[{"doi":"10.1016/j.isci.2019.11.025","citation":{"short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268.","mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>.","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>.","ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>iScience</i>. 2019;22(12):256-268. doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>","ieee":"S. Tabata <i>et al.</i>, “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” <i>iScience</i>, vol. 22, no. 12. Elsevier, pp. 256–268, 2019.","ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268."},"related_material":{"record":[{"relation":"dissertation_contains","id":"11393","status":"public"}]},"title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","day":"20","project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"department":[{"_id":"RySh"}],"publisher":"Elsevier","publication":"iScience","ddc":["570"],"issue":"12","page":"256-268","pmid":1,"file":[{"access_level":"open_access","creator":"dernst","content_type":"application/pdf","checksum":"f3e90056a49f09b205b1c4f8c739ffd1","relation":"main_file","date_updated":"2020-07-14T12:47:57Z","file_size":7197776,"file_id":"7448","file_name":"2019_iScience_Tabata.pdf","date_created":"2020-02-04T10:48:36Z"}],"abstract":[{"lang":"eng","text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM."}],"volume":22,"publication_identifier":{"issn":["2589-0042"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-01-29T15:56:56Z","type":"journal_article","has_accepted_license":"1","date_published":"2019-12-20T00:00:00Z","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2024-03-25T23:30:07Z","year":"2019","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"month":"12","external_id":{"isi":[":000504652000020"],"pmid":["31786521"]},"intvolume":"        22","publication_status":"published","_id":"7391","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:57Z","status":"public","article_type":"original","author":[{"id":"4427179E-F248-11E8-B48F-1D18A9856A87","last_name":"Tabata","full_name":"Tabata, Shigekazu","first_name":"Shigekazu"},{"last_name":"Jevtic","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","first_name":"Marijo","full_name":"Jevtic, Marijo"},{"full_name":"Kurashige, Nobutaka","first_name":"Nobutaka","last_name":"Kurashige"},{"last_name":"Fuchida","full_name":"Fuchida, Hirokazu","first_name":"Hirokazu"},{"last_name":"Kido","full_name":"Kido, Munetsugu","first_name":"Munetsugu"},{"first_name":"Kazushi","full_name":"Tani, Kazushi","last_name":"Tani"},{"last_name":"Zenmyo","full_name":"Zenmyo, Naoki","first_name":"Naoki"},{"last_name":"Uchinomiya","full_name":"Uchinomiya, Shohei","first_name":"Shohei"},{"id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","first_name":"Harumi"},{"last_name":"Itakura","first_name":"Makoto","full_name":"Itakura, Makoto"},{"first_name":"Itaru","full_name":"Hamachi, Itaru","last_name":"Hamachi"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"first_name":"Akio","full_name":"Ojida, Akio","last_name":"Ojida"}],"quality_controlled":"1","article_processing_charge":"No"},{"doi":"10.1126/sciadv.aav9963","isi":1,"department":[{"_id":"NiBa"}],"publisher":"AAAS","publication":"Science Advances","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"day":"04","title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","citation":{"ieee":"H. E. Morales <i>et al.</i>, “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” <i>Science Advances</i>, vol. 5, no. 12. AAAS, 2019.","ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. <i>Science Advances</i>. 2019;5(12). doi:<a href=\"https://doi.org/10.1126/sciadv.aav9963\">10.1126/sciadv.aav9963</a>","ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019).","mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” <i>Science Advances</i>, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:<a href=\"https://doi.org/10.1126/sciadv.aav9963\">10.1126/sciadv.aav9963</a>.","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., &#38; Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.aav9963\">https://doi.org/10.1126/sciadv.aav9963</a>","chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” <i>Science Advances</i>. AAAS, 2019. <a href=\"https://doi.org/10.1126/sciadv.aav9963\">https://doi.org/10.1126/sciadv.aav9963</a>."},"issue":"12","article_number":"eaav9963","ddc":["570"],"abstract":[{"lang":"eng","text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow."}],"pmid":1,"file":[{"file_id":"7442","file_size":1869449,"date_updated":"2020-07-14T12:47:57Z","relation":"main_file","checksum":"af99a5dcdc66c6d6102051faf3be48d8","access_level":"open_access","content_type":"application/pdf","creator":"dernst","date_created":"2020-02-03T13:33:25Z","file_name":"2019_ScienceAdvances_Morales.pdf"}],"date_published":"2019-12-04T00:00:00Z","has_accepted_license":"1","date_created":"2020-01-29T15:58:27Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"type":"journal_article","volume":5,"publication_identifier":{"issn":["2375-2548"]},"ec_funded":1,"oa":1,"year":"2019","scopus_import":"1","date_updated":"2023-09-06T15:35:56Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"original","_id":"7393","oa_version":"Published Version","status":"public","file_date_updated":"2020-07-14T12:47:57Z","language":[{"iso":"eng"}],"publication_status":"published","month":"12","intvolume":"         5","external_id":{"isi":["000505069600008"],"pmid":["31840052"]},"article_processing_charge":"No","quality_controlled":"1","author":[{"last_name":"Morales","full_name":"Morales, Hernán E.","first_name":"Hernán E."},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}]},{"language":[{"iso":"eng"}],"external_id":{"isi":["000502890600001"],"pmid":["31787165"]},"publication_status":"published","intvolume":"        52","month":"12","oa_version":"None","_id":"7394","status":"public","article_type":"letter_note","author":[{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"last_name":"Dagdas","full_name":"Dagdas, Yasin","first_name":"Yasin"}],"quality_controlled":"1","article_processing_charge":"No","volume":52,"publication_identifier":{"issn":["1369-5266"]},"date_created":"2020-01-29T16:00:07Z","type":"journal_article","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","date_updated":"2023-09-07T14:56:55Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","issue":"12","page":"A1-A2","pmid":1,"doi":"10.1016/j.pbi.2019.11.002","isi":1,"citation":{"ista":"Benková E, Dagdas Y. 2019. Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. 52(12), A1–A2.","ama":"Benková E, Dagdas Y. Editorial overview: Cell biology in the era of omics? <i>Current Opinion in Plant Biology</i>. 2019;52(12):A1-A2. doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.11.002\">10.1016/j.pbi.2019.11.002</a>","ieee":"E. Benková and Y. Dagdas, “Editorial overview: Cell biology in the era of omics?,” <i>Current Opinion in Plant Biology</i>, vol. 52, no. 12. Elsevier, pp. A1–A2, 2019.","chicago":"Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era of Omics?” <i>Current Opinion in Plant Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.pbi.2019.11.002\">https://doi.org/10.1016/j.pbi.2019.11.002</a>.","short":"E. Benková, Y. Dagdas, Current Opinion in Plant Biology 52 (2019) A1–A2.","mla":"Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era of Omics?” <i>Current Opinion in Plant Biology</i>, vol. 52, no. 12, Elsevier, 2019, pp. A1–2, doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.11.002\">10.1016/j.pbi.2019.11.002</a>.","apa":"Benková, E., &#38; Dagdas, Y. (2019). Editorial overview: Cell biology in the era of omics? <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2019.11.002\">https://doi.org/10.1016/j.pbi.2019.11.002</a>"},"title":"Editorial overview: Cell biology in the era of omics?","day":"01","department":[{"_id":"EvBe"}],"publisher":"Elsevier","publication":"Current Opinion in Plant Biology"},{"project":[{"call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309"}],"day":"19","publication":"Molecular Cell","publisher":"Cell Press","department":[{"_id":"LeSa"}],"citation":{"ama":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. <i>Molecular Cell</i>. 2019;75(6):1131-1146.e6. doi:<a href=\"https://doi.org/10.1016/j.molcel.2019.07.022\">10.1016/j.molcel.2019.07.022</a>","ieee":"J. A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, and L. A. Sazanov, “Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk,” <i>Molecular Cell</i>, vol. 75, no. 6. Cell Press, p. 1131–1146.e6, 2019.","ista":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. 2019. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 75(6), 1131–1146.e6.","short":"J.A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, L.A. Sazanov, Molecular Cell 75 (2019) 1131–1146.e6.","mla":"Letts, James A., et al. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” <i>Molecular Cell</i>, vol. 75, no. 6, Cell Press, 2019, p. 1131–1146.e6, doi:<a href=\"https://doi.org/10.1016/j.molcel.2019.07.022\">10.1016/j.molcel.2019.07.022</a>.","apa":"Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., &#38; Sazanov, L. A. (2019). Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2019.07.022\">https://doi.org/10.1016/j.molcel.2019.07.022</a>","chicago":"Letts, James A, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, and Leonid A Sazanov. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” <i>Molecular Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.molcel.2019.07.022\">https://doi.org/10.1016/j.molcel.2019.07.022</a>."},"title":"Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk","isi":1,"doi":"10.1016/j.molcel.2019.07.022","abstract":[{"lang":"eng","text":"The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII2. CI shows a transition between “closed” and “open” conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII2, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs."}],"page":"1131-1146.e6","pmid":1,"file":[{"file_id":"7447","file_size":9654895,"date_updated":"2020-07-14T12:47:57Z","relation":"main_file","checksum":"5202f53a237d6650ece038fbf13bdcea","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2020-02-04T10:37:28Z","file_name":"2019_MolecularCell_Letts.pdf"}],"issue":"6","ddc":["570"],"oa":1,"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T14:53:06Z","scopus_import":"1","year":"2019","has_accepted_license":"1","date_published":"2019-09-19T00:00:00Z","publication_identifier":{"issn":["1097-2765"]},"volume":75,"type":"journal_article","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-01-29T16:02:33Z","article_processing_charge":"No","author":[{"orcid":"0000-0002-9864-3586","full_name":"Letts, James A","first_name":"James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87","last_name":"Letts"},{"last_name":"Fiedorczuk","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol","full_name":"Fiedorczuk, Karol"},{"first_name":"Gianluca","full_name":"Degliesposti, Gianluca","last_name":"Degliesposti"},{"full_name":"Skehel, Mark","first_name":"Mark","last_name":"Skehel"},{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"quality_controlled":"1","article_type":"original","intvolume":"        75","external_id":{"pmid":["31492636"],"isi":["000486614200006"]},"month":"09","publication_status":"published","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:57Z","status":"public","oa_version":"Published Version","_id":"7395"},{"quality_controlled":"1","author":[{"last_name":"Koch","first_name":"Christiane P.","full_name":"Koch, Christiane P."},{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sugny","first_name":"Dominique","full_name":"Sugny, Dominique"}],"article_processing_charge":"No","oa_version":"Preprint","_id":"7396","status":"public","language":[{"iso":"eng"}],"intvolume":"        91","publication_status":"published","external_id":{"arxiv":["1810.11338"],"isi":["000486661700001"]},"month":"09","article_type":"original","year":"2019","scopus_import":"1","date_updated":"2024-02-28T13:15:33Z","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_created":"2020-01-29T16:04:19Z","type":"journal_article","volume":91,"publication_identifier":{"issn":["0034-6861"],"eissn":["1539-0756"]},"date_published":"2019-09-18T00:00:00Z","abstract":[{"lang":"eng","text":"The angular momentum of molecules, or, equivalently, their rotation in three-dimensional space, is ideally suited for quantum control. Molecular angular momentum is naturally quantized, time evolution is governed by a well-known Hamiltonian with only a few accurately known parameters, and transitions between rotational levels can be driven by external fields from various parts of the electromagnetic spectrum. Control over the rotational motion can be exerted in one-, two-, and many-body scenarios, thereby allowing one to probe Anderson localization, target stereoselectivity of bimolecular reactions, or encode quantum information to name just a few examples. The corresponding approaches to quantum control are pursued within separate, and typically disjoint, subfields of physics, including ultrafast science, cold collisions, ultracold gases, quantum information science, and condensed-matter physics. It is the purpose of this review to present the various control phenomena, which all rely on the same underlying physics, within a unified framework. To this end, recall the Hamiltonian for free rotations, assuming the rigid rotor approximation to be valid, and summarize the different ways for a rotor to interact with external electromagnetic fields. These interactions can be exploited for control—from achieving alignment, orientation, or laser cooling in a one-body framework, steering bimolecular collisions, or realizing a quantum computer or quantum simulator in the many-body setting."}],"article_number":"035005 ","issue":"3","title":"Quantum control of molecular rotation","citation":{"ama":"Koch CP, Lemeshko M, Sugny D. Quantum control of molecular rotation. <i>Reviews of Modern Physics</i>. 2019;91(3). doi:<a href=\"https://doi.org/10.1103/revmodphys.91.035005\">10.1103/revmodphys.91.035005</a>","ieee":"C. P. Koch, M. Lemeshko, and D. Sugny, “Quantum control of molecular rotation,” <i>Reviews of Modern Physics</i>, vol. 91, no. 3. American Physical Society, 2019.","ista":"Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation. Reviews of Modern Physics. 91(3), 035005.","short":"C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (2019).","mla":"Koch, Christiane P., et al. “Quantum Control of Molecular Rotation.” <i>Reviews of Modern Physics</i>, vol. 91, no. 3, 035005, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/revmodphys.91.035005\">10.1103/revmodphys.91.035005</a>.","apa":"Koch, C. P., Lemeshko, M., &#38; Sugny, D. (2019). Quantum control of molecular rotation. <i>Reviews of Modern Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/revmodphys.91.035005\">https://doi.org/10.1103/revmodphys.91.035005</a>","chicago":"Koch, Christiane P., Mikhail Lemeshko, and Dominique Sugny. “Quantum Control of Molecular Rotation.” <i>Reviews of Modern Physics</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/revmodphys.91.035005\">https://doi.org/10.1103/revmodphys.91.035005</a>."},"department":[{"_id":"MiLe"}],"main_file_link":[{"url":"https://arxiv.org/abs/1810.11338","open_access":"1"}],"publisher":"American Physical Society","publication":"Reviews of Modern Physics","day":"18","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"doi":"10.1103/revmodphys.91.035005","isi":1},{"volume":874,"publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"date_created":"2020-01-29T16:05:19Z","type":"journal_article","date_published":"2019-09-10T00:00:00Z","scopus_import":"1","date_updated":"2023-09-06T15:36:36Z","arxiv":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","oa":1,"language":[{"iso":"eng"}],"month":"09","intvolume":"       874","publication_status":"published","external_id":{"isi":["000475349900001"],"arxiv":["1808.04080"]},"_id":"7397","oa_version":"Preprint","status":"public","article_type":"original","author":[{"last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87","first_name":"Jose M","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M"},{"first_name":"George H","full_name":"Choueiri, George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1017/jfm.2019.486","isi":1,"citation":{"chicago":"Lopez Alonso, Jose M, George H Choueiri, and Björn Hof. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” <i>Journal of Fluid Mechanics</i>. CUP, 2019. <a href=\"https://doi.org/10.1017/jfm.2019.486\">https://doi.org/10.1017/jfm.2019.486</a>.","apa":"Lopez Alonso, J. M., Choueiri, G. H., &#38; Hof, B. (2019). Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. <i>Journal of Fluid Mechanics</i>. CUP. <a href=\"https://doi.org/10.1017/jfm.2019.486\">https://doi.org/10.1017/jfm.2019.486</a>","short":"J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874 (2019) 699–719.","mla":"Lopez Alonso, Jose M., et al. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” <i>Journal of Fluid Mechanics</i>, vol. 874, CUP, 2019, pp. 699–719, doi:<a href=\"https://doi.org/10.1017/jfm.2019.486\">10.1017/jfm.2019.486</a>.","ista":"Lopez Alonso JM, Choueiri GH, Hof B. 2019. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 874, 699–719.","ama":"Lopez Alonso JM, Choueiri GH, Hof B. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. <i>Journal of Fluid Mechanics</i>. 2019;874:699-719. doi:<a href=\"https://doi.org/10.1017/jfm.2019.486\">10.1017/jfm.2019.486</a>","ieee":"J. M. Lopez Alonso, G. H. Choueiri, and B. Hof, “Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit,” <i>Journal of Fluid Mechanics</i>, vol. 874. CUP, pp. 699–719, 2019."},"title":"Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit","day":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04080"}],"department":[{"_id":"BjHo"}],"publication":"Journal of Fluid Mechanics","publisher":"CUP","page":"699-719","abstract":[{"text":"Polymer additives can substantially reduce the drag of turbulent flows and the upperlimit, the so called “maximum drag reduction” (MDR) asymptote is universal, i.e. inde-pendent of the type of polymer and solvent used. Until recently, the consensus was that,in this limit, flows are in a marginal state where only a minimal level of turbulence activ-ity persists. Observations in direct numerical simulations using minimal sized channelsappeared  to  support  this  view  and  reported  long  “hibernation”  periods  where  turbu-lence is marginalized. In simulations of pipe flow we find that, indeed, with increasingWeissenberg number (Wi), turbulence expresses long periods of hibernation if the domainsize is small. However, with increasing pipe length, the temporal hibernation continuouslyalters to spatio-temporal intermittency and here the flow consists of turbulent puffs sur-rounded by laminar flow. Moreover, upon an increase in Wi, the flow fully relaminarises,in agreement with recent experiments. At even larger Wi, a different instability is en-countered causing a drag increase towards MDR. Our findings hence link earlier minimalflow unit simulations with recent experiments and confirm that the addition of polymersinitially suppresses Newtonian turbulence and leads to a reverse transition. The MDRstate on the other hand results from a separate instability and the underlying dynamicscorresponds to the recently proposed state of elasto-inertial-turbulence (EIT).","lang":"eng"}]},{"issue":"8","ddc":["570"],"abstract":[{"lang":"eng","text":"Transporters of the solute carrier 6 (SLC6) family translocate their cognate substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4). Here, we posited that the transport cycle of individual SLC6 transporters reflects the physiological requirements they operate under. We tested this hypothesis by analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions in real time by electrophysiological recordings. Contrary to monoamine transporters, both GlyTs were found to have a high transport capacity driven by rapid return of the empty transporter after release of Cl− on the intracellular side. Rapid cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate ions and substrate such that their forward transport mode was maintained even under conditions of elevated intracellular Na+ or Cl−. The most important differences in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1 were governed by transition of the substrate-bound transporter from outward- to inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+ binding (or a related conformational change). Kinetic modeling showed that the kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels required for NMDA receptor activation."}],"page":"1035-1050","file":[{"file_size":2641297,"file_id":"7450","date_updated":"2020-07-14T12:47:57Z","checksum":"5706b4ccd74ee3e50bf7ecb2a203df71","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_created":"2020-02-05T07:20:32Z","file_name":"2019_JGP_Erdem.pdf"}],"pmid":1,"doi":"10.1085/jgp.201912318","isi":1,"day":"03","department":[{"_id":"RySh"}],"publication":"The Journal of General Physiology","publisher":"Rockefeller University Press","citation":{"short":"F.A. Erdem, M. Ilic, P. Koppensteiner, J. Gołacki, G. Lubec, M. Freissmuth, W. Sandtner, The Journal of General Physiology 151 (2019) 1035–1050.","mla":"Erdem, Fatma Asli, et al. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” <i>The Journal of General Physiology</i>, vol. 151, no. 8, Rockefeller University Press, 2019, pp. 1035–50, doi:<a href=\"https://doi.org/10.1085/jgp.201912318\">10.1085/jgp.201912318</a>.","apa":"Erdem, F. A., Ilic, M., Koppensteiner, P., Gołacki, J., Lubec, G., Freissmuth, M., &#38; Sandtner, W. (2019). A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. <i>The Journal of General Physiology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1085/jgp.201912318\">https://doi.org/10.1085/jgp.201912318</a>","chicago":"Erdem, Fatma Asli, Marija Ilic, Peter Koppensteiner, Jakub Gołacki, Gert Lubec, Michael Freissmuth, and Walter Sandtner. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” <i>The Journal of General Physiology</i>. Rockefeller University Press, 2019. <a href=\"https://doi.org/10.1085/jgp.201912318\">https://doi.org/10.1085/jgp.201912318</a>.","ama":"Erdem FA, Ilic M, Koppensteiner P, et al. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. <i>The Journal of General Physiology</i>. 2019;151(8):1035-1050. doi:<a href=\"https://doi.org/10.1085/jgp.201912318\">10.1085/jgp.201912318</a>","ieee":"F. A. Erdem <i>et al.</i>, “A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2,” <i>The Journal of General Physiology</i>, vol. 151, no. 8. Rockefeller University Press, pp. 1035–1050, 2019.","ista":"Erdem FA, Ilic M, Koppensteiner P, Gołacki J, Lubec G, Freissmuth M, Sandtner W. 2019. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 151(8), 1035–1050."},"title":"A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2","article_type":"original","language":[{"iso":"eng"}],"month":"07","external_id":{"isi":["000478792500008"],"pmid":["31270129"]},"intvolume":"       151","publication_status":"published","_id":"7398","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:57Z","status":"public","article_processing_charge":"No","author":[{"last_name":"Erdem","full_name":"Erdem, Fatma Asli","first_name":"Fatma Asli"},{"last_name":"Ilic","full_name":"Ilic, Marija","first_name":"Marija"},{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner"},{"last_name":"Gołacki","first_name":"Jakub","full_name":"Gołacki, Jakub"},{"last_name":"Lubec","full_name":"Lubec, Gert","first_name":"Gert"},{"last_name":"Freissmuth","full_name":"Freissmuth, Michael","first_name":"Michael"},{"full_name":"Sandtner, Walter","first_name":"Walter","last_name":"Sandtner"}],"quality_controlled":"1","has_accepted_license":"1","date_published":"2019-07-03T00:00:00Z","volume":151,"publication_identifier":{"issn":["0022-1295"],"eissn":["1540-7748"]},"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"date_created":"2020-01-29T16:06:29Z","type":"journal_article","oa":1,"scopus_import":"1","date_updated":"2023-09-07T14:52:23Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019"},{"abstract":[{"text":"Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.","lang":"eng"}],"file":[{"file_name":"2019_PlosGenetics_Andergassen.pdf","date_created":"2020-02-04T10:11:55Z","relation":"main_file","checksum":"2f51fc91e4a4199827adc51d432ad864","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_id":"7446","file_size":2302307,"date_updated":"2020-07-14T12:47:57Z"}],"pmid":1,"issue":"7","article_number":"e1008268","ddc":["570"],"day":"22","department":[{"_id":"SiHi"}],"publisher":"Public Library of Science","publication":"PLoS Genetics","citation":{"mla":"Andergassen, Daniel, et al. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” <i>PLoS Genetics</i>, vol. 15, no. 7, e1008268, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008268\">10.1371/journal.pgen.1008268</a>.","short":"D. Andergassen, M. Muckenhuber, P.C. Bammer, T.M. Kulinski, H.-C. Theussl, T. Shimizu, J.M. Penninger, F. Pauler, Q.J. Hudson, PLoS Genetics 15 (2019).","apa":"Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl, H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1008268\">https://doi.org/10.1371/journal.pgen.1008268</a>","chicago":"Andergassen, Daniel, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski, Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian Pauler, and Quanah J. Hudson. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” <i>PLoS Genetics</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pgen.1008268\">https://doi.org/10.1371/journal.pgen.1008268</a>.","ama":"Andergassen D, Muckenhuber M, Bammer PC, et al. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. <i>PLoS Genetics</i>. 2019;15(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008268\">10.1371/journal.pgen.1008268</a>","ieee":"D. Andergassen <i>et al.</i>, “The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes,” <i>PLoS Genetics</i>, vol. 15, no. 7. Public Library of Science, 2019.","ista":"Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl H-C, Shimizu T, Penninger JM, Pauler F, Hudson QJ. 2019. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 15(7), e1008268."},"title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","doi":"10.1371/journal.pgen.1008268","isi":1,"article_processing_charge":"No","author":[{"full_name":"Andergassen, Daniel","first_name":"Daniel","last_name":"Andergassen"},{"full_name":"Muckenhuber, Markus","first_name":"Markus","last_name":"Muckenhuber"},{"first_name":"Philipp C.","full_name":"Bammer, Philipp C.","last_name":"Bammer"},{"last_name":"Kulinski","first_name":"Tomasz M.","full_name":"Kulinski, Tomasz M."},{"full_name":"Theussl, Hans-Christian","first_name":"Hans-Christian","last_name":"Theussl"},{"last_name":"Shimizu","full_name":"Shimizu, Takahiko","first_name":"Takahiko"},{"full_name":"Penninger, Josef M.","first_name":"Josef M.","last_name":"Penninger"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"last_name":"Hudson","first_name":"Quanah J.","full_name":"Hudson, Quanah J."}],"quality_controlled":"1","article_type":"original","language":[{"iso":"eng"}],"external_id":{"pmid":["31329595"],"isi":["000478689100025"]},"month":"07","intvolume":"        15","publication_status":"published","_id":"7399","oa_version":"Published Version","status":"public","file_date_updated":"2020-07-14T12:47:57Z","oa":1,"scopus_import":"1","date_updated":"2023-10-17T12:30:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","has_accepted_license":"1","date_published":"2019-07-22T00:00:00Z","volume":15,"publication_identifier":{"issn":["1553-7404"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-01-29T16:14:07Z","type":"journal_article"},{"date_created":"2020-01-29T16:15:44Z","type":"journal_article","volume":212,"publication_identifier":{"issn":["0016-6731"],"eissn":["1943-2631"]},"date_published":"2019-07-01T00:00:00Z","year":"2019","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T14:49:29Z","ec_funded":1,"oa":1,"oa_version":"Published Version","_id":"7400","status":"public","language":[{"iso":"eng"}],"month":"07","publication_status":"published","external_id":{"isi":["000474809300015"],"pmid":["31113811"]},"intvolume":"       212","article_type":"original","quality_controlled":"1","author":[{"full_name":"Veltsos, Paris","first_name":"Paris","last_name":"Veltsos"},{"last_name":"Ridout","full_name":"Ridout, Kate E.","first_name":"Kate E."},{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups"},{"last_name":"González-Martínez","first_name":"Santiago C.","full_name":"González-Martínez, Santiago C."},{"last_name":"Muyle","full_name":"Muyle, Aline","first_name":"Aline"},{"last_name":"Emery","full_name":"Emery, Olivier","first_name":"Olivier"},{"full_name":"Rastas, Pasi","first_name":"Pasi","last_name":"Rastas"},{"full_name":"Hudzieczek, Vojtech","first_name":"Vojtech","last_name":"Hudzieczek"},{"full_name":"Hobza, Roman","first_name":"Roman","last_name":"Hobza"},{"last_name":"Vyskot","full_name":"Vyskot, Boris","first_name":"Boris"},{"last_name":"Marais","full_name":"Marais, Gabriel A. B.","first_name":"Gabriel A. B."},{"full_name":"Filatov, Dmitry A.","first_name":"Dmitry A.","last_name":"Filatov"},{"last_name":"Pannell","first_name":"John R.","full_name":"Pannell, John R."}],"article_processing_charge":"No","doi":"10.1534/genetics.119.302045","isi":1,"title":"Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua","citation":{"apa":"Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle, A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.119.302045\">https://doi.org/10.1534/genetics.119.302045</a>","mla":"Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” <i>Genetics</i>, vol. 212, no. 3, Genetics Society of America, 2019, pp. 815–35, doi:<a href=\"https://doi.org/10.1534/genetics.119.302045\">10.1534/genetics.119.302045</a>.","short":"P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O. Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov, J.R. Pannell, Genetics 212 (2019) 815–835.","chicago":"Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez, Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” <i>Genetics</i>. Genetics Society of America, 2019. <a href=\"https://doi.org/10.1534/genetics.119.302045\">https://doi.org/10.1534/genetics.119.302045</a>.","ama":"Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. <i>Genetics</i>. 2019;212(3):815-835. doi:<a href=\"https://doi.org/10.1534/genetics.119.302045\">10.1534/genetics.119.302045</a>","ieee":"P. Veltsos <i>et al.</i>, “Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua,” <i>Genetics</i>, vol. 212, no. 3. Genetics Society of America, pp. 815–835, 2019.","ista":"Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 212(3), 815–835."},"main_file_link":[{"url":"https://doi.org/10.1534/genetics.119.302045","open_access":"1"}],"department":[{"_id":"BeVi"}],"publisher":"Genetics Society of America","publication":"Genetics","day":"01","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","call_identifier":"H2020"}],"issue":"3","pmid":1,"page":"815-835","abstract":[{"lang":"eng","text":"Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination."}]},{"publication":"35th International Symposium on Computational Geometry (SoCG 2019)","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"project":[{"grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"day":"01","title":"Z_2-Genus of graphs and minimum rank of partial symmetric matrices","citation":{"ama":"Fulek R, Kyncl J. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In: <i>35th International Symposium on Computational Geometry (SoCG 2019)</i>. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.SOCG.2019.39\">10.4230/LIPICS.SOCG.2019.39</a>","ieee":"R. Fulek and J. Kyncl, “Z_2-Genus of graphs and minimum rank of partial symmetric matrices,” in <i>35th International Symposium on Computational Geometry (SoCG 2019)</i>, Portland, OR, United States, 2019, vol. 129.","ista":"Fulek R, Kyncl J. 2019. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. 35th International Symposium on Computational Geometry (SoCG 2019). SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 39.","apa":"Fulek, R., &#38; Kyncl, J. (2019). Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In <i>35th International Symposium on Computational Geometry (SoCG 2019)</i> (Vol. 129). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.SOCG.2019.39\">https://doi.org/10.4230/LIPICS.SOCG.2019.39</a>","mla":"Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” <i>35th International Symposium on Computational Geometry (SoCG 2019)</i>, vol. 129, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.SOCG.2019.39\">10.4230/LIPICS.SOCG.2019.39</a>.","short":"R. Fulek, J. Kyncl, in:, 35th International Symposium on Computational Geometry (SoCG 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” In <i>35th International Symposium on Computational Geometry (SoCG 2019)</i>, Vol. 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.SOCG.2019.39\">https://doi.org/10.4230/LIPICS.SOCG.2019.39</a>."},"doi":"10.4230/LIPICS.SOCG.2019.39","abstract":[{"text":"The genus g(G) of a graph G is the minimum g such that G has an embedding on the orientable surface M_g of genus g. A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum g such that G has an independently even drawing on M_g. By a result of Battle, Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph is additive over 2-connected blocks as well, and asked whether this result can be extended to so-called 2-amalgamations, as an analogue of results by Decker, Glover, Huneke, and Stahl for the genus. We give the following partial answer. If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1. For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest. ","lang":"eng"}],"file":[{"date_created":"2020-02-04T09:14:31Z","file_name":"2019_LIPIcs_Fulek.pdf","date_updated":"2020-07-14T12:47:57Z","file_size":628347,"file_id":"7445","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"aac37b09118cc0ab58cf77129e691f8c","relation":"main_file"}],"ddc":["000"],"article_number":"39","oa":1,"year":"2019","arxiv":1,"date_updated":"2021-01-12T08:13:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"date_published":"2019-06-01T00:00:00Z","has_accepted_license":"1","type":"conference","date_created":"2020-01-29T16:17:05Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_identifier":{"isbn":["978-3-95977-104-7"],"issn":["1868-8969"]},"volume":129,"article_processing_charge":"No","alternative_title":["LIPIcs"],"quality_controlled":"1","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","first_name":"Radoslav"},{"first_name":"Jan","full_name":"Kyncl, Jan","last_name":"Kyncl"}],"conference":{"end_date":"2019-06-21","start_date":"2019-06-18","location":"Portland, OR, United States","name":"SoCG: Symposium on Computational Geometry"},"status":"public","file_date_updated":"2020-07-14T12:47:57Z","oa_version":"Published Version","_id":"7401","intvolume":"       129","month":"06","publication_status":"published","external_id":{"arxiv":["1903.08637"]},"language":[{"iso":"eng"}]},{"arxiv":1,"date_updated":"2025-07-14T09:09:54Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","year":"2019","oa":1,"publication_identifier":{"isbn":["9781728136080"]},"type":"conference","date_created":"2020-01-29T16:18:33Z","date_published":"2019-06-01T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"quality_controlled":"1","article_processing_charge":"No","month":"06","external_id":{"arxiv":["1802.03642"],"isi":["000805002800001"]},"publication_status":"published","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","_id":"7402","conference":{"name":"LICS: Symposium on Logic in Computer Science","location":"Vancouver, BC, Canada","start_date":"2019-06-24","end_date":"2019-06-27"},"citation":{"ista":"Chatterjee K, Doyen L. 2019. Graph planning with expected finite horizon. 34th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.","ieee":"K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” in <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Vancouver, BC, Canada, 2019, pp. 1–13.","ama":"Chatterjee K, Doyen L. Graph planning with expected finite horizon. In: <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. IEEE; 2019:1-13. doi:<a href=\"https://doi.org/10.1109/lics.2019.8785706\">10.1109/lics.2019.8785706</a>","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” In <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 1–13. IEEE, 2019. <a href=\"https://doi.org/10.1109/lics.2019.8785706\">https://doi.org/10.1109/lics.2019.8785706</a>.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, IEEE, 2019, pp. 1–13, doi:<a href=\"https://doi.org/10.1109/lics.2019.8785706\">10.1109/lics.2019.8785706</a>.","short":"K. Chatterjee, L. Doyen, in:, 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13.","apa":"Chatterjee, K., &#38; Doyen, L. (2019). Graph planning with expected finite horizon. In <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 1–13). Vancouver, BC, Canada: IEEE. <a href=\"https://doi.org/10.1109/lics.2019.8785706\">https://doi.org/10.1109/lics.2019.8785706</a>"},"title":"Graph planning with expected finite horizon","related_material":{"record":[{"relation":"later_version","status":"public","id":"11402"}]},"day":"01","publication":"34th Annual ACM/IEEE Symposium on Logic in Computer Science","publisher":"IEEE","department":[{"_id":"KrCh"}],"main_file_link":[{"url":"https://arxiv.org/abs/1802.03642","open_access":"1"}],"isi":1,"doi":"10.1109/lics.2019.8785706","page":"1-13","abstract":[{"lang":"eng","text":"Graph planning gives rise to fundamental algorithmic questions such as shortest path, traveling salesman problem, etc. A classical problem in discrete planning is to consider a weighted graph and construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary, to represent the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time. Consequently, our polynomial-time algorithm for adversarial stopping time also computes an optimal plan among all possible plans."}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T14:47:00Z","scopus_import":"1","year":"2019","oa":1,"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"volume":146,"type":"journal_article","date_created":"2020-01-29T16:27:10Z","date_published":"2019-04-04T00:00:00Z","author":[{"first_name":"Tomke","full_name":"Stürner, Tomke","last_name":"Stürner"},{"last_name":"Tatarnikova","full_name":"Tatarnikova, Anastasia","first_name":"Anastasia"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","last_name":"Müller","full_name":"Müller, Jan","first_name":"Jan"},{"full_name":"Schaffran, Barbara","first_name":"Barbara","last_name":"Schaffran"},{"last_name":"Cuntz","first_name":"Hermann","full_name":"Cuntz, Hermann"},{"last_name":"Zhang","first_name":"Yun","full_name":"Zhang, Yun"},{"last_name":"Nemethova","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Nemethova, Maria"},{"last_name":"Bogdan","full_name":"Bogdan, Sven","first_name":"Sven"},{"last_name":"Small","full_name":"Small, Vic","first_name":"Vic"},{"first_name":"Gaia","full_name":"Tavosanis, Gaia","last_name":"Tavosanis"}],"quality_controlled":"1","article_processing_charge":"No","month":"04","intvolume":"       146","publication_status":"published","external_id":{"pmid":["30910826"],"isi":["000464583200006"]},"language":[{"iso":"eng"}],"status":"public","_id":"7404","oa_version":"Published Version","article_type":"original","citation":{"ama":"Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. <i>Development</i>. 2019;146(7). doi:<a href=\"https://doi.org/10.1242/dev.171397\">10.1242/dev.171397</a>","ieee":"T. Stürner <i>et al.</i>, “Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo,” <i>Development</i>, vol. 146, no. 7. The Company of Biologists, 2019.","ista":"Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397.","short":"T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang, M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019).","mla":"Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” <i>Development</i>, vol. 146, no. 7, dev171397, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.171397\">10.1242/dev.171397</a>.","apa":"Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang, Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.171397\">https://doi.org/10.1242/dev.171397</a>","chicago":"Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.171397\">https://doi.org/10.1242/dev.171397</a>."},"title":"Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo","day":"04","publisher":"The Company of Biologists","publication":"Development","department":[{"_id":"MiSi"}],"main_file_link":[{"url":"https://doi.org/10.1242/dev.171397","open_access":"1"}],"isi":1,"doi":"10.1242/dev.171397","pmid":1,"abstract":[{"text":"The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation.","lang":"eng"}],"article_number":"dev171397","issue":"7"},{"article_type":"original","language":[{"iso":"eng"}],"month":"05","external_id":{"pmid":["31025934"],"isi":["000468968400001"]},"intvolume":"         8","publication_status":"published","oa_version":"Published Version","_id":"7405","status":"public","file_date_updated":"2020-07-14T12:47:57Z","article_processing_charge":"No","author":[{"last_name":"Dura-Bernal","full_name":"Dura-Bernal, Salvador","first_name":"Salvador"},{"first_name":"Benjamin","orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin","last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Padraig","full_name":"Gleeson, Padraig","last_name":"Gleeson"},{"first_name":"Matteo","full_name":"Cantarelli, Matteo","last_name":"Cantarelli"},{"last_name":"Quintana","full_name":"Quintana, Adrian","first_name":"Adrian"},{"full_name":"Rodriguez, Facundo","first_name":"Facundo","last_name":"Rodriguez"},{"full_name":"Kedziora, David J","first_name":"David J","last_name":"Kedziora"},{"last_name":"Chadderdon","full_name":"Chadderdon, George L","first_name":"George L"},{"last_name":"Kerr","first_name":"Cliff C","full_name":"Kerr, Cliff C"},{"first_name":"Samuel A","full_name":"Neymotin, Samuel A","last_name":"Neymotin"},{"last_name":"McDougal","full_name":"McDougal, Robert A","first_name":"Robert A"},{"full_name":"Hines, Michael","first_name":"Michael","last_name":"Hines"},{"last_name":"Shepherd","full_name":"Shepherd, Gordon MG","first_name":"Gordon MG"},{"last_name":"Lytton","full_name":"Lytton, William W","first_name":"William W"}],"quality_controlled":"1","has_accepted_license":"1","date_published":"2019-05-31T00:00:00Z","volume":8,"publication_identifier":{"issn":["2050-084X"]},"date_created":"2020-01-30T09:08:01Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","oa":1,"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T14:27:52Z","year":"2019","article_number":"e44494","ddc":["570"],"abstract":[{"text":"Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena.","lang":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:57Z","file_size":6182359,"file_id":"7444","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"7014189c11c10a12feeeae37f054871d","relation":"main_file","date_created":"2020-02-04T08:41:47Z","file_name":"2019_eLife_DuraBernal.pdf"}],"pmid":1,"doi":"10.7554/elife.44494","isi":1,"day":"31","department":[{"_id":"PeJo"}],"publisher":"eLife Sciences Publications","publication":"eLife","citation":{"ieee":"S. Dura-Bernal <i>et al.</i>, “NetPyNE, a tool for data-driven multiscale modeling of brain circuits,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ama":"Dura-Bernal S, Suter B, Gleeson P, et al. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.44494\">10.7554/elife.44494</a>","ista":"Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. 2019. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 8, e44494.","apa":"Dura-Bernal, S., Suter, B., Gleeson, P., Cantarelli, M., Quintana, A., Rodriguez, F., … Lytton, W. W. (2019). NetPyNE, a tool for data-driven multiscale modeling of brain circuits. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.44494\">https://doi.org/10.7554/elife.44494</a>","short":"S. Dura-Bernal, B. Suter, P. Gleeson, M. Cantarelli, A. Quintana, F. Rodriguez, D.J. Kedziora, G.L. Chadderdon, C.C. Kerr, S.A. Neymotin, R.A. McDougal, M. Hines, G.M. Shepherd, W.W. Lytton, ELife 8 (2019).","mla":"Dura-Bernal, Salvador, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” <i>ELife</i>, vol. 8, e44494, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.44494\">10.7554/elife.44494</a>.","chicago":"Dura-Bernal, Salvador, Benjamin Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.44494\">https://doi.org/10.7554/elife.44494</a>."},"title":"NetPyNE, a tool for data-driven multiscale modeling of brain circuits"},{"author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie","full_name":"Mckenzie, Catherine","first_name":"Catherine"},{"first_name":"Miroslava","full_name":"Spanova, Miroslava","last_name":"Spanova","id":"44A924DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"full_name":"Kainrath, Stephanie","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","first_name":"Vanessa"},{"full_name":"Sitte, Harald H.","first_name":"Harald H.","last_name":"Sitte"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak"}],"quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"month":"01","intvolume":"       312","publication_status":"published","external_id":{"isi":["000456220900013"],"pmid":["30496761"]},"oa_version":"None","_id":"7406","status":"public","article_type":"original","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-06T15:27:29Z","year":"2019","ec_funded":1,"volume":312,"publication_identifier":{"issn":["0165-0270"]},"date_created":"2020-01-30T09:12:19Z","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"date_published":"2019-01-15T00:00:00Z","page":"114-121","pmid":1,"abstract":[{"text":"Background\r\nSynaptic vesicles (SVs) are an integral part of the neurotransmission machinery, and isolation of SVs from their host neuron is necessary to reveal their most fundamental biochemical and functional properties in in vitro assays. Isolated SVs from neurons that have been genetically engineered, e.g. to introduce genetically encoded indicators, are not readily available but would permit new insights into SV structure and function. Furthermore, it is unclear if cultured neurons can provide sufficient starting material for SV isolation procedures.\r\n\r\nNew method\r\nHere, we demonstrate an efficient ex vivo procedure to obtain functional SVs from cultured rat cortical neurons after genetic engineering with a lentivirus.\r\n\r\nResults\r\nWe show that ∼108 plated cortical neurons allow isolation of suitable SV amounts for functional analysis and imaging. We found that SVs isolated from cultured neurons have neurotransmitter uptake comparable to that of SVs isolated from intact cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized an exogenous SV-targeted marker protein and demonstrated the high efficiency of SV modification.\r\n\r\nComparison with existing methods\r\nObtaining SVs from genetically engineered neurons currently generally requires the availability of transgenic animals, which is constrained by technical (e.g. cost and time) and biological (e.g. developmental defects and lethality) limitations.\r\n\r\nConclusions\r\nThese results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts.","lang":"eng"}],"citation":{"ista":"Mckenzie C, Spanova M, Johnson AJ, Kainrath S, Zheden V, Sitte HH, Janovjak HL. 2019. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 312, 114–121.","ama":"Mckenzie C, Spanova M, Johnson AJ, et al. Isolation of synaptic vesicles from genetically engineered cultured neurons. <i>Journal of Neuroscience Methods</i>. 2019;312:114-121. doi:<a href=\"https://doi.org/10.1016/j.jneumeth.2018.11.018\">10.1016/j.jneumeth.2018.11.018</a>","ieee":"C. Mckenzie <i>et al.</i>, “Isolation of synaptic vesicles from genetically engineered cultured neurons,” <i>Journal of Neuroscience Methods</i>, vol. 312. Elsevier, pp. 114–121, 2019.","chicago":"Mckenzie, Catherine, Miroslava Spanova, Alexander J Johnson, Stephanie Kainrath, Vanessa Zheden, Harald H. Sitte, and Harald L Janovjak. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” <i>Journal of Neuroscience Methods</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jneumeth.2018.11.018\">https://doi.org/10.1016/j.jneumeth.2018.11.018</a>.","apa":"Mckenzie, C., Spanova, M., Johnson, A. J., Kainrath, S., Zheden, V., Sitte, H. H., &#38; Janovjak, H. L. (2019). Isolation of synaptic vesicles from genetically engineered cultured neurons. <i>Journal of Neuroscience Methods</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jneumeth.2018.11.018\">https://doi.org/10.1016/j.jneumeth.2018.11.018</a>","short":"C. Mckenzie, M. Spanova, A.J. Johnson, S. Kainrath, V. Zheden, H.H. Sitte, H.L. Janovjak, Journal of Neuroscience Methods 312 (2019) 114–121.","mla":"Mckenzie, Catherine, et al. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” <i>Journal of Neuroscience Methods</i>, vol. 312, Elsevier, 2019, pp. 114–21, doi:<a href=\"https://doi.org/10.1016/j.jneumeth.2018.11.018\">10.1016/j.jneumeth.2018.11.018</a>."},"title":"Isolation of synaptic vesicles from genetically engineered cultured neurons","project":[{"call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"day":"15","department":[{"_id":"HaJa"},{"_id":"Bio"}],"publication":"Journal of Neuroscience Methods","publisher":"Elsevier","doi":"10.1016/j.jneumeth.2018.11.018","isi":1},{"conference":{"name":"International Conference on the Theory and Applications of Cryptographic Techniques","start_date":"2019-05-19","end_date":"2019-05-23","location":"Darmstadt, Germany"},"status":"public","_id":"7411","oa_version":"Submitted Version","external_id":{"isi":["000483516200010"]},"publication_status":"published","intvolume":"     11477","month":"04","language":[{"iso":"eng"}],"article_processing_charge":"No","alternative_title":["LNCS"],"quality_controlled":"1","author":[{"last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M","full_name":"Abusalah, Hamza M"},{"last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan"},{"last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","full_name":"Klein, Karen"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"},{"first_name":"Michael","full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2019-04-24T00:00:00Z","type":"conference","date_created":"2020-01-30T09:26:14Z","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030176556","9783030176563"],"issn":["0302-9743"]},"volume":11477,"ec_funded":1,"oa":1,"year":"2019","date_updated":"2023-09-06T15:26:06Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","abstract":[{"text":"Proofs of sequential work (PoSW) are proof systems where a prover, upon receiving a statement χ and a time parameter T computes a proof ϕ(χ,T) which is efficiently and publicly verifiable. The proof can be computed in T sequential steps, but not much less, even by a malicious party having large parallelism. A PoSW thus serves as a proof that T units of time have passed since χ\r\n\r\nwas received.\r\n\r\nPoSW were introduced by Mahmoody, Moran and Vadhan [MMV11], a simple and practical construction was only recently proposed by Cohen and Pietrzak [CP18].\r\n\r\nIn this work we construct a new simple PoSW in the random permutation model which is almost as simple and efficient as [CP18] but conceptually very different. Whereas the structure underlying [CP18] is a hash tree, our construction is based on skip lists and has the interesting property that computing the PoSW is a reversible computation.\r\nThe fact that the construction is reversible can potentially be used for new applications like constructing proofs of replication. We also show how to “embed” the sloth function of Lenstra and Weselowski [LW17] into our PoSW to get a PoSW where one additionally can verify correctness of the output much more efficiently than recomputing it (though recent constructions of “verifiable delay functions” subsume most of the applications this construction was aiming at).","lang":"eng"}],"page":"277-291","isi":1,"doi":"10.1007/978-3-030-17656-3_10","publisher":"Springer International Publishing","publication":"Advances in Cryptology – EUROCRYPT 2019","department":[{"_id":"KrPi"}],"main_file_link":[{"url":"https://eprint.iacr.org/2019/252","open_access":"1"}],"project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"24","title":"Reversible proofs of sequential work","citation":{"mla":"Abusalah, Hamza M., et al. “Reversible Proofs of Sequential Work.” <i>Advances in Cryptology – EUROCRYPT 2019</i>, vol. 11477, Springer International Publishing, 2019, pp. 277–91, doi:<a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">10.1007/978-3-030-17656-3_10</a>.","short":"H.M. Abusalah, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2019, Springer International Publishing, 2019, pp. 277–291.","apa":"Abusalah, H. M., Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., &#38; Walter, M. (2019). Reversible proofs of sequential work. In <i>Advances in Cryptology – EUROCRYPT 2019</i> (Vol. 11477, pp. 277–291). Darmstadt, Germany: Springer International Publishing. <a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">https://doi.org/10.1007/978-3-030-17656-3_10</a>","chicago":"Abusalah, Hamza M, Chethan Kamath Hosdurg, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “Reversible Proofs of Sequential Work.” In <i>Advances in Cryptology – EUROCRYPT 2019</i>, 11477:277–91. Springer International Publishing, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">https://doi.org/10.1007/978-3-030-17656-3_10</a>.","ama":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. Reversible proofs of sequential work. In: <i>Advances in Cryptology – EUROCRYPT 2019</i>. Vol 11477. Springer International Publishing; 2019:277-291. doi:<a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">10.1007/978-3-030-17656-3_10</a>","ieee":"H. M. Abusalah, C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “Reversible proofs of sequential work,” in <i>Advances in Cryptology – EUROCRYPT 2019</i>, Darmstadt, Germany, 2019, vol. 11477, pp. 277–291.","ista":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2019. Reversible proofs of sequential work. Advances in Cryptology – EUROCRYPT 2019. International Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol. 11477, 277–291."}},{"abstract":[{"text":"We develop a framework for the rigorous analysis of focused stochastic local search algorithms. These algorithms search a state space by repeatedly selecting some constraint that is violated in the current state and moving to a random nearby state that addresses the violation, while (we hope) not introducing many new violations. An important class of focused local search algorithms with provable performance guarantees has recently arisen from algorithmizations of the Lovász local lemma (LLL), a nonconstructive tool for proving the existence of satisfying states by introducing a background measure on the state space. While powerful, the state transitions of algorithms in this class must be, in a precise sense, perfectly compatible with the background measure. In many applications this is a very restrictive requirement, and one needs to step outside the class. Here we introduce the notion of measure distortion and develop a framework for analyzing arbitrary focused stochastic local search algorithms, recovering LLL algorithmizations as the special case of no distortion. Our framework takes as input an arbitrary algorithm of such type and an arbitrary probability measure and shows how to use the measure as a yardstick of algorithmic progress, even for algorithms designed independently of the measure.","lang":"eng"}],"page":"1583-1602","issue":"5","publisher":"SIAM","publication":"SIAM Journal on Computing","main_file_link":[{"url":"https://arxiv.org/abs/1809.01537","open_access":"1"}],"department":[{"_id":"VlKo"}],"project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"day":"31","title":"A local lemma for focused stochastical algorithms","citation":{"ista":"Achlioptas D, Iliopoulos F, Kolmogorov V. 2019. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 48(5), 1583–1602.","ama":"Achlioptas D, Iliopoulos F, Kolmogorov V. A local lemma for focused stochastical algorithms. <i>SIAM Journal on Computing</i>. 2019;48(5):1583-1602. doi:<a href=\"https://doi.org/10.1137/16m109332x\">10.1137/16m109332x</a>","ieee":"D. Achlioptas, F. Iliopoulos, and V. Kolmogorov, “A local lemma for focused stochastical algorithms,” <i>SIAM Journal on Computing</i>, vol. 48, no. 5. SIAM, pp. 1583–1602, 2019.","chicago":"Achlioptas, Dimitris, Fotis Iliopoulos, and Vladimir Kolmogorov. “A Local Lemma for Focused Stochastical Algorithms.” <i>SIAM Journal on Computing</i>. SIAM, 2019. <a href=\"https://doi.org/10.1137/16m109332x\">https://doi.org/10.1137/16m109332x</a>.","apa":"Achlioptas, D., Iliopoulos, F., &#38; Kolmogorov, V. (2019). A local lemma for focused stochastical algorithms. <i>SIAM Journal on Computing</i>. SIAM. <a href=\"https://doi.org/10.1137/16m109332x\">https://doi.org/10.1137/16m109332x</a>","mla":"Achlioptas, Dimitris, et al. “A Local Lemma for Focused Stochastical Algorithms.” <i>SIAM Journal on Computing</i>, vol. 48, no. 5, SIAM, 2019, pp. 1583–602, doi:<a href=\"https://doi.org/10.1137/16m109332x\">10.1137/16m109332x</a>.","short":"D. Achlioptas, F. Iliopoulos, V. Kolmogorov, SIAM Journal on Computing 48 (2019) 1583–1602."},"isi":1,"doi":"10.1137/16m109332x","article_processing_charge":"No","quality_controlled":"1","author":[{"full_name":"Achlioptas, Dimitris","first_name":"Dimitris","last_name":"Achlioptas"},{"full_name":"Iliopoulos, Fotis","first_name":"Fotis","last_name":"Iliopoulos"},{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"}],"article_type":"original","status":"public","oa_version":"Preprint","_id":"7412","publication_status":"published","month":"10","intvolume":"        48","external_id":{"arxiv":["1809.01537"],"isi":["000493900200005"]},"language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"date_updated":"2023-09-06T15:25:29Z","scopus_import":"1","date_published":"2019-10-31T00:00:00Z","type":"journal_article","date_created":"2020-01-30T09:27:32Z","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"volume":48},{"citation":{"ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Bogoliubov theory in the Gross–Pitaevskii limit. <i>Acta Mathematica</i>. 2019;222(2):219-335. doi:<a href=\"https://doi.org/10.4310/acta.2019.v222.n2.a1\">10.4310/acta.2019.v222.n2.a1</a>","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Bogoliubov theory in the Gross–Pitaevskii limit,” <i>Acta Mathematica</i>, vol. 222, no. 2. International Press of Boston, pp. 219–335, 2019.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2019. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 222(2), 219–335.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., &#38; Schlein, B. (2019). Bogoliubov theory in the Gross–Pitaevskii limit. <i>Acta Mathematica</i>. International Press of Boston. <a href=\"https://doi.org/10.4310/acta.2019.v222.n2.a1\">https://doi.org/10.4310/acta.2019.v222.n2.a1</a>","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Acta Mathematica 222 (2019) 219–335.","mla":"Boccato, Chiara, et al. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” <i>Acta Mathematica</i>, vol. 222, no. 2, International Press of Boston, 2019, pp. 219–335, doi:<a href=\"https://doi.org/10.4310/acta.2019.v222.n2.a1\">10.4310/acta.2019.v222.n2.a1</a>.","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” <i>Acta Mathematica</i>. International Press of Boston, 2019. <a href=\"https://doi.org/10.4310/acta.2019.v222.n2.a1\">https://doi.org/10.4310/acta.2019.v222.n2.a1</a>."},"title":"Bogoliubov theory in the Gross–Pitaevskii limit","day":"07","publication":"Acta Mathematica","publisher":"International Press of Boston","department":[{"_id":"RoSe"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.01389"}],"isi":1,"doi":"10.4310/acta.2019.v222.n2.a1","page":"219-335","abstract":[{"text":"We consider Bose gases consisting of N particles trapped in a box with volume one and interacting through a repulsive potential with scattering length of order N−1 (Gross–Pitaevskii regime). We determine the ground state energy and the low-energy excitation spectrum, up to errors vanishing as N→∞. Our results confirm Bogoliubov’s predictions.","lang":"eng"}],"issue":"2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-06T15:24:31Z","arxiv":1,"scopus_import":"1","year":"2019","oa":1,"publication_identifier":{"eissn":["1871-2509"],"issn":["0001-5962"]},"volume":222,"type":"journal_article","date_created":"2020-01-30T09:30:41Z","date_published":"2019-06-07T00:00:00Z","author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","last_name":"Boccato","full_name":"Boccato, Chiara","first_name":"Chiara"},{"first_name":"Christian","full_name":"Brennecke, Christian","last_name":"Brennecke"},{"last_name":"Cenatiempo","first_name":"Serena","full_name":"Cenatiempo, Serena"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"}],"quality_controlled":"1","article_processing_charge":"No","publication_status":"published","external_id":{"arxiv":["1801.01389"],"isi":["000495865300001"]},"intvolume":"       222","month":"06","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","_id":"7413","article_type":"original"},{"volume":29,"publication_identifier":{"issn":["0924-977X"]},"date_created":"2020-01-30T10:06:15Z","type":"journal_article","doi":"10.1016/j.euroneuro.2019.09.039","isi":1,"date_published":"2019-12-13T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T14:55:23Z","citation":{"chicago":"Knaus, Lisa, Dora-Clara Tarlungeanu, and Gaia Novarino. “S.16.03 A Homozygous Missense Mutation in SLC7A5 Leads to Autism Spectrum Disorder and Microcephaly.” <i>European Neuropsychopharmacology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.039\">https://doi.org/10.1016/j.euroneuro.2019.09.039</a>.","mla":"Knaus, Lisa, et al. “S.16.03 A Homozygous Missense Mutation in SLC7A5 Leads to Autism Spectrum Disorder and Microcephaly.” <i>European Neuropsychopharmacology</i>, vol. 29, no. Supplement 6, Elsevier, 2019, p. S11, doi:<a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.039\">10.1016/j.euroneuro.2019.09.039</a>.","short":"L. Knaus, D.-C. Tarlungeanu, G. Novarino, European Neuropsychopharmacology 29 (2019) S11.","apa":"Knaus, L., Tarlungeanu, D.-C., &#38; Novarino, G. (2019). S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly. <i>European Neuropsychopharmacology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.039\">https://doi.org/10.1016/j.euroneuro.2019.09.039</a>","ista":"Knaus L, Tarlungeanu D-C, Novarino G. 2019. S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly. European Neuropsychopharmacology. 29(Supplement 6), S11.","ieee":"L. Knaus, D.-C. Tarlungeanu, and G. Novarino, “S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly,” <i>European Neuropsychopharmacology</i>, vol. 29, no. Supplement 6. Elsevier, p. S11, 2019.","ama":"Knaus L, Tarlungeanu D-C, Novarino G. S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly. <i>European Neuropsychopharmacology</i>. 2019;29(Supplement 6):S11. doi:<a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.039\">10.1016/j.euroneuro.2019.09.039</a>"},"title":"S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly","year":"2019","day":"13","department":[{"_id":"GaNo"}],"publication":"European Neuropsychopharmacology","publisher":"Elsevier","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"        29","external_id":{"isi":["000502657500020"]},"month":"12","_id":"7414","oa_version":"None","status":"public","article_type":"original","issue":"Supplement 6","page":"S11","author":[{"full_name":"Knaus, Lisa","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus"},{"last_name":"Tarlungeanu","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","first_name":"Dora-Clara","full_name":"Tarlungeanu, Dora-Clara"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"quality_controlled":"1","article_processing_charge":"No"},{"date_created":"2020-01-30T10:07:41Z","type":"journal_article","volume":29,"publication_identifier":{"issn":["0924-977X"]},"date_published":"2019-12-13T00:00:00Z","doi":"10.1016/j.euroneuro.2019.09.040","isi":1,"title":"S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism","year":"2019","citation":{"chicago":"Morandell, Jasmin, Armel Nicolas, Lena A Schwarz, and Gaia Novarino. “S.16.05 Illuminating the Role of the E3 Ubiquitin Ligase Cullin3 in Brain Development and Autism.” <i>European Neuropsychopharmacology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.040\">https://doi.org/10.1016/j.euroneuro.2019.09.040</a>.","apa":"Morandell, J., Nicolas, A., Schwarz, L. A., &#38; Novarino, G. (2019). S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism. <i>European Neuropsychopharmacology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.040\">https://doi.org/10.1016/j.euroneuro.2019.09.040</a>","short":"J. Morandell, A. Nicolas, L.A. Schwarz, G. Novarino, European Neuropsychopharmacology 29 (2019) S11–S12.","mla":"Morandell, Jasmin, et al. “S.16.05 Illuminating the Role of the E3 Ubiquitin Ligase Cullin3 in Brain Development and Autism.” <i>European Neuropsychopharmacology</i>, vol. 29, no. Supplement 6, Elsevier, 2019, pp. S11–12, doi:<a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.040\">10.1016/j.euroneuro.2019.09.040</a>.","ista":"Morandell J, Nicolas A, Schwarz LA, Novarino G. 2019. S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism. European Neuropsychopharmacology. 29(Supplement 6), S11–S12.","ieee":"J. Morandell, A. Nicolas, L. A. Schwarz, and G. Novarino, “S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism,” <i>European Neuropsychopharmacology</i>, vol. 29, no. Supplement 6. Elsevier, pp. S11–S12, 2019.","ama":"Morandell J, Nicolas A, Schwarz LA, Novarino G. S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism. <i>European Neuropsychopharmacology</i>. 2019;29(Supplement 6):S11-S12. doi:<a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.040\">10.1016/j.euroneuro.2019.09.040</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T14:56:17Z","department":[{"_id":"GaNo"},{"_id":"LifeSc"}],"publisher":"Elsevier","publication":"European Neuropsychopharmacology","day":"13","_id":"7415","oa_version":"None","status":"public","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000502657500021"]},"month":"12","intvolume":"        29","issue":"Supplement 6","article_type":"original","quality_controlled":"1","page":"S11-S12","author":[{"last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","full_name":"Morandell, Jasmin"},{"last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","full_name":"Nicolas, Armel"},{"full_name":"Schwarz, Lena A","first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"}],"article_processing_charge":"No"},{"date_published":"2019-11-01T00:00:00Z","volume":38,"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"date_created":"2020-01-30T10:19:43Z","type":"journal_article","scopus_import":"1","date_updated":"2023-09-06T15:22:23Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","article_type":"original","language":[{"iso":"eng"}],"external_id":{"isi":["000498397300001"]},"month":"11","intvolume":"        38","publication_status":"published","oa_version":"None","_id":"7418","status":"public","article_processing_charge":"No","author":[{"first_name":"Ondřej","full_name":"Karlík, Ondřej","last_name":"Karlík"},{"full_name":"Šik, Martin","first_name":"Martin","last_name":"Šik"},{"first_name":"Petr","full_name":"Vévoda, Petr","last_name":"Vévoda"},{"last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","full_name":"Skrivan, Tomas"},{"first_name":"Jaroslav","full_name":"Křivánek, Jaroslav","last_name":"Křivánek"}],"quality_controlled":"1","doi":"10.1145/3355089.3356565","isi":1,"day":"01","department":[{"_id":"ChWo"}],"publisher":"ACM","publication":"ACM Transactions on Graphics","citation":{"ista":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. 2019. MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. 38(6), 151.","ama":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. MIS compensation: Optimizing sampling techniques in multiple importance sampling. <i>ACM Transactions on Graphics</i>. 2019;38(6). doi:<a href=\"https://doi.org/10.1145/3355089.3356565\">10.1145/3355089.3356565</a>","ieee":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, and J. Křivánek, “MIS compensation: Optimizing sampling techniques in multiple importance sampling,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6. ACM, 2019.","chicago":"Karlík, Ondřej, Martin Šik, Petr Vévoda, Tomas Skrivan, and Jaroslav Křivánek. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3355089.3356565\">https://doi.org/10.1145/3355089.3356565</a>.","apa":"Karlík, O., Šik, M., Vévoda, P., Skrivan, T., &#38; Křivánek, J. (2019). MIS compensation: Optimizing sampling techniques in multiple importance sampling. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3355089.3356565\">https://doi.org/10.1145/3355089.3356565</a>","mla":"Karlík, Ondřej, et al. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6, 151, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3355089.3356565\">10.1145/3355089.3356565</a>.","short":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, J. Křivánek, ACM Transactions on Graphics 38 (2019)."},"title":"MIS compensation: Optimizing sampling techniques in multiple importance sampling","issue":"6","article_number":"151","abstract":[{"text":"Multiple importance sampling (MIS) has become an indispensable tool in Monte Carlo rendering, widely accepted as a near-optimal solution for combining different sampling techniques. But an MIS combination, using the common balance or power heuristics, often results in an overly defensive estimator, leading to high variance. We show that by generalizing the MIS framework, variance can be substantially reduced. Specifically, we optimize one of the combined sampling techniques so as to decrease the overall variance of the resulting MIS estimator. We apply the approach to the computation of direct illumination due to an HDR environment map and to the computation of global illumination using a path guiding algorithm. The implementation can be as simple as subtracting a constant value from the tabulated sampling density done entirely in a preprocessing step. This produces a consistent noise reduction in all our tests with no negative influence on run time, no artifacts or bias, and no failure cases.","lang":"eng"}]}]