00Z","citation":{"ama":"Schwartz EA, Bravo JPK, Macias LA, et al. Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.06.13.496011\">10.1101/2022.06.13.496011</a>","ista":"Schwartz EA, Bravo JPK, Macias LA, McCafferty CL, Dangerfield TL, Walker JN, Brodbelt JS, Fineran PC, Fagerlund RD, Taylor DW. Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex. bioRxiv, <a href=\"https://doi.org/10.1101/2022.06.13.496011\">10.1101/2022.06.13.496011</a>.","chicago":"Schwartz, Evan A., Jack Peter Kelly Bravo, Luis A. Macias, Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, Jennifer S. Brodbelt, Peter C. Fineran, Robert D. Fagerlund, and David W. Taylor. “Assembly of Multi-Subunit Fusion Proteins into the RNA-Targeting Type III-D CRISPR-Cas Effector Complex.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.06.13.496011\">https://doi.org/10.1101/2022.06.13.496011</a>.","short":"E.A. Schwartz, J.P.K. Bravo, L.A. Macias, C.L. McCafferty, T.L. Dangerfield, J.N. Walker, J.S. Brodbelt, P.C. Fineran, R.D. Fagerlund, D.W. Taylor, BioRxiv (n.d.).","apa":"Schwartz, E. A., Bravo, J. P. K., Macias, L. A., McCafferty, C. L., Dangerfield, T. L., Walker, J. N., … Taylor, D. W. (n.d.). Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.06.13.496011\">https://doi.org/10.1101/2022.06.13.496011</a>","ieee":"E. A. Schwartz <i>et al.</i>, “Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","mla":"Schwartz, Evan A., et al. “Assembly of Multi-Subunit Fusion Proteins into the RNA-Targeting Type III-D CRISPR-Cas Effector Complex.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.06.13.496011\">10.1101/2022.06.13.496011</a>."},"month":"06","type":"preprint","title":"Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex","author":[{"last_name":"Schwartz","first_name":"Evan A.","full_name":"Schwartz, Evan A."},{"first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753"},{"last_name":"Macias","first_name":"Luis A.","full_name":"Macias, Luis A."},{"last_name":"McCafferty","first_name":"Caitlyn L.","full_name":"McCafferty, Caitlyn L."},{"last_name":"Dangerfield","first_name":"Tyler L.","full_name":"Dangerfield, Tyler L."},{"last_name":"Walker","first_name":"Jada N.","full_name":"Walker, Jada N."},{"last_name":"Brodbelt","full_name":"Brodbelt, Jennifer S.","first_name":"Jennifer S."},{"last_name":"Fineran","first_name":"Peter C.","full_name":"Fineran, Peter C."},{"last_name":"Fagerlund","full_name":"Fagerlund, Robert D.","first_name":"Robert D."},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"date_created":"2024-06-04T06:44:16Z","oa":1},{"publication_identifier":{"issn":["0004-637X","1538-4357"]},"day":"23","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3847/1538-4357/ac7daa"}],"publication_status":"published","extern":"1","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2022-08-23T00:00:00Z","article_type":"original","title":"Supercritical growth pathway to overmassive black holes at cosmic dawn: Coevolution with massive quasar hosts","date_created":"2024-09-05T12:00:42Z","article_number":"140","author":[{"last_name":"Hu","full_name":"Hu, Haojie","first_name":"Haojie"},{"full_name":"Inayoshi, Kohei","first_name":"Kohei","last_name":"Inayoshi"},{"full_name":"Haiman, Zoltán","first_name":"Zoltán","last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"},{"last_name":"Li","full_name":"Li, Wenxiu","first_name":"Wenxiu"},{"last_name":"Quataert","full_name":"Quataert, Eliot","first_name":"Eliot"},{"first_name":"Rolf","full_name":"Kuiper, Rolf","last_name":"Kuiper"}],"issue":"2","doi":"10.3847/1538-4357/ac7daa","intvolume":"       935","publication":"The Astrophysical Journal","year":"2022","scopus_import":"1","volume":935,"quality_controlled":"1","publisher":"American Astronomical Society","oa_version":"Published Version","date_updated":"2024-09-18T12:31:26Z","language":[{"iso":"eng"}],"_id":"17560","abstract":[{"text":"Observations of the most luminous quasars at high redshifts (z>6) have revealed that the largest supermassive black holes (SMBHs) at those epochs tend to be substantially overmassive relative to their host galaxies compared to the local relations, suggesting they experienced rapid early growth phases. We propose an assembly model for the SMBHs that end up in rare massive ∼1012 M⊙ host halos at z∼6−7, applying a kinetic feedback prescription for BHs accreting above the Eddington rate, provided by radiation hydrodynamic simulations for the long-term evolution of the accretion-flow structure. The large inflow rates into these halos during their assembly enable the formation of >109 M⊙ SMBHs by z∼6, even starting from stellar-mass seeds at z∼30, and even in the presence of outflows that reduce the BH feeding rate, especially at early times. This mechanism also naturally yields a high BH-to-galaxy mass ratio of >0.01 before the SMBH mass reaches MBH>109 M⊙ by z∼6. These fast-growing SMBH progenitors are bright enough to be detected by upcoming observations with the James Webb Space Telescope over a wide range of redshift (7<z<15), regardless of how they were seeded.","lang":"eng"}],"oa":1,"type":"journal_article","citation":{"mla":"Hu, Haojie, et al. “Supercritical Growth Pathway to Overmassive Black Holes at Cosmic Dawn: Coevolution with Massive Quasar Hosts.” <i>The Astrophysical Journal</i>, vol. 935, no. 2, 140, American Astronomical Society, 2022, doi:<a href=\"https://doi.org/10.3847/1538-4357/ac7daa\">10.3847/1538-4357/ac7daa</a>.","ieee":"H. Hu, K. Inayoshi, Z. Haiman, W. Li, E. Quataert, and R. Kuiper, “Supercritical growth pathway to overmassive black holes at cosmic dawn: Coevolution with massive quasar hosts,” <i>The Astrophysical Journal</i>, vol. 935, no. 2. American Astronomical Society, 2022.","short":"H. Hu, K. Inayoshi, Z. Haiman, W. Li, E. Quataert, R. Kuiper, The Astrophysical Journal 935 (2022).","apa":"Hu, H., Inayoshi, K., Haiman, Z., Li, W., Quataert, E., &#38; Kuiper, R. (2022). Supercritical growth pathway to overmassive black holes at cosmic dawn: Coevolution with massive quasar hosts. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.3847/1538-4357/ac7daa\">https://doi.org/10.3847/1538-4357/ac7daa</a>","chicago":"Hu, Haojie, Kohei Inayoshi, Zoltán Haiman, Wenxiu Li, Eliot Quataert, and Rolf Kuiper. “Supercritical Growth Pathway to Overmassive Black Holes at Cosmic Dawn: Coevolution with Massive Quasar Hosts.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2022. <a href=\"https://doi.org/10.3847/1538-4357/ac7daa\">https://doi.org/10.3847/1538-4357/ac7daa</a>.","ista":"Hu H, Inayoshi K, Haiman Z, Li W, Quataert E, Kuiper R. 2022. Supercritical growth pathway to overmassive black holes at cosmic dawn: Coevolution with massive quasar hosts. The Astrophysical Journal. 935(2), 140.","ama":"Hu H, Inayoshi K, Haiman Z, Li W, Quataert E, Kuiper R. Supercritical growth pathway to overmassive black holes at cosmic dawn: Coevolution with massive quasar hosts. <i>The Astrophysical Journal</i>. 2022;935(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ac7daa\">10.3847/1538-4357/ac7daa</a>"},"month":"08"},{"intvolume":"         5","acknowledgement":"We thank Dr, Luke Formosa (Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia) for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology [VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry, Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00 to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025 to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an NHMRC Project grant to M.R. (GNT1164459).\r\n","doi":"10.1038/s42003-022-03568-6","ddc":["570"],"volume":5,"scopus_import":"1","pmid":1,"publication":"Communications Biology","year":"2022","date_published":"2022-06-23T00:00:00Z","issue":"1","file":[{"date_created":"2022-07-13T07:44:58Z","creator":"kschuh","file_size":2335369,"content_type":"application/pdf","checksum":"965f88bbcef3fd0c3e121340555c4467","success":1,"file_id":"11571","access_level":"open_access","date_updated":"2022-07-13T07:44:58Z","relation":"main_file","file_name":"2022_communicationsbiology_Molina-Granada.pdf"}],"title":"Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit","article_number":"620","author":[{"first_name":"David","full_name":"Molina-Granada, David","last_name":"Molina-Granada"},{"full_name":"González-Vioque, Emiliano","first_name":"Emiliano","last_name":"González-Vioque"},{"last_name":"Dibley","first_name":"Marris G.","full_name":"Dibley, Marris G."},{"full_name":"Cabrera-Pérez, Raquel","first_name":"Raquel","last_name":"Cabrera-Pérez"},{"full_name":"Vallbona-Garcia, Antoni","first_name":"Antoni","last_name":"Vallbona-Garcia"},{"last_name":"Torres-Torronteras","first_name":"Javier","full_name":"Torres-Torronteras, Javier"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A","full_name":"Sazanov, Leonid A"},{"full_name":"Ryan, Michael T.","first_name":"Michael T.","last_name":"Ryan"},{"full_name":"Cámara, Yolanda","first_name":"Yolanda","last_name":"Cámara"},{"last_name":"Martí","first_name":"Ramon","full_name":"Martí, Ramon"}],"date_created":"2022-07-10T22:01:52Z","file_date_updated":"2022-07-13T07:44:58Z","has_accepted_license":"1","isi":1,"status":"public","day":"23","publication_identifier":{"eissn":["2399-3642"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"LeSa"}],"article_processing_charge":"No","publication_status":"published","external_id":{"isi":["000815098500002"],"pmid":[" 35739187"]},"abstract":[{"text":"Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance.","lang":"eng"}],"_id":"11551","type":"journal_article","month":"06","citation":{"ieee":"D. Molina-Granada <i>et al.</i>, “Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit,” <i>Communications Biology</i>, vol. 5, no. 1. Springer Nature, 2022.","mla":"Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>, vol. 5, no. 1, 620, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>.","apa":"Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R., Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>","short":"D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A. Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R. Martí, Communications Biology 5 (2022).","ama":"Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. 2022;5(1). doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>","ista":"Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. 5(1), 620.","chicago":"Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov, Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>."},"oa":1,"oa_version":"Published Version","publisher":"Springer Nature","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2026-04-02T13:22:53Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TiBr"}],"article_processing_charge":"No","publication_status":"draft","external_id":{"arxiv":["2208.05422"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.05422"}],"day":"10","date_updated":"2026-04-07T12:53:53Z","language":[{"iso":"eng"}],"oa_version":"Preprint","corr_author":"1","citation":{"ista":"Glas J, Hochfilzer L. On a question of Davenport and diagonal cubic forms over Fq(t). arXiv, 2208.05422.","chicago":"Glas, Jakob, and Leonhard Hochfilzer. “On a Question of Davenport and Diagonal Cubic Forms over Fq(T).” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2208.05422\">https://doi.org/10.48550/arXiv.2208.05422</a>.","ama":"Glas J, Hochfilzer L. On a question of Davenport and diagonal cubic forms over Fq(t). <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2208.05422\">10.48550/arXiv.2208.05422</a>","apa":"Glas, J., &#38; Hochfilzer, L. (n.d.). On a question of Davenport and diagonal cubic forms over Fq(t). <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2208.05422\">https://doi.org/10.48550/arXiv.2208.05422</a>","short":"J. Glas, L. Hochfilzer, ArXiv (n.d.).","mla":"Glas, Jakob, and Leonhard Hochfilzer. “On a Question of Davenport and Diagonal Cubic Forms over Fq(T).” <i>ArXiv</i>, 2208.05422, doi:<a href=\"https://doi.org/10.48550/arXiv.2208.05422\">10.48550/arXiv.2208.05422</a>.","ieee":"J. Glas and L. Hochfilzer, “On a question of Davenport and diagonal cubic forms over Fq(t),” <i>arXiv</i>. ."},"related_material":{"record":[{"relation":"later_version","id":"18705","status":"public"},{"relation":"dissertation_contains","id":"18132","status":"public"}]},"month":"08","type":"preprint","author":[{"id":"d6423cba-dc74-11ea-a0a7-ee61689ff5fb","last_name":"Glas","first_name":"Jakob","full_name":"Glas, Jakob"},{"last_name":"Hochfilzer","first_name":"Leonhard","full_name":"Hochfilzer, Leonhard"}],"title":"On a question of Davenport and diagonal cubic forms over Fq(t)","article_number":"2208.05422","date_created":"2024-10-10T12:46:41Z","oa":1,"abstract":[{"lang":"eng","text":"Given a non-singular diagonal cubic hypersurface X⊂Pn−1 over Fq(t) with char(Fq)≠3, we show that the number of rational points of height at most |P| is O(|P|3+ε) for n=6 and O(|P|2+ε) for n=4. In fact, if n=4 and char(Fq)>3 we prove that the number of rational points away from any rational line contained in X is bounded by O(|P|3/2+ε). From the result in 6 variables we deduce weak approximation for diagonal cubic hypersurfaces for n≥7 over Fq(t) when char(Fq)>3 and handle Waring's problem for cubes in 7 variables over Fq(t) when char(Fq)≠3. Our results answer a question of Davenport regarding the number of solutions of bounded height to x31+x32+x33=x34+x35+x36 with xi∈Fq[t]."}],"_id":"18293","date_published":"2022-08-10T00:00:00Z","publication":"arXiv","year":"2022","arxiv":1,"OA_place":"repository","doi":"10.48550/arXiv.2208.05422"},{"file_date_updated":"2022-05-17T15:19:39Z","alternative_title":["ISTA Thesis"],"supervisor":[{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"has_accepted_license":"1","status":"public","publication_identifier":{"isbn":["978-3-99078-017-6"]},"day":"12","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","publication_status":"published","doi":"10.15479/at:ista:11362","ddc":["004"],"year":"2022","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"date_published":"2022-05-12T00:00:00Z","file":[{"file_size":13210143,"date_created":"2022-05-13T12:33:26Z","creator":"mlechner","file_name":"src.zip","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","content_type":"application/zip","access_level":"closed","file_id":"11378","relation":"source_file","date_updated":"2022-05-13T12:49:00Z"},{"file_name":"thesis_main-a2.pdf","relation":"main_file","date_updated":"2022-05-17T15:19:39Z","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","content_type":"application/pdf","access_level":"open_access","file_id":"11382","file_size":2732536,"creator":"mlechner","date_created":"2022-05-16T08:02:28Z"}],"author":[{"first_name":"Mathias","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner"}],"date_created":"2022-05-12T07:14:01Z","title":"Learning verifiable representations","ec_funded":1,"oa_version":"Published Version","corr_author":"1","publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png"},"date_updated":"2026-04-16T09:46:06Z","language":[{"iso":"eng"}],"OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nd/4.0/","degree_awarded":"PhD","abstract":[{"text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks.","lang":"eng"}],"_id":"11362","keyword":["neural networks","verification","machine learning"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"11366","status":"public"},{"id":"10665","status":"public","relation":"part_of_dissertation"},{"id":"10667","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"10666","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7808"}]},"type":"dissertation","citation":{"ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","mla":"Lechner, Mathias. <i>Learning Verifiable Representations</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>.","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","apa":"Lechner, M. (2022). <i>Learning verifiable representations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>","chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>.","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria.","ama":"Lechner M. Learning verifiable representations. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>"},"month":"05","page":"124","oa":1},{"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaNo"}],"external_id":{"pmid":["35675510"],"isi":["000807770000001"]},"publication_status":"published","isi":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/brain/awac145"}],"day":"01","publication_identifier":{"issn":["0006-8950"],"eissn":["1460-2156"]},"volume":145,"publication":"Brain","year":"2022","pmid":1,"scopus_import":"1","intvolume":"       145","ddc":["570"],"doi":"10.1093/brain/awac145","acknowledgement":"We thank all patients and family members for their participation in this study. We thank Melanie Pieraks and Eva Reinthaler (Neurolentech, Austria) for generating the human iPSC lines and\r\nfor performing quality checks. We thank Vanessa Zheden and Daniel Gütl for their excellent technical support in the specimen preparation for transmission electron microscopy and Flavia Leite for preparing the lentiviruses. The support from Electron Microscopy Facility and Molecular Biology Services at IST Austria is greatly acknowledged. We would like to thank Doctors Jane Hurst and Richard Scott for their help in retrieving the detailed clinical information of Patient 17. The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. See Supplementary Material for Undiagnosed Disease Network consortium details. Genetic information on Patient 23 was made available through access to the data and findings generated by the 100 000 Genomes\r\nProject; www.genomicsengland.co.uk (to K.L.). \r\nThis work was supported by the EU 7th Framework Programme (FP7) under the project DESIRE grant N602531 (to R.G.); the Regione Toscana under the Call for Health 2018 (grant\r\nDECODE-EE) (to R.G.); the ‘Brain Project’ by Fondazione Cassa di Risparmio di Firenze (to R.G.); IRCCS Ospedale Policlinico San Martino 5×1000 and Ricerca Corrente (to A.F. and F.B.). The European Reference Network (ERN) for rare and complex epilepsies (EpiCARE) provided financial support for meetings organization. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute (grant number WT098051). The views expressed in this publication\r\nare those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). This study makes use of DECIPHER (https://www.deciphergenomics.org), which is funded by Wellcome. K.K.-S. was supported by the ISTplus fellowship. ","issue":"8","ec_funded":1,"title":"Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis","author":[{"last_name":"Guerrini","full_name":"Guerrini, Renzo","first_name":"Renzo"},{"last_name":"Mei","first_name":"Davide","full_name":"Mei, Davide"},{"orcid":"0000-0001-9500-8758","last_name":"Szigeti","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","full_name":"Szigeti, Margit Katalin","first_name":"Margit Katalin"},{"first_name":"Sara","full_name":"Pepe, Sara","last_name":"Pepe"},{"last_name":"Koenig","full_name":"Koenig, Mary Kay","first_name":"Mary Kay"},{"full_name":"Von Allmen, Gretchen","first_name":"Gretchen","last_name":"Von Allmen"},{"last_name":"Cho","first_name":"Megan T","full_name":"Cho, Megan T"},{"last_name":"McDonald","full_name":"McDonald, Kimberly","first_name":"Kimberly"},{"first_name":"Janice","full_name":"Baker, Janice","last_name":"Baker"},{"first_name":"Vikas","full_name":"Bhambhani, Vikas","last_name":"Bhambhani"},{"full_name":"Powis, Zöe","first_name":"Zöe","last_name":"Powis"},{"first_name":"Lance","full_name":"Rodan, Lance","last_name":"Rodan"},{"last_name":"Nabbout","first_name":"Rima","full_name":"Nabbout, Rima"},{"last_name":"Barcia","first_name":"Giulia","full_name":"Barcia, Giulia"},{"last_name":"Rosenfeld","first_name":"Jill A","full_name":"Rosenfeld, Jill A"},{"last_name":"Bacino","full_name":"Bacino, Carlos A","first_name":"Carlos A"},{"first_name":"Cyril","full_name":"Mignot, Cyril","last_name":"Mignot"},{"last_name":"Power","full_name":"Power, Lillian H","first_name":"Lillian H"},{"last_name":"Harris","full_name":"Harris, Catharine J","first_name":"Catharine J"},{"first_name":"Dragan","full_name":"Marjanovic, Dragan","last_name":"Marjanovic"},{"last_name":"Møller","first_name":"Rikke S","full_name":"Møller, Rikke S"},{"first_name":"Trine B","full_name":"Hammer, Trine B","last_name":"Hammer"},{"last_name":"Keski Filppula","first_name":"Riikka","full_name":"Keski Filppula, Riikka"},{"last_name":"Vieira","first_name":"Päivi","full_name":"Vieira, Päivi"},{"last_name":"Hildebrandt","first_name":"Clara","full_name":"Hildebrandt, Clara"},{"full_name":"Sacharow, Stephanie","first_name":"Stephanie","last_name":"Sacharow"},{"first_name":"Luca","full_name":"Maragliano, Luca","last_name":"Maragliano"},{"first_name":"Fabio","full_name":"Benfenati, Fabio","last_name":"Benfenati"},{"last_name":"Lachlan","first_name":"Katherine","full_name":"Lachlan, Katherine"},{"full_name":"Benneche, Andreas","first_name":"Andreas","last_name":"Benneche"},{"full_name":"Petit, Florence","first_name":"Florence","last_name":"Petit"},{"last_name":"de Sainte Agathe","full_name":"de Sainte Agathe, Jean Madeleine","first_name":"Jean Madeleine"},{"last_name":"Hallinan","first_name":"Barbara","full_name":"Hallinan, Barbara"},{"first_name":"Yue","full_name":"Si, Yue","last_name":"Si"},{"last_name":"Wentzensen","full_name":"Wentzensen, Ingrid M","first_name":"Ingrid M"},{"last_name":"Zou","first_name":"Fanggeng","full_name":"Zou, Fanggeng"},{"full_name":"Narayanan, Vinodh","first_name":"Vinodh","last_name":"Narayanan"},{"first_name":"Naomichi","full_name":"Matsumoto, Naomichi","last_name":"Matsumoto"},{"full_name":"Boncristiano, Alessandra","first_name":"Alessandra","last_name":"Boncristiano"},{"full_name":"la Marca, Giancarlo","first_name":"Giancarlo","last_name":"la Marca"},{"last_name":"Kato","first_name":"Mitsuhiro","full_name":"Kato, Mitsuhiro"},{"full_name":"Anderson, Kristin","first_name":"Kristin","last_name":"Anderson"},{"full_name":"Barba, Carmen","first_name":"Carmen","last_name":"Barba"},{"first_name":"Luisa","full_name":"Sturiale, Luisa","last_name":"Sturiale"},{"full_name":"Garozzo, Domenico","first_name":"Domenico","last_name":"Garozzo"},{"last_name":"Bei","first_name":"Roberto","full_name":"Bei, Roberto"},{"last_name":"Masuelli","first_name":"Laura","full_name":"Masuelli, Laura"},{"first_name":"Valerio","full_name":"Conti, Valerio","last_name":"Conti"},{"first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"last_name":"Fassio","full_name":"Fassio, Anna","first_name":"Anna"}],"date_created":"2023-01-12T12:11:45Z","article_type":"original","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"date_published":"2022-08-01T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2026-06-18T17:24:52Z","oa_version":"Published Version","quality_controlled":"1","publisher":"Oxford University Press","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"month":"08","citation":{"ista":"Guerrini R, Mei D, Szigeti MK, Pepe S, Koenig MK, Von Allmen G, Cho MT, McDonald K, Baker J, Bhambhani V, Powis Z, Rodan L, Nabbout R, Barcia G, Rosenfeld JA, Bacino CA, Mignot C, Power LH, Harris CJ, Marjanovic D, Møller RS, Hammer TB, Keski Filppula R, Vieira P, Hildebrandt C, Sacharow S, Maragliano L, Benfenati F, Lachlan K, Benneche A, Petit F, de Sainte Agathe JM, Hallinan B, Si Y, Wentzensen IM, Zou F, Narayanan V, Matsumoto N, Boncristiano A, la Marca G, Kato M, Anderson K, Barba C, Sturiale L, Garozzo D, Bei R, Masuelli L, Conti V, Novarino G, Fassio A. 2022. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 145(8), 2687–2703.","chicago":"Guerrini, Renzo, Davide Mei, Margit Katalin Szigeti, Sara Pepe, Mary Kay Koenig, Gretchen Von Allmen, Megan T Cho, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” <i>Brain</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/brain/awac145\">https://doi.org/10.1093/brain/awac145</a>.","ama":"Guerrini R, Mei D, Szigeti MK, et al. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. <i>Brain</i>. 2022;145(8):2687-2703. doi:<a href=\"https://doi.org/10.1093/brain/awac145\">10.1093/brain/awac145</a>","short":"R. Guerrini, D. Mei, M.K. Szigeti, S. Pepe, M.K. Koenig, G. Von Allmen, M.T. Cho, K. McDonald, J. Baker, V. Bhambhani, Z. Powis, L. Rodan, R. Nabbout, G. Barcia, J.A. Rosenfeld, C.A. Bacino, C. Mignot, L.H. Power, C.J. Harris, D. Marjanovic, R.S. Møller, T.B. Hammer, R. Keski Filppula, P. Vieira, C. Hildebrandt, S. Sacharow, L. Maragliano, F. Benfenati, K. Lachlan, A. Benneche, F. Petit, J.M. de Sainte Agathe, B. Hallinan, Y. Si, I.M. Wentzensen, F. Zou, V. Narayanan, N. Matsumoto, A. Boncristiano, G. la Marca, M. Kato, K. Anderson, C. Barba, L. Sturiale, D. Garozzo, R. Bei, L. Masuelli, V. Conti, G. Novarino, A. Fassio, Brain 145 (2022) 2687–2703.","apa":"Guerrini, R., Mei, D., Szigeti, M. K., Pepe, S., Koenig, M. K., Von Allmen, G., … Fassio, A. (2022). Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. <i>Brain</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awac145\">https://doi.org/10.1093/brain/awac145</a>","mla":"Guerrini, Renzo, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” <i>Brain</i>, vol. 145, no. 8, Oxford University Press, 2022, pp. 2687–703, doi:<a href=\"https://doi.org/10.1093/brain/awac145\">10.1093/brain/awac145</a>.","ieee":"R. Guerrini <i>et al.</i>, “Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis,” <i>Brain</i>, vol. 145, no. 8. Oxford University Press, pp. 2687–2703, 2022."},"type":"journal_article","oa":1,"page":"2687-2703","abstract":[{"lang":"eng","text":"Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease.\r\nHere we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs.</jats:p>\r\n               <jats:p>Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes.\r\nATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants."}],"keyword":["Neurology (clinical)"],"_id":"12174"},{"file_date_updated":"2023-02-02T09:39:25Z","has_accepted_license":"1","status":"public","supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"isbn":["978-3-99078-020-6"],"issn":["2663-337X"]},"day":"22","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publication_status":"published","ddc":["000","620"],"doi":"10.15479/at:ista:12103","year":"2022","project":[{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"date_published":"2022-09-22T00:00:00Z","file":[{"file_size":104497530,"creator":"cchlebak","description":"This is the main PDF file of the thesis. File size: 105 MB","date_created":"2023-01-25T12:04:41Z","title":"Thesis","file_name":"thesis_gsperl.pdf","date_updated":"2023-02-02T09:29:57Z","relation":"main_file","file_id":"12371","access_level":"open_access","content_type":"application/pdf","checksum":"083722acbb8115e52e3b0fdec6226769"},{"date_created":"2023-02-02T09:33:37Z","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","title":"Thesis (compressed 23MB)","creator":"cchlebak","file_size":23183710,"checksum":"511f82025e5fcb70bff4731d6896ca07","content_type":"application/pdf","file_id":"12483","access_level":"open_access","date_updated":"2023-02-02T09:33:37Z","relation":"main_file","file_name":"thesis_gsperl_compressed.pdf"},{"file_name":"thesis-source.zip","date_updated":"2023-02-02T09:39:25Z","relation":"source_file","access_level":"open_access","file_id":"12484","content_type":"application/x-zip-compressed","checksum":"ed4cb85225eedff761c25bddfc37a2ed","file_size":98382247,"creator":"cchlebak","date_created":"2023-02-02T09:39:25Z"}],"ec_funded":1,"date_created":"2023-01-24T10:49:46Z","author":[{"full_name":"Sperl, Georg","first_name":"Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"}],"title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","corr_author":"1","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","date_updated":"2026-06-18T19:57:47Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"OA_place":"publisher","abstract":[{"lang":"eng","text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n"}],"degree_awarded":"PhD","_id":"12358","citation":{"ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","mla":"Sperl, Georg. <i>Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>.","apa":"Sperl, G. (2022). <i>Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>"},"type":"dissertation","month":"09","related_material":{"record":[{"id":"8385","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11736"},{"id":"9818","status":"public","relation":"part_of_dissertation"}]},"oa":1,"page":"138"},{"date_updated":"2026-06-20T22:30:36Z","language":[{"iso":"eng"}],"corr_author":"1","oa_version":"Preprint","publisher":"Cold Spring Harbor Laboratory","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"}],"publication_status":"draft","status":"public","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.16.484431","open_access":"1"}],"day":"09","year":"2022","publication":"bioRxiv","doi":"10.1101/2022.03.16.484431","OA_place":"repository","citation":{"ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Donglai Wei, Zudi Lin, Jake Watson, Jakob Troidl, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. Saturated reconstruction of living brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, BioRxiv (n.d.).","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Wei, D., Lin, Z., Watson, J., … Danzl, J. G. (n.d.). Saturated reconstruction of living brain tissue. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.03.16.484431\">https://doi.org/10.1101/2022.03.16.484431</a>","mla":"Velicky, Philipp, et al. “Saturated Reconstruction of Living Brain Tissue.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2022.03.16.484431\">10.1101/2022.03.16.484431</a>.","ieee":"P. Velicky <i>et al.</i>, “Saturated reconstruction of living brain tissue,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory."},"type":"preprint","related_material":{"record":[{"id":"13267","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"12470"}]},"month":"05","oa":1,"author":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","orcid":"0000-0002-2340-7431","first_name":"Philipp","full_name":"Velicky, Philipp"},{"full_name":"Miguel Villalba, Eder","first_name":"Eder","orcid":"0000-0001-5665-0430","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba"},{"first_name":"Julia M","full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","orcid":"0000-0003-3862-1235"},{"full_name":"Wei, Donglai","first_name":"Donglai","last_name":"Wei"},{"last_name":"Lin","full_name":"Lin, Zudi","first_name":"Zudi"},{"full_name":"Watson, Jake","first_name":"Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"last_name":"Troidl","first_name":"Jakob","full_name":"Troidl, Jakob"},{"last_name":"Beyer","first_name":"Johanna","full_name":"Beyer, Johanna"},{"full_name":"Ben Simon, Yoav","first_name":"Yoav","last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer"},{"orcid":"0000-0003-0201-2315","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","full_name":"Jahr, Wiebke","first_name":"Wiebke"},{"last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","full_name":"Cenameri, Alban"},{"full_name":"Broichhagen, Johannes","first_name":"Johannes","last_name":"Broichhagen"},{"first_name":"Seth G. N.","full_name":"Grant, Seth G. N.","last_name":"Grant"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","first_name":"Gaia"},{"last_name":"Pfister","first_name":"Hanspeter","full_name":"Pfister, Hanspeter"},{"first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385"},{"orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G"}],"title":"Saturated reconstruction of living brain tissue","date_created":"2022-08-23T11:07:59Z","abstract":[{"lang":"eng","text":"Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full <jats:italic>in-silico</jats:italic> reconstruction<jats:sup>1–5</jats:sup>, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches<jats:sup>6–12</jats:sup> facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy<jats:sup>6,13</jats:sup> in extracellularly labelled tissue<jats:sup>14</jats:sup> for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue."}],"date_published":"2022-05-09T00:00:00Z","_id":"11943"},{"_id":"12244","keyword":["General Neuroscience"],"abstract":[{"text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology.","lang":"eng"}],"page":"1379-1393","oa":1,"month":"10","citation":{"ama":"Colombo G, Cubero RJ, Kanari L, et al. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. 2022;25(10):1379-1393. doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>","chicago":"Colombo, Gloria, Ryan J Cubero, Lida Kanari, Alessandro Venturino, Rouven Schulz, Martina Scolamiero, Jens Agerberg, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>.","ista":"Colombo G, Cubero RJ, Kanari L, Venturino A, Schulz R, Scolamiero M, Agerberg J, Mathys H, Tsai L-H, Chachólski W, Hess K, Siegert S. 2022. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. Nature Neuroscience. 25(10), 1379–1393.","apa":"Colombo, G., Cubero, R. J., Kanari, L., Venturino, A., Schulz, R., Scolamiero, M., … Siegert, S. (2022). A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>","short":"G. Colombo, R.J. Cubero, L. Kanari, A. Venturino, R. Schulz, M. Scolamiero, J. Agerberg, H. Mathys, L.-H. Tsai, W. Chachólski, K. Hess, S. Siegert, Nature Neuroscience 25 (2022) 1379–1393.","ieee":"G. Colombo <i>et al.</i>, “A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes,” <i>Nature Neuroscience</i>, vol. 25, no. 10. Springer Nature, pp. 1379–1393, 2022.","mla":"Colombo, Gloria, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>, vol. 25, no. 10, Springer Nature, 2022, pp. 1379–93, doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>."},"type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12378"}],"link":[{"url":"https://ista.ac.at/en/news/morphomics-revealing-the-hidden-meaning-of-microglia-shape/","relation":"press_release","description":"News on ISTA website"}]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"publisher":"Springer Nature","quality_controlled":"1","oa_version":"Published Version","corr_author":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2026-06-20T22:30:38Z","language":[{"iso":"eng"}],"date_published":"2022-10-01T00:00:00Z","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"article_type":"original","title":"A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes","author":[{"orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","last_name":"Colombo","full_name":"Colombo, Gloria","first_name":"Gloria"},{"orcid":"0000-0003-0002-1867","id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","full_name":"Cubero, Ryan J","first_name":"Ryan J"},{"last_name":"Kanari","full_name":"Kanari, Lida","first_name":"Lida"},{"full_name":"Venturino, Alessandro","first_name":"Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","full_name":"Schulz, Rouven","first_name":"Rouven"},{"first_name":"Martina","full_name":"Scolamiero, Martina","last_name":"Scolamiero"},{"first_name":"Jens","full_name":"Agerberg, Jens","last_name":"Agerberg"},{"full_name":"Mathys, Hansruedi","first_name":"Hansruedi","last_name":"Mathys"},{"last_name":"Tsai","full_name":"Tsai, Li-Huei","first_name":"Li-Huei"},{"first_name":"Wojciech","full_name":"Chachólski, Wojciech","last_name":"Chachólski"},{"last_name":"Hess","first_name":"Kathryn","full_name":"Hess, Kathryn"},{"full_name":"Siegert, Sandra","first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-01-16T09:53:07Z","ec_funded":1,"issue":"10","file":[{"creator":"dernst","date_created":"2023-01-30T08:06:56Z","file_size":23789835,"relation":"main_file","date_updated":"2023-01-30T08:06:56Z","checksum":"28431146873096f52e0107b534f178c9","content_type":"application/pdf","file_id":"12437","access_level":"open_access","success":1,"file_name":"2022_NatureNeuroscience_Colombo.pdf"}],"doi":"10.1038/s41593-022-01167-6","acknowledgement":"We thank the scientific service units at ISTA, in particular M. Schunn’s team at the preclinical facility, and especially our colony manager S. Haslinger, for excellent support. We are also grateful to the ISTA Imaging & Optics Facility, and in particular C. Sommer for helping with the data file conversions. We thank R. Erhart from the ISTA Scientific Computing Unit for improving the script performance. We thank M. Maes, B. Nagy, S. Oakeley and M. Benevento and all members of the Siegert group for constant feedback on the project and on the manuscript. This research was supported by the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (754411 to R.J.A.C.), and by the European Research Council (grant no. 715571 to S.S.). L.K. was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne, from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. L.-H.T. was supported by NIH (grant no. R37NS051874) and by the JPB Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","ddc":["570"],"intvolume":"        25","scopus_import":"1","pmid":1,"year":"2022","publication":"Nature Neuroscience","volume":25,"day":"01","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"has_accepted_license":"1","status":"public","isi":1,"publication_status":"published","external_id":{"pmid":["36180790"],"isi":["000862214700001"]},"department":[{"_id":"SaSi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","file_date_updated":"2023-01-30T08:06:56Z"},{"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publication_identifier":{"isbn":["978-3-99078-018-3"]},"day":"18","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"status":"public","file_date_updated":"2023-05-20T22:30:03Z","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","author":[{"full_name":"Belohlavy, Stefanie","first_name":"Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy"}],"date_created":"2022-05-16T16:49:18Z","file":[{"file_name":"thesis_sb_final_pdfa.pdf","file_id":"11398","access_level":"open_access","checksum":"4d75e6a619df7e8a9d6e840aee182380","content_type":"application/pdf","embargo":"2023-05-19","date_updated":"2023-05-20T22:30:03Z","relation":"main_file","file_size":8247240,"date_created":"2022-05-19T13:03:13Z","creator":"sbelohla"},{"file_id":"11399","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","relation":"source_file","date_updated":"2023-05-20T22:30:03Z","file_name":"thesis_sb_final.zip","date_created":"2022-05-19T13:07:47Z","creator":"sbelohla","embargo_to":"open_access","file_size":7094}],"date_published":"2022-05-18T00:00:00Z","year":"2022","doi":"10.15479/at:ista:11388","ddc":["576"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_updated":"2026-04-07T14:29:57Z","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","corr_author":"1","page":"98","oa":1,"citation":{"apa":"Belohlavy, S. (2022). <i>The genetic basis of complex traits studied via analysis of evolve and resequence experiments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","mla":"Belohlavy, Stefanie. <i>The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>."},"related_material":{"record":[{"status":"public","id":"6713","relation":"part_of_dissertation"}]},"month":"05","type":"dissertation","_id":"11388","degree_awarded":"PhD","abstract":[{"text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work.","lang":"eng"}],"OA_place":"publisher"},{"abstract":[{"lang":"eng","text":"Rest-frame ultraviolet (UV) emission lines probe electron densities, gas-phase abundances, metallicities, and ionization parameters of the emitting star-forming galaxies and their environments. The strongest main UV emission line, Lyα, has been instrumental in advancing the general knowledge of galaxy formation in the early universe. However, observing Lyα emission becomes increasingly challenging at z ≳ 6 when the neutral hydrogen fraction of the circumgalactic and intergalactic media increases. Secondary weaker UV emission lines provide important alternative methods for studying galaxy properties at high redshift. We present a large sample of rest-frame UV emission line sources at intermediate redshift for calibrating and exploring the connection between secondary UV lines and the emitting galaxies’ physical properties and their Lyα emission. The sample of 2052 emission line sources with 1.5 < z < 6.4 was collected from integral field data from the MUSE-Wide and MUSE-Deep surveys taken as part of Guaranteed Time Observations. The objects were selected through untargeted source detection (i.e., no preselection of sources as in dedicated spectroscopic campaigns) in the three-dimensional MUSE data cubes. We searched optimally extracted one-dimensional spectra of the full sample for UV emission features via emission line template matching, resulting in a sample of more than 100 rest-frame UV emission line detections. We show that the detection efficiency of (non-Lyα) UV emission lines increases with survey depth, and that the emission line strength of He IIλ1640 Å, [O III] λ1661 + O III] λ1666, and [Si III] λ1883 + Si III] λ1892 correlate with the strength of [C III] λ1907 + C III] λ1909. The rest-frame equivalent width (EW0) of [C III] λ1907 + C III] λ1909 is found to be roughly 0.22 ± 0.18 of EW0(Lyα). We measured the velocity offsets of resonant emission lines with respect to systemic tracers. For C IVλ1548 + C IVλ1551 we find that ΔvC IV ≲ 250 km s−1, whereas ΔvLyα falls in the range of 250−500 km s−1 which is in agreement with previous results from the literature. The electron density ne measured from [Si III] λ1883 + Si III] λ1892 and [C III] λ1907 + C III] λ1909 line flux ratios is generally < 105 cm−3 and the gas-phase abundance is below solar at 12 + log10(O/H)≈8. Lastly, we used “PhotoIonization Model Probability Density Functions” to infer physical parameters of the full sample and individual systems based on photoionization model parameter grids and observational constraints from our UV emission line searches. This reveals that the UV line emitters generally have ionization parameter log10(U) ≈ −2.5 and metal mass fractions that scatter around Z ≈ 10−2, that is Z ≈ 0.66 Z⊙. Value-added catalogs of the full sample of MUSE objects studied in this work and a collection of UV line emitters from the literature are provided with this paper."}],"keyword":["Space and Planetary Science","Astronomy and Astrophysics","ultraviolet: galaxies / galaxies: high-redshift / galaxies: ISM / ISM: lines and bands / methods: observational / techniques: imaging spectroscopy"],"_id":"11498","month":"10","citation":{"ieee":"K. B. Schmidt <i>et al.</i>, “Recovery and analysis of rest-frame UV emission lines in 2052 galaxies observed with MUSE at 1.5 &#60; z &#60; 6.4,” <i>Astronomy &#38; Astrophysics</i>, vol. 654. EDP Sciences, 2021.","mla":"Schmidt, K. B., et al. “Recovery and Analysis of Rest-Frame UV Emission Lines in 2052 Galaxies Observed with MUSE at 1.5 &#60; z &#60; 6.4.” <i>Astronomy &#38; Astrophysics</i>, vol. 654, A80, EDP Sciences, 2021, doi:<a href=\"https://doi.org/10.1051/0004-6361/202140876\">10.1051/0004-6361/202140876</a>.","ama":"Schmidt KB, Kerutt J, Wisotzki L, et al. Recovery and analysis of rest-frame UV emission lines in 2052 galaxies observed with MUSE at 1.5 &#60; z &#60; 6.4. <i>Astronomy &#38; Astrophysics</i>. 2021;654. doi:<a href=\"https://doi.org/10.1051/0004-6361/202140876\">10.1051/0004-6361/202140876</a>","chicago":"Schmidt, K. B., J. Kerutt, L. Wisotzki, T. Urrutia, A. Feltre, M. V. Maseda, T. Nanayakkara, et al. “Recovery and Analysis of Rest-Frame UV Emission Lines in 2052 Galaxies Observed with MUSE at 1.5 &#60; z &#60; 6.4.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2021. <a href=\"https://doi.org/10.1051/0004-6361/202140876\">https://doi.org/10.1051/0004-6361/202140876</a>.","ista":"Schmidt KB, Kerutt J, Wisotzki L, Urrutia T, Feltre A, Maseda MV, Nanayakkara T, Bacon R, Boogaard LA, Conseil S, Contini T, Herenz EC, Kollatschny W, Krumpe M, Leclercq F, Mahler G, Matthee JJ, Mauerhofer V, Richard J, Schaye J. 2021. Recovery and analysis of rest-frame UV emission lines in 2052 galaxies observed with MUSE at 1.5 &#60; z &#60; 6.4. Astronomy &#38; Astrophysics. 654, A80.","short":"K.B. Schmidt, J. Kerutt, L. Wisotzki, T. Urrutia, A. Feltre, M.V. Maseda, T. Nanayakkara, R. Bacon, L.A. Boogaard, S. Conseil, T. Contini, E.C. Herenz, W. Kollatschny, M. Krumpe, F. Leclercq, G. Mahler, J.J. Matthee, V. Mauerhofer, J. Richard, J. Schaye, Astronomy &#38; Astrophysics 654 (2021).","apa":"Schmidt, K. B., Kerutt, J., Wisotzki, L., Urrutia, T., Feltre, A., Maseda, M. V., … Schaye, J. (2021). Recovery and analysis of rest-frame UV emission lines in 2052 galaxies observed with MUSE at 1.5 &#60; z &#60; 6.4. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202140876\">https://doi.org/10.1051/0004-6361/202140876</a>"},"type":"journal_article","oa":1,"arxiv":1,"oa_version":"Published Version","quality_controlled":"1","publisher":"EDP Sciences","date_updated":"2022-07-19T09:34:36Z","language":[{"iso":"eng"}],"article_type":"original","date_published":"2021-10-15T00:00:00Z","article_number":"A80","date_created":"2022-07-06T08:49:03Z","title":"Recovery and analysis of rest-frame UV emission lines in 2052 galaxies observed with MUSE at 1.5 < z < 6.4","author":[{"full_name":"Schmidt, K. B.","first_name":"K. B.","last_name":"Schmidt"},{"first_name":"J.","full_name":"Kerutt, J.","last_name":"Kerutt"},{"full_name":"Wisotzki, L.","first_name":"L.","last_name":"Wisotzki"},{"full_name":"Urrutia, T.","first_name":"T.","last_name":"Urrutia"},{"first_name":"A.","full_name":"Feltre, A.","last_name":"Feltre"},{"full_name":"Maseda, M. V.","first_name":"M. V.","last_name":"Maseda"},{"last_name":"Nanayakkara","full_name":"Nanayakkara, T.","first_name":"T."},{"last_name":"Bacon","first_name":"R.","full_name":"Bacon, R."},{"full_name":"Boogaard, L. A.","first_name":"L. A.","last_name":"Boogaard"},{"full_name":"Conseil, S.","first_name":"S.","last_name":"Conseil"},{"first_name":"T.","full_name":"Contini, T.","last_name":"Contini"},{"last_name":"Herenz","full_name":"Herenz, E. C.","first_name":"E. C."},{"full_name":"Kollatschny, W.","first_name":"W.","last_name":"Kollatschny"},{"full_name":"Krumpe, M.","first_name":"M.","last_name":"Krumpe"},{"full_name":"Leclercq, F.","first_name":"F.","last_name":"Leclercq"},{"last_name":"Mahler","first_name":"G.","full_name":"Mahler, G."},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"},{"first_name":"V.","full_name":"Mauerhofer, V.","last_name":"Mauerhofer"},{"last_name":"Richard","first_name":"J.","full_name":"Richard, J."},{"full_name":"Schaye, J.","first_name":"J.","last_name":"Schaye"}],"intvolume":"       654","doi":"10.1051/0004-6361/202140876","acknowledgement":"We would like to thank Charlotte Mason for useful discussions and for providing the data for the curves shown in Fig. 13 and Dawn Erb for providing the observational data for the comparison sample studied by Steidel et al. (2014), also shown in Fig. 13. This work has been supported by the BMBF grant 05A14BAC and we acknowledge support by the Competitive Fund of the Leibniz Association through grant SAW-2015-AIP-2. AF acknowledges the support from grant PRIN MIUR2017-20173ML3WW_001. JS acknowledges the support from Vici grant 639.043.409 from the Dutch Research Council (NWO). GM received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No MARACAS – DLV-896778. This paper is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 094.A-0289(B), 095.A-0010(A), 096.A-0045(A), 096.A-0045(B), 094.A-0205, 095.A-0240, 096.A-0090, 097.A-0160, and 098.A-0017. This paper also makes use of observations made with the NASA/ESA Hubble Space Telescope obtained at STScI. This research made use of the following programs and open-source packages for Python and we are thankful to their developers: DS9 (Joye & Mandel 2003), Astropy (Astropy Collaboration 2013, 2018), APLpy (Robitaille & Bressert 2012), iPython (Pérez & Granger 2007), numpy (van der Walt et al. 2011), matplotlib (Hunter 2007), and SciPy (Jones et al. 2001).","volume":654,"publication":"Astronomy & Astrophysics","year":"2021","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2108.01713","open_access":"1"}],"status":"public","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"day":"15","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2108.01713"]},"extern":"1","publication_status":"published"},{"abstract":[{"text":"We report the discovery of diffuse extended Lyα emission from redshift 3.1 to 4.5, tracing cosmic web filaments on scales of 2.5−4 cMpc. These structures have been observed in overdensities of Lyα emitters in the MUSE Extremely Deep Field, a 140 h deep MUSE observation located in the Hubble Ultra-Deep Field. Among the 22 overdense regions identified, five are likely to harbor very extended Lyα emission at high significance with an average surface brightness of 5 × 10−20 erg s−1 cm−2 arcsec−2. Remarkably, 70% of the total Lyα luminosity from these filaments comes from beyond the circumgalactic medium of any identified Lyα emitter. Fluorescent Lyα emission powered by the cosmic UV background can only account for less than 34% of this emission at z ≈ 3 and for not more than 10% at higher redshift. We find that the bulk of this diffuse emission can be reproduced by the unresolved Lyα emission of a large population of ultra low-luminosity Lyα emitters (< 1040 erg s−1), provided that the faint end of the Lyα luminosity function is steep (α ⪅ −1.8), it extends down to luminosities lower than 1038 − 1037 erg s−1, and the clustering of these Lyα emitters is significant (filling factor < 1/6). If these Lyα emitters are powered by star formation, then this implies their luminosity function needs to extend down to star formation rates < 10−4 M⊙ yr−1. These observations provide the first detection of the cosmic web in Lyα emission in typical filamentary environments and the first observational clue indicating the existence of a large population of ultra low-luminosity Lyα emitters at high redshift.","lang":"eng"}],"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: groups: general / cosmology: observations"],"_id":"11500","type":"journal_article","month":"03","citation":{"ama":"Bacon R, Mary D, Garel T, et al. The MUSE Extremely Deep Field: The cosmic web in emission at high redshift. <i>Astronomy &#38; Astrophysics</i>. 2021;647. doi:<a href=\"https://doi.org/10.1051/0004-6361/202039887\">10.1051/0004-6361/202039887</a>","ista":"Bacon R, Mary D, Garel T, Blaizot J, Maseda M, Schaye J, Wisotzki L, Conseil S, Brinchmann J, Leclercq F, Abril-Melgarejo V, Boogaard L, Bouché NF, Contini T, Feltre A, Guiderdoni B, Herenz C, Kollatschny W, Kusakabe H, Matthee JJ, Michel-Dansac L, Nanayakkara T, Richard J, Roth M, Schmidt KB, Steinmetz M, Tresse L, Urrutia T, Verhamme A, Weilbacher PM, Zabl J, Zoutendijk SL. 2021. The MUSE Extremely Deep Field: The cosmic web in emission at high redshift. Astronomy &#38; Astrophysics. 647, A107.","chicago":"Bacon, R., D. Mary, T. Garel, J. Blaizot, M. Maseda, J. Schaye, L. Wisotzki, et al. “The MUSE Extremely Deep Field: The Cosmic Web in Emission at High Redshift.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2021. <a href=\"https://doi.org/10.1051/0004-6361/202039887\">https://doi.org/10.1051/0004-6361/202039887</a>.","short":"R. Bacon, D. Mary, T. Garel, J. Blaizot, M. Maseda, J. Schaye, L. Wisotzki, S. Conseil, J. Brinchmann, F. Leclercq, V. Abril-Melgarejo, L. Boogaard, N.F. Bouché, T. Contini, A. Feltre, B. Guiderdoni, C. Herenz, W. Kollatschny, H. Kusakabe, J.J. Matthee, L. Michel-Dansac, T. Nanayakkara, J. Richard, M. Roth, K.B. Schmidt, M. Steinmetz, L. Tresse, T. Urrutia, A. Verhamme, P.M. Weilbacher, J. Zabl, S.L. Zoutendijk, Astronomy &#38; Astrophysics 647 (2021).","apa":"Bacon, R., Mary, D., Garel, T., Blaizot, J., Maseda, M., Schaye, J., … Zoutendijk, S. L. (2021). The MUSE Extremely Deep Field: The cosmic web in emission at high redshift. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202039887\">https://doi.org/10.1051/0004-6361/202039887</a>","ieee":"R. Bacon <i>et al.</i>, “The MUSE Extremely Deep Field: The cosmic web in emission at high redshift,” <i>Astronomy &#38; Astrophysics</i>, vol. 647. EDP Sciences, 2021.","mla":"Bacon, R., et al. “The MUSE Extremely Deep Field: The Cosmic Web in Emission at High Redshift.” <i>Astronomy &#38; Astrophysics</i>, vol. 647, A107, EDP Sciences, 2021, doi:<a href=\"https://doi.org/10.1051/0004-6361/202039887\">10.1051/0004-6361/202039887</a>."},"oa":1,"arxiv":1,"oa_version":"Published Version","publisher":"EDP Sciences","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2022-07-19T09:34:57Z","article_type":"original","date_published":"2021-03-18T00:00:00Z","article_number":"A107","title":"The MUSE Extremely Deep Field: The cosmic web in emission at high redshift","date_created":"2022-07-06T09:31:50Z","author":[{"first_name":"R.","full_name":"Bacon, R.","last_name":"Bacon"},{"last_name":"Mary","full_name":"Mary, D.","first_name":"D."},{"full_name":"Garel, T.","first_name":"T.","last_name":"Garel"},{"last_name":"Blaizot","full_name":"Blaizot, J.","first_name":"J."},{"full_name":"Maseda, M.","first_name":"M.","last_name":"Maseda"},{"first_name":"J.","full_name":"Schaye, J.","last_name":"Schaye"},{"full_name":"Wisotzki, L.","first_name":"L.","last_name":"Wisotzki"},{"last_name":"Conseil","first_name":"S.","full_name":"Conseil, S."},{"first_name":"J.","full_name":"Brinchmann, J.","last_name":"Brinchmann"},{"first_name":"F.","full_name":"Leclercq, F.","last_name":"Leclercq"},{"first_name":"V.","full_name":"Abril-Melgarejo, V.","last_name":"Abril-Melgarejo"},{"first_name":"L.","full_name":"Boogaard, L.","last_name":"Boogaard"},{"last_name":"Bouché","first_name":"N. F.","full_name":"Bouché, N. F."},{"first_name":"T.","full_name":"Contini, T.","last_name":"Contini"},{"first_name":"A.","full_name":"Feltre, A.","last_name":"Feltre"},{"last_name":"Guiderdoni","first_name":"B.","full_name":"Guiderdoni, B."},{"last_name":"Herenz","full_name":"Herenz, C.","first_name":"C."},{"first_name":"W.","full_name":"Kollatschny, W.","last_name":"Kollatschny"},{"last_name":"Kusakabe","first_name":"H.","full_name":"Kusakabe, H."},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"},{"full_name":"Michel-Dansac, L.","first_name":"L.","last_name":"Michel-Dansac"},{"first_name":"T.","full_name":"Nanayakkara, T.","last_name":"Nanayakkara"},{"last_name":"Richard","full_name":"Richard, J.","first_name":"J."},{"last_name":"Roth","first_name":"M.","full_name":"Roth, M."},{"full_name":"Schmidt, K. B.","first_name":"K. B.","last_name":"Schmidt"},{"last_name":"Steinmetz","first_name":"M.","full_name":"Steinmetz, M."},{"first_name":"L.","full_name":"Tresse, L.","last_name":"Tresse"},{"full_name":"Urrutia, T.","first_name":"T.","last_name":"Urrutia"},{"last_name":"Verhamme","full_name":"Verhamme, A.","first_name":"A."},{"full_name":"Weilbacher, P. M.","first_name":"P. M.","last_name":"Weilbacher"},{"full_name":"Zabl, J.","first_name":"J.","last_name":"Zabl"},{"full_name":"Zoutendijk, S. L.","first_name":"S. L.","last_name":"Zoutendijk"}],"intvolume":"       647","acknowledgement":"We warmly thank ESO Paranal staff for their great professional support during all MXDF GTO observing runs. We thank the anonymous referee for a careful reading of the manuscript and helpful comments. We also thank Matthew Lehnert for fruitful discussions. RB, AF, SC acknowledge support from the ERC advanced grant 339659-MUSICOS. JB acknowledges support by Fundação para a Ciência e a Tecnologia (FCT) through the research grants UID/FIS/04434/2019, UIDB/04434/2020, UIDP/04434/2020 and through the Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003. TG, AV acknowledges support from the European Research Council under grant agreement ERC-stg-757258 (TRIPLE). DM acknowledges A. Dabbech for useful interactions about IUWT and support from the GDR ISIS through the Projets exploratoires program (project TASTY). AF acknowledges the support from grant PRIN MIUR2017-20173ML3WW_001. SLZ acknowledges support by The Netherlands Organisation for Scientific Research (NWO) through a TOP Grant Module 1 under project number 614.001.652. This research made use of the following open-source software and we are thankful to the developers of these: GNU Octave (Eaton et al. 2018) and its statistics, signal and image packages, the Python packages Matplotlib (Hunter 2007), Numpy (van der Walt et al. 2010), MPDAF (Piqueras et al. 2017), Astropy (Astropy Collaboration 2018), PyWavelets (Lee et al. 2019).","doi":"10.1051/0004-6361/202039887","volume":647,"scopus_import":"1","year":"2021","publication":"Astronomy & Astrophysics","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.05516"}],"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","extern":"1","publication_status":"published","external_id":{"arxiv":["2102.05516"]}},{"external_id":{"arxiv":["2004.14496"]},"publication_status":"published","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.14496"}],"status":"public","year":"2021","publication":"Monthly Notices of the Royal Astronomical Society","scopus_import":"1","volume":508,"doi":"10.1093/mnras/stab2762","acknowledgement":"The authors thank the referee for constructive feedback that improved the outcome of this study. We are grateful to Antoinette Songaila Cowie for sharing the ‘NEPLA4’ spectrum with us. This research has made use of NASA’s Astrophysics Data System, and many open source projects such as trident (Hummels et al. 2017), IPython (Pérez & Granger 2007), SciPy (Virtanen et al. 2019), NumPy (Walt et al. 2011), matplotlib (Hunter 2007), pandas (McKinney 2010), and the yt-project (Turk et al. 2011). MG was supported by NASA through the NASA Hubble Fellowship grant HST-HF2-51409 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. MG acknowledges support from NASA grants HST-GO-15643.017, and HST-AR15797.001 as well as XSEDE grant TG-AST180036. CAM acknowledges support by NASA Headquarters through the NASA Hubble Fellowship grant HST-HF2-51413.001-A. PRS was supported in part by U.S. NSF grant AST-1009799, NASA grant NNX11AE09G, and supercomputer resources from NSF XSEDE grant TG AST090005 and the Texas Advanced Computing Center (TACC) at The University of Texas at Austin. JM acknowledges a Zwicky Prize Fellowship from ETH Zurich. GY acknowledges financial support by MICIU/FEDER under project grant PGC2018-094975-C21. SEIB acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 669253). ITI was supported by the Science and Technology Facilities Council [grants ST/I000976/1, ST/F002858/1, ST/P000525/1, and ST/T000473/1]; and The Southeast Physics Network (SEPNet). KA was supported by NRF2016R1D1A1B04935414 and NRF-2016R1A5A1013277. KA also appreciates APCTP for its hospitality during completion of this work. PO acknowledges support from the French ANR funded project ORAGE (ANR-14-CE33-0016). ND and DA acknowledge funding from the French ANR for project ANR-12-JS05- 0001 (EMMA). The CoDa II simulation was performed at Oak Ridge National Laboratory/Oak Ridge Leadership Computing Facility on the Titan supercomputer (INCITE 2016 award AST031). Processing was performed on the Eos and Rhea clusters. Resolution study simulations were performed on Piz Daint at the Swiss National Supercomputing Center (PRACE Tier 0 award, project id pr37). The authors would like to acknowledge the High Performance Computing center of the University of Strasbourg for supporting this work by providing scientific support and access to computing resources. Part of the computing resources were funded by the Equipex EquipMeso project (Programme Investissements d’Avenir) and the CPER Alsacalcul/Big Data.","intvolume":"       508","title":"Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation","author":[{"last_name":"Gronke","full_name":"Gronke, Max","first_name":"Max"},{"last_name":"Ocvirk","full_name":"Ocvirk, Pierre","first_name":"Pierre"},{"full_name":"Mason, Charlotte","first_name":"Charlotte","last_name":"Mason"},{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee"},{"last_name":"Bosman","full_name":"Bosman, Sarah E I","first_name":"Sarah E I"},{"full_name":"Sorce, Jenny G","first_name":"Jenny G","last_name":"Sorce"},{"last_name":"Lewis","first_name":"Joseph","full_name":"Lewis, Joseph"},{"first_name":"Kyungjin","full_name":"Ahn, Kyungjin","last_name":"Ahn"},{"last_name":"Aubert","full_name":"Aubert, Dominique","first_name":"Dominique"},{"first_name":"Taha","full_name":"Dawoodbhoy, Taha","last_name":"Dawoodbhoy"},{"first_name":"Ilian T","full_name":"Iliev, Ilian T","last_name":"Iliev"},{"first_name":"Paul R","full_name":"Shapiro, Paul R","last_name":"Shapiro"},{"full_name":"Yepes, Gustavo","first_name":"Gustavo","last_name":"Yepes"}],"date_created":"2022-07-07T09:30:21Z","issue":"3","date_published":"2021-12-01T00:00:00Z","article_type":"original","language":[{"iso":"eng"}],"date_updated":"2022-08-18T10:45:56Z","quality_controlled":"1","publisher":"Oxford University Press","oa_version":"Preprint","arxiv":1,"oa":1,"page":"3697-3709","month":"12","citation":{"chicago":"Gronke, Max, Pierre Ocvirk, Charlotte Mason, Jorryt J Matthee, Sarah E I Bosman, Jenny G Sorce, Joseph Lewis, et al. “Lyman-α Transmission Properties of the Intergalactic Medium in the CoDaII Simulation.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/mnras/stab2762\">https://doi.org/10.1093/mnras/stab2762</a>.","ista":"Gronke M, Ocvirk P, Mason C, Matthee JJ, Bosman SEI, Sorce JG, Lewis J, Ahn K, Aubert D, Dawoodbhoy T, Iliev IT, Shapiro PR, Yepes G. 2021. Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation. Monthly Notices of the Royal Astronomical Society. 508(3), 3697–3709.","ama":"Gronke M, Ocvirk P, Mason C, et al. Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation. <i>Monthly Notices of the Royal Astronomical Society</i>. 2021;508(3):3697-3709. doi:<a href=\"https://doi.org/10.1093/mnras/stab2762\">10.1093/mnras/stab2762</a>","apa":"Gronke, M., Ocvirk, P., Mason, C., Matthee, J. J., Bosman, S. E. I., Sorce, J. G., … Yepes, G. (2021). Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stab2762\">https://doi.org/10.1093/mnras/stab2762</a>","short":"M. Gronke, P. Ocvirk, C. Mason, J.J. Matthee, S.E.I. Bosman, J.G. Sorce, J. Lewis, K. Ahn, D. Aubert, T. Dawoodbhoy, I.T. Iliev, P.R. Shapiro, G. Yepes, Monthly Notices of the Royal Astronomical Society 508 (2021) 3697–3709.","mla":"Gronke, Max, et al. “Lyman-α Transmission Properties of the Intergalactic Medium in the CoDaII Simulation.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 508, no. 3, Oxford University Press, 2021, pp. 3697–709, doi:<a href=\"https://doi.org/10.1093/mnras/stab2762\">10.1093/mnras/stab2762</a>.","ieee":"M. Gronke <i>et al.</i>, “Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 508, no. 3. Oxford University Press, pp. 3697–3709, 2021."},"type":"journal_article","keyword":["dark ages","reionization","first stars","intergalactic medium","galaxies: formation"],"_id":"11522","abstract":[{"lang":"eng","text":"The decline in abundance of Lyman-α (Lyα) emitting galaxies at z ≳ 6 is a powerful and commonly used probe to constrain the progress of cosmic reionization. We use the CODAII simulation, which is a radiation hydrodynamic simulation featuring a box of ∼94 comoving Mpc side length, to compute the Lyα transmission properties of the intergalactic medium (IGM) at z ∼ 5.8 to 7. Our results mainly confirm previous studies, i.e. we find a declining Lyα transmission with redshift and a large sightline-to-sightline variation. However, motivated by the recent discovery of blue Lyα peaks at high redshift, we also analyse the IGM transmission on the blue side, which shows a rapid decline at z ≳ 6 of the blue transmission. This low transmission can be attributed not only to the presence of neutral regions but also to the residual neutral hydrogen within ionized regions, for which a density even as low as nHI∼10−9cm−3 (sometimes combined with kinematic effects) leads to a significantly reduced visibility. Still, we find that ∼1 per cent of sightlines towards M1600AB ∼ −21 galaxies at z ∼ 7 are transparent enough to allow a transmission of a blue Lyα peak. We discuss our results in the context of the interpretation of observations."}]},{"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: luminosity function","mass function"],"_id":"11524","abstract":[{"lang":"eng","text":"We measure the evolution of the rest-frame UV luminosity function (LF) and the stellar mass function (SMF) of Lyman-α (Ly α) emitters (LAEs) from z ∼ 2 to z ∼ 6 by exploring ∼4000 LAEs from the SC4K sample. We find a correlation between Ly α luminosity (LLy α) and rest-frame UV (MUV), with best fit MUV=−1.6+0.2−0.3log10(LLyα/ergs−1)+47+12−11 and a shallower relation between LLy α and stellar mass (M⋆), with best fit log10(M⋆/M⊙)=0.9+0.1−0.1log10(LLyα/ergs−1)−28+4.0−3.8⁠. An increasing LLy α cut predominantly lowers the number density of faint MUV and low M⋆ LAEs. We estimate a proxy for the full UV LFs and SMFs of LAEs with simple assumptions of the faint end slope. For the UV LF, we find a brightening of the characteristic UV luminosity (M∗UV⁠) with increasing redshift and a decrease of the characteristic number density (Φ*). For the SMF, we measure a characteristic stellar mass (⁠M∗⋆/M⊙⁠) increase with increasing redshift, and a Φ* decline. However, if we apply a uniform luminosity cut of log10(LLyα/ergs−1)≥43.0⁠, we find much milder to no evolution in the UV and SMF of LAEs. The UV luminosity density (ρUV) of the full sample of LAEs shows moderate evolution and the stellar mass density (ρM) decreases, with both being always lower than the total ρUV and ρM of more typical galaxies but slowly approaching them with increasing redshift. Overall, our results indicate that both ρUV and ρM of LAEs slowly approach the measurements of continuum-selected galaxies at z > 6, which suggests a key role of LAEs in the epoch of reionization."}],"oa":1,"page":"1117-1134","citation":{"mla":"Santos, S., et al. “The Evolution of the UV Luminosity and Stellar Mass Functions of Lyman-α Emitters from z ∼ 2 to z ∼ 6.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 505, no. 1, Oxford University Press, 2021, pp. 1117–34, doi:<a href=\"https://doi.org/10.1093/mnras/stab1218\">10.1093/mnras/stab1218</a>.","ieee":"S. Santos <i>et al.</i>, “The evolution of the UV luminosity and stellar mass functions of Lyman-α emitters from z ∼ 2 to z ∼ 6,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 505, no. 1. Oxford University Press, pp. 1117–1134, 2021.","ista":"Santos S, Sobral D, Butterworth J, Paulino-Afonso A, Ribeiro B, da Cunha E, Calhau J, Khostovan AA, Matthee JJ, Arrabal Haro P. 2021. The evolution of the UV luminosity and stellar mass functions of Lyman-α emitters from z ∼ 2 to z ∼ 6. Monthly Notices of the Royal Astronomical Society. 505(1), 1117–1134.","chicago":"Santos, S, D Sobral, J Butterworth, A Paulino-Afonso, B Ribeiro, E da Cunha, J Calhau, A A Khostovan, Jorryt J Matthee, and P Arrabal Haro. “The Evolution of the UV Luminosity and Stellar Mass Functions of Lyman-α Emitters from z ∼ 2 to z ∼ 6.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/mnras/stab1218\">https://doi.org/10.1093/mnras/stab1218</a>.","ama":"Santos S, Sobral D, Butterworth J, et al. The evolution of the UV luminosity and stellar mass functions of Lyman-α emitters from z ∼ 2 to z ∼ 6. <i>Monthly Notices of the Royal Astronomical Society</i>. 2021;505(1):1117-1134. doi:<a href=\"https://doi.org/10.1093/mnras/stab1218\">10.1093/mnras/stab1218</a>","apa":"Santos, S., Sobral, D., Butterworth, J., Paulino-Afonso, A., Ribeiro, B., da Cunha, E., … Arrabal Haro, P. (2021). The evolution of the UV luminosity and stellar mass functions of Lyman-α emitters from z ∼ 2 to z ∼ 6. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stab1218\">https://doi.org/10.1093/mnras/stab1218</a>","short":"S. Santos, D. Sobral, J. Butterworth, A. Paulino-Afonso, B. Ribeiro, E. da Cunha, J. Calhau, A.A. Khostovan, J.J. Matthee, P. Arrabal Haro, Monthly Notices of the Royal Astronomical Society 505 (2021) 1117–1134."},"month":"07","type":"journal_article","arxiv":1,"quality_controlled":"1","publisher":"Oxford University Press","oa_version":"Preprint","date_updated":"2022-08-18T10:51:47Z","language":[{"iso":"eng"}],"date_published":"2021-07-01T00:00:00Z","article_type":"original","date_created":"2022-07-07T10:02:59Z","title":"The evolution of the UV luminosity and stellar mass functions of Lyman-α emitters from z ∼ 2 to z ∼ 6","author":[{"last_name":"Santos","full_name":"Santos, S","first_name":"S"},{"last_name":"Sobral","first_name":"D","full_name":"Sobral, D"},{"first_name":"J","full_name":"Butterworth, J","last_name":"Butterworth"},{"full_name":"Paulino-Afonso, A","first_name":"A","last_name":"Paulino-Afonso"},{"last_name":"Ribeiro","full_name":"Ribeiro, B","first_name":"B"},{"last_name":"da Cunha","full_name":"da Cunha, E","first_name":"E"},{"full_name":"Calhau, J","first_name":"J","last_name":"Calhau"},{"last_name":"Khostovan","full_name":"Khostovan, A A","first_name":"A A"},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"},{"full_name":"Arrabal Haro, P","first_name":"P","last_name":"Arrabal Haro"}],"issue":"1","doi":"10.1093/mnras/stab1218","acknowledgement":"This research made use of Astropy, a community developed core Python package for Astronomy (Astropy Collaboration et al. 2013). topcat, a graphical tool for manipulating tabular data, was also utilized in this analysis (Taylor 2005). SG would like to thank Nastasha Wijers for the discussion on the column density distribution in EAGLE. SC gratefully acknowledges support from Swiss National Science Foundation grants PP00P2 163824 and PP00P2 190092, and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No 864361. GP acknowledges support from the Swiss National Science Foundation (SNF) and from the Netherlands Research School for Astronomy (NOVA).","intvolume":"       505","year":"2021","publication":"Monthly Notices of the Royal Astronomical Society","scopus_import":"1","volume":505,"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"day":"01","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2105.00007"}],"external_id":{"arxiv":["2105.00007"]},"extern":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"date_updated":"2024-11-06T12:09:22Z","oa_version":"Preprint","quality_controlled":"1","publisher":"Elsevier","arxiv":1,"type":"journal_article","citation":{"apa":"Henzinger, M., &#38; Peng, P. (2021). Constant-time dynamic weight approximation for minimum spanning forest. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2021.104805\">https://doi.org/10.1016/j.ic.2021.104805</a>","short":"M. Henzinger, P. Peng, Information and Computation 281 (2021).","ama":"Henzinger M, Peng P. Constant-time dynamic weight approximation for minimum spanning forest. <i>Information and Computation</i>. 2021;281(12). doi:<a href=\"https://doi.org/10.1016/j.ic.2021.104805\">10.1016/j.ic.2021.104805</a>","ista":"Henzinger M, Peng P. 2021. Constant-time dynamic weight approximation for minimum spanning forest. Information and Computation. 281(12), 104805.","chicago":"Henzinger, Monika, and Pan Peng. “Constant-Time Dynamic Weight Approximation for Minimum Spanning Forest.” <i>Information and Computation</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ic.2021.104805\">https://doi.org/10.1016/j.ic.2021.104805</a>.","ieee":"M. Henzinger and P. Peng, “Constant-time dynamic weight approximation for minimum spanning forest,” <i>Information and Computation</i>, vol. 281, no. 12. Elsevier, 2021.","mla":"Henzinger, Monika, and Pan Peng. “Constant-Time Dynamic Weight Approximation for Minimum Spanning Forest.” <i>Information and Computation</i>, vol. 281, no. 12, 104805, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.ic.2021.104805\">10.1016/j.ic.2021.104805</a>."},"month":"12","oa":1,"abstract":[{"lang":"eng","text":"We give two fully dynamic algorithms that maintain a (1 + ε)-approximation of the weight M of a minimum spanning forest (MSF) of an n-node graph G with edges weights in [1, W ], for any ε > 0. (1) Our deterministic algorithm takes O (W 2 log W /ε3) worst-case update time, which is O (1) if both W and ε are constants. (2) Our randomized (Monte-Carlo style) algorithm works with high probability and runs in worst-case O (log W /ε4) update time if W = O ((m∗)1/6/log2/3 n), where m∗ is the minimum number of edges in the graph throughout all the updates. It works even against an adaptive adversary. We complement our algorithmic results with two cell-probe lower bounds for dynamically maintaining an approximation of the weight of an MSF of a graph."}],"_id":"11756","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2011.00977"]},"publication_status":"published","extern":"1","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/2011.00977","open_access":"1"}],"day":"01","publication_identifier":{"issn":["0890-5401"]},"volume":281,"publication":"Information and Computation","year":"2021","scopus_import":"1","intvolume":"       281","doi":"10.1016/j.ic.2021.104805","issue":"12","title":"Constant-time dynamic weight approximation for minimum spanning forest","article_number":"104805","date_created":"2022-08-08T10:58:29Z","author":[{"first_name":"Monika H","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"full_name":"Peng, Pan","first_name":"Pan","last_name":"Peng"}],"article_type":"original","date_published":"2021-12-01T00:00:00Z"},{"extern":"1","publication_status":"published","external_id":{"arxiv":["1504.07056"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.07056"}],"status":"public","scopus_import":"1","year":"2021","publication":"SIAM Journal on Computing","volume":50,"doi":"10.1137/16m1097808","intvolume":"        50","date_created":"2022-08-17T07:54:45Z","author":[{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"first_name":"Danupon","full_name":"Nanongkai, Danupon","last_name":"Nanongkai"}],"title":"A deterministic almost-tight distributed algorithm for approximating single-source shortest paths","issue":"3","date_published":"2021-05-01T00:00:00Z","article_type":"original","date_updated":"2024-11-06T12:22:31Z","language":[{"iso":"eng"}],"publisher":"Society for Industrial & Applied Mathematics","quality_controlled":"1","oa_version":"Preprint","arxiv":1,"page":"STOC16-98-STOC16-137","oa":1,"citation":{"apa":"Henzinger, M., Krinninger, S., &#38; Nanongkai, D. (2021). A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. <i>SIAM Journal on Computing</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/16m1097808\">https://doi.org/10.1137/16m1097808</a>","short":"M. Henzinger, S. Krinninger, D. Nanongkai, SIAM Journal on Computing 50 (2021) STOC16-98-STOC16-137.","ama":"Henzinger M, Krinninger S, Nanongkai D. A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. <i>SIAM Journal on Computing</i>. 2021;50(3):STOC16-98-STOC16-137. doi:<a href=\"https://doi.org/10.1137/16m1097808\">10.1137/16m1097808</a>","ista":"Henzinger M, Krinninger S, Nanongkai D. 2021. A deterministic almost-tight distributed algorithm for approximating single-source shortest paths. SIAM Journal on Computing. 50(3), STOC16-98-STOC16-137.","chicago":"Henzinger, Monika, Sebastian Krinninger, and Danupon Nanongkai. “A Deterministic Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.” <i>SIAM Journal on Computing</i>. Society for Industrial &#38; Applied Mathematics, 2021. <a href=\"https://doi.org/10.1137/16m1097808\">https://doi.org/10.1137/16m1097808</a>.","mla":"Henzinger, Monika, et al. “A Deterministic Almost-Tight Distributed Algorithm for Approximating Single-Source Shortest Paths.” <i>SIAM Journal on Computing</i>, vol. 50, no. 3, Society for Industrial &#38; Applied Mathematics, 2021, pp. STOC16-98-STOC16-137, doi:<a href=\"https://doi.org/10.1137/16m1097808\">10.1137/16m1097808</a>.","ieee":"M. Henzinger, S. Krinninger, and D. Nanongkai, “A deterministic almost-tight distributed algorithm for approximating single-source shortest paths,” <i>SIAM Journal on Computing</i>, vol. 50, no. 3. Society for Industrial &#38; Applied Mathematics, pp. STOC16-98-STOC16-137, 2021."},"month":"05","type":"journal_article","_id":"11886","abstract":[{"text":"We present a deterministic (1+𝑜(1))-approximation (𝑛1/2+𝑜(1)+𝐷1+𝑜(1))-time algorithm for solving the single-source shortest paths problem on distributed weighted networks (the \\sf CONGEST model); here 𝑛 is the number of nodes in the network, 𝐷 is its (hop) diameter, and edge weights are positive integers from 1 to poly(𝑛). This is the first nontrivial deterministic algorithm for this problem. It also improves (i) the running time of the randomized (1+𝑜(1))-approximation 𝑂̃ (𝑛√𝐷1/4+𝐷)-time algorithm of Nanongkai [in Proceedings of STOC, 2014, pp. 565--573] by a factor of as large as 𝑛1/8, and (ii) the 𝑂(𝜖−1log𝜖−1)-approximation factor of Lenzen and Patt-Shamir's 𝑂̃ (𝑛1/2+𝜖+𝐷)-time algorithm [in Proceedings of STOC, 2013, pp. 381--390] within the same running time. (Throughout, we use 𝑂̃ (⋅) to hide polylogarithmic factors in 𝑛.) Our running time matches the known time lower bound of Ω(𝑛/log𝑛‾‾‾‾‾‾‾√+𝐷) [M. Elkin, SIAM J. Comput., 36 (2006), pp. 433--456], thus essentially settling the status of this problem which was raised at least a decade ago [M. Elkin, SIGACT News, 35 (2004), pp. 40--57]. It also implies a (2+𝑜(1))-approximation (𝑛1/2+𝑜(1)+𝐷1+𝑜(1))-time algorithm for approximating a network's weighted diameter which almost matches the lower bound by Holzer and Pinsker [in Proceedings of OPODIS, 2015, Schloss Dagstuhl. Leibniz-Zent. Inform., Wadern, Germany, 2016, 6]. In achieving this result, we develop two techniques which might be of independent interest and useful in other settings: (i) a deterministic process that replaces the “hitting set argument” commonly used for shortest paths computation in various settings, and (ii) a simple, deterministic construction of an (𝑛𝑜(1),𝑜(1))-hop set of size 𝑛1+𝑜(1). We combine these techniques with many distributed algorithmic techniques, some of which are from problems that are not directly related to shortest paths, e.g., ruling sets [A. V. Goldberg, S. A. Plotkin, and G. E. Shannon, SIAM J. Discrete Math., 1 (1988), pp. 434--446], source detection [C. Lenzen and D. Peleg, in Proceedings of PODC, 2013, pp. 375--382], and partial distance estimation [C. Lenzen and B. Patt-Shamir, in Proceedings of PODC, 2015, pp. 153--162]. Our hop set construction also leads to single-source shortest paths algorithms in two other settings: (i) a (1+𝑜(1))-approximation 𝑛𝑜(1)-time algorithm on congested cliques, and (ii) a (1+𝑜(1))-approximation 𝑛𝑜(1)-pass 𝑛1+𝑜(1)-space streaming algorithm. The first result answers an open problem in [D. Nanongkai, in Proceedings of STOC, 2014, pp. 565--573]. The second result partially answers an open problem raised by McGregor in 2006 [List of Open Problems in Sublinear Algorithms: Problem 14].","lang":"eng"}]},{"page":"313-317","citation":{"ama":"Greenwald JE, Cameron J, Findlay NJ, et al. Highly nonlinear transport across single-molecule junctions via destructive quantum interference. <i>Nature Nanotechnology</i>. 2021;16(3):313-317. doi:<a href=\"https://doi.org/10.1038/s41565-020-00807-x\">10.1038/s41565-020-00807-x</a>","chicago":"Greenwald, Julia E., Joseph Cameron, Neil J. Findlay, Tianren Fu, Suman Gunasekaran, Peter J. Skabara, and Latha Venkataraman. “Highly Nonlinear Transport across Single-Molecule Junctions via Destructive Quantum Interference.” <i>Nature Nanotechnology</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41565-020-00807-x\">https://doi.org/10.1038/s41565-020-00807-x</a>.","ista":"Greenwald JE, Cameron J, Findlay NJ, Fu T, Gunasekaran S, Skabara PJ, Venkataraman L. 2021. Highly nonlinear transport across single-molecule junctions via destructive quantum interference. Nature Nanotechnology. 16(3), 313–317.","short":"J.E. Greenwald, J. Cameron, N.J. Findlay, T. Fu, S. Gunasekaran, P.J. Skabara, L. Venkataraman, Nature Nanotechnology 16 (2021) 313–317.","apa":"Greenwald, J. E., Cameron, J., Findlay, N. J., Fu, T., Gunasekaran, S., Skabara, P. J., &#38; Venkataraman, L. (2021). Highly nonlinear transport across single-molecule junctions via destructive quantum interference. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41565-020-00807-x\">https://doi.org/10.1038/s41565-020-00807-x</a>","mla":"Greenwald, Julia E., et al. “Highly Nonlinear Transport across Single-Molecule Junctions via Destructive Quantum Interference.” <i>Nature Nanotechnology</i>, vol. 16, no. 3, Springer Nature, 2021, pp. 313–17, doi:<a href=\"https://doi.org/10.1038/s41565-020-00807-x\">10.1038/s41565-020-00807-x</a>.","ieee":"J. E. Greenwald <i>et al.</i>, “Highly nonlinear transport across single-molecule junctions via destructive quantum interference,” <i>Nature Nanotechnology</i>, vol. 16, no. 3. Springer Nature, pp. 313–317, 2021."},"type":"journal_article","month":"03","_id":"17900","abstract":[{"lang":"eng","text":"To rival the performance of modern integrated circuits, single-molecule devices must be designed to exhibit extremely nonlinear current–voltage (I–V) characteristics1,2,3,4. A common approach is to design molecular backbones where destructive quantum interference (QI) between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) produces a nonlinear energy-dependent tunnelling probability near the electrode Fermi energy (EF)5,6,7,8. However, tuning such systems is not straightforward, as aligning the frontier orbitals to EF is hard to control9. Here, we instead create a molecular system where constructive QI between the HOMO and LUMO is suppressed and destructive QI between the HOMO and strongly coupled occupied orbitals of opposite phase is enhanced. We use a series of fluorene oligomers containing a central benzothiadiazole10 unit to demonstrate that this strategy can be used to create highly nonlinear single-molecule circuits. Notably, we are able to reproducibly modulate the conductance of a 6-nm molecule by a factor of more than 10^4."}],"date_updated":"2024-12-10T10:20:32Z","language":[{"iso":"eng"}],"publisher":"Springer Nature","quality_controlled":"1","oa_version":"None","title":"Highly nonlinear transport across single-molecule junctions via destructive quantum interference","author":[{"first_name":"Julia E.","full_name":"Greenwald, Julia E.","last_name":"Greenwald"},{"full_name":"Cameron, Joseph","first_name":"Joseph","last_name":"Cameron"},{"last_name":"Findlay","first_name":"Neil J.","full_name":"Findlay, Neil J."},{"last_name":"Fu","full_name":"Fu, Tianren","first_name":"Tianren"},{"first_name":"Suman","full_name":"Gunasekaran, Suman","last_name":"Gunasekaran"},{"last_name":"Skabara","first_name":"Peter J.","full_name":"Skabara, Peter J."},{"id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","first_name":"Latha","full_name":"Venkataraman, Latha"}],"date_created":"2024-09-09T06:43:51Z","issue":"3","date_published":"2021-03-01T00:00:00Z","pmid":1,"scopus_import":"1","year":"2021","publication":"Nature Nanotechnology","volume":16,"doi":"10.1038/s41565-020-00807-x","intvolume":"        16","publication_status":"published","extern":"1","external_id":{"pmid":["33288949"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"status":"public","OA_type":"closed access"}]