[{"year":"2018","abstract":[{"text":"We consider the problem of learning a Bayesian network or directed acyclic graph model from observational data. A number of constraint‐based, score‐based and hybrid algorithms have been developed for this purpose. Statistical consistency guarantees of these algorithms rely on the faithfulness assumption, which has been shown to be restrictive especially for graphs with cycles in the skeleton. We here propose the sparsest permutation (SP) algorithm, showing that learning Bayesian networks is possible under strictly weaker assumptions than faithfulness. This comes at a computational price, thereby indicating a statistical‐computational trade‐off for causal inference algorithms. In the Gaussian noiseless setting, we prove that the SP algorithm boils down to finding the permutation of the variables with the sparsest Cholesky decomposition of the inverse covariance matrix, which is equivalent to ℓ0‐penalized maximum likelihood estimation. We end with a simulation study showing that in line with the proven stronger consistency guarantees, and the SP algorithm compares favourably to standard causal inference algorithms in terms of accuracy for a given sample size.","lang":"eng"}],"date_created":"2018-12-11T11:55:13Z","month":"04","_id":"2015","publisher":"Wiley","external_id":{"arxiv":["1307.0366"]},"publication_status":"published","fulldoi":"https://doi.org/10.1002/sta4.183","issue":"1","arxiv":1,"date_published":"2018-04-17T00:00:00Z","article_number":"e183","status":"public","language":[{"iso":"eng"}],"publist_id":"5061","volume":7,"publication":"STAT","author":[{"full_name":"Raskutti, Garvesh","first_name":"Garvesh","last_name":"Raskutti"},{"orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"}],"title":"Learning directed acyclic graphs based on sparsest permutations","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2021-01-12T06:54:44Z","oa_version":"Preprint","quality_controlled":"1","intvolume":"         7","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.0366"}],"doi":"10.1002/sta4.183","citation":{"short":"G. Raskutti, C. Uhler, STAT 7 (2018).","chicago":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” <i>STAT</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/sta4.183\">https://doi.org/10.1002/sta4.183</a>.","mla":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” <i>STAT</i>, vol. 7, no. 1, e183, Wiley, 2018, doi:<a href=\"https://doi.org/10.1002/sta4.183\">10.1002/sta4.183</a>.","ieee":"G. Raskutti and C. Uhler, “Learning directed acyclic graphs based on sparsest permutations,” <i>STAT</i>, vol. 7, no. 1. Wiley, 2018.","apa":"Raskutti, G., &#38; Uhler, C. (2018). Learning directed acyclic graphs based on sparsest permutations. <i>STAT</i>. Wiley. <a href=\"https://doi.org/10.1002/sta4.183\">https://doi.org/10.1002/sta4.183</a>","ama":"Raskutti G, Uhler C. Learning directed acyclic graphs based on sparsest permutations. <i>STAT</i>. 2018;7(1). doi:<a href=\"https://doi.org/10.1002/sta4.183\">10.1002/sta4.183</a>","ista":"Raskutti G, Uhler C. 2018. Learning directed acyclic graphs based on sparsest permutations. STAT. 7(1), e183."},"article_type":"original","extern":"1","day":"17"},{"oa_version":"Submitted Version","date_updated":"2026-04-28T08:29:26Z","OA_place":"repository","article_processing_charge":"No","title":"Auxin methylation is required for differential growth in Arabidopsis","author":[{"id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abbas, Mohamad","last_name":"Abbas","first_name":"Mohamad"},{"last_name":"Hernández","first_name":"García J","full_name":"Hernández, García J"},{"last_name":"Pollmann","first_name":"Stephan","full_name":"Pollmann, Stephan"},{"full_name":"Samodelov, Sophia L","first_name":"Sophia L","last_name":"Samodelov"},{"first_name":"Martina","last_name":"Kolb","full_name":"Kolb, Martina"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml"},{"first_name":"Ulrich Z","last_name":"Hammes","full_name":"Hammes, Ulrich Z"},{"last_name":"Zurbriggen","first_name":"Matias D","full_name":"Zurbriggen, Matias D"},{"full_name":"Blázquez, Miguel","last_name":"Blázquez","first_name":"Miguel"},{"first_name":"David","last_name":"Alabadí","full_name":"Alabadí, David"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":115,"publication":"PNAS","day":"26","article_type":"original","page":"6864-6869","citation":{"ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. 2018;115(26):6864-6869. doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>","ieee":"M. Abbas <i>et al.</i>, “Auxin methylation is required for differential growth in Arabidopsis,” <i>PNAS</i>, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>.","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869."},"doi":"10.1073/pnas.1806565115","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"main_file_link":[{"url":"http://eprints.nottingham.ac.uk/52388/","open_access":"1"}],"intvolume":"       115","oa":1,"quality_controlled":"1","publication_status":"published","publisher":"National Academy of Sciences","external_id":{"isi":["000436245000096"]},"_id":"203","month":"06","abstract":[{"text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.","lang":"eng"}],"OA_type":"green","date_created":"2018-12-11T11:45:11Z","year":"2018","language":[{"iso":"eng"}],"publist_id":"7710","status":"public","date_published":"2018-06-26T00:00:00Z","department":[{"_id":"JiFr"}],"scopus_import":"1","isi":1,"ec_funded":1,"issue":"26","fulldoi":"https://doi.org/10.1073/pnas.1806565115"},{"language":[{"iso":"eng"}],"status":"public","acknowledgement":"We acknowledge support from the Schiff Foundation (A.J.D.), the Royal Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC (T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several useful discussions.","date_published":"2018-10-18T00:00:00Z","scopus_import":"1","issue":"49","fulldoi":"https://doi.org/10.1021/acs.jpcb.8b07805","pmid":1,"publication_status":"published","external_id":{"pmid":["30336667"]},"publisher":"American Chemical Society","month":"10","_id":"10357","publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"date_created":"2021-11-26T11:55:12Z","abstract":[{"text":"The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements.","lang":"eng"}],"year":"2018","day":"18","page":"11721-11730","article_type":"original","extern":"1","citation":{"ista":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 122(49), 11721–11730.","apa":"Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., &#38; Knowles, T. P. J. (2018). Statistical mechanics of globular oligomer formation by protein molecules. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">https://doi.org/10.1021/acs.jpcb.8b07805</a>","ama":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics of globular oligomer formation by protein molecules. <i>The Journal of Physical Chemistry B</i>. 2018;122(49):11721-11730. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">10.1021/acs.jpcb.8b07805</a>","ieee":"A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles, “Statistical mechanics of globular oligomer formation by protein molecules,” <i>The Journal of Physical Chemistry B</i>, vol. 122, no. 49. American Chemical Society, pp. 11721–11730, 2018.","chicago":"Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M. Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">https://doi.org/10.1021/acs.jpcb.8b07805</a>.","short":"A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal of Physical Chemistry B 122 (2018) 11721–11730.","mla":"Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” <i>The Journal of Physical Chemistry B</i>, vol. 122, no. 49, American Chemical Society, 2018, pp. 11721–30, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">10.1021/acs.jpcb.8b07805</a>."},"keyword":["materials chemistry"],"doi":"10.1021/acs.jpcb.8b07805","intvolume":"       122","quality_controlled":"1","date_updated":"2021-11-26T12:40:02Z","oa_version":"None","article_processing_charge":"No","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Statistical mechanics of globular oligomer formation by protein molecules","author":[{"first_name":"Alexander J.","last_name":"Dear","full_name":"Dear, Alexander J."},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."}],"publication":"The Journal of Physical Chemistry B","volume":122},{"day":"24","article_type":"original","extern":"1","page":"3055-3065","citation":{"ama":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate theory for supramolecular kinetics: application to protein aggregation. <i>Molecular Physics</i>. 2018;116(21-22):3055-3065. doi:<a href=\"https://doi.org/10.1080/00268976.2018.1474280\">10.1080/00268976.2018.1474280</a>","apa":"Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., &#38; Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. <i>Molecular Physics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00268976.2018.1474280\">https://doi.org/10.1080/00268976.2018.1474280</a>","ista":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 116(21–22), 3055–3065.","mla":"Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” <i>Molecular Physics</i>, vol. 116, no. 21–22, Taylor &#38; Francis, 2018, pp. 3055–65, doi:<a href=\"https://doi.org/10.1080/00268976.2018.1474280\">10.1080/00268976.2018.1474280</a>.","chicago":"Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” <i>Molecular Physics</i>. Taylor &#38; Francis, 2018. <a href=\"https://doi.org/10.1080/00268976.2018.1474280\">https://doi.org/10.1080/00268976.2018.1474280</a>.","short":"T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles, Molecular Physics 116 (2018) 3055–3065.","ieee":"T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P. J. Knowles, “Reaction rate theory for supramolecular kinetics: application to protein aggregation,” <i>Molecular Physics</i>, vol. 116, no. 21–22. Taylor &#38; Francis, pp. 3055–3065, 2018."},"keyword":["physical chemistry"],"doi":"10.1080/00268976.2018.1474280","main_file_link":[{"url":"https://arxiv.org/abs/1803.04851","open_access":"1"}],"intvolume":"       116","oa":1,"quality_controlled":"1","date_updated":"2021-11-26T12:39:58Z","oa_version":"Preprint","article_processing_charge":"No","author":[{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"last_name":"Liu","first_name":"Lucie X.","full_name":"Liu, Lucie X."},{"first_name":"Samo","last_name":"Curk","full_name":"Curk, Samo"},{"full_name":"Bolhuis, Peter G.","first_name":"Peter G.","last_name":"Bolhuis"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}],"title":"Reaction rate theory for supramolecular kinetics: application to protein aggregation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":116,"publication":"Molecular Physics","language":[{"iso":"eng"}],"status":"public","date_published":"2018-05-24T00:00:00Z","acknowledgement":"We thank Claudia Flandoli for the help with illustrations.","scopus_import":"1","arxiv":1,"issue":"21-22","fulldoi":"https://doi.org/10.1080/00268976.2018.1474280","publication_status":"published","publisher":"Taylor & Francis","external_id":{"arxiv":["1803.04851"]},"_id":"10358","month":"05","publication_identifier":{"issn":["0026-8976"],"eissn":["1362-3028"]},"abstract":[{"lang":"eng","text":"Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements."}],"date_created":"2021-11-26T12:08:02Z","year":"2018"},{"issue":"9","pmid":1,"fulldoi":"https://doi.org/10.1021/acs.nanolett.8b00786","date_published":"2018-04-18T00:00:00Z","acknowledgement":"We acknowledge discussions with Giuseppe Battaglia as well as support from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.). We thank Claudia Flandoli for help with Figure 1.","scopus_import":"1","language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets."}],"date_created":"2021-11-26T12:15:47Z","year":"2018","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"month":"04","_id":"10359","publication_status":"published","publisher":"American Chemical Society","external_id":{"pmid":["29667410"]},"intvolume":"        18","oa":1,"quality_controlled":"1","keyword":["mechanical engineering","condensed matter physics"],"doi":"10.1021/acs.nanolett.8b00786","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.10147"}],"citation":{"ista":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.","apa":"Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., &#38; Šarić, A. (2018). Controlling cargo trafficking in multicomponent membranes. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">https://doi.org/10.1021/acs.nanolett.8b00786</a>","ama":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking in multicomponent membranes. <i>Nano Letters</i>. 2018;18(9):5350-5356. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">10.1021/acs.nanolett.8b00786</a>","ieee":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling cargo trafficking in multicomponent membranes,” <i>Nano Letters</i>, vol. 18, no. 9. American Chemical Society, pp. 5350–5356, 2018.","short":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters 18 (2018) 5350–5356.","chicago":"Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” <i>Nano Letters</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">https://doi.org/10.1021/acs.nanolett.8b00786</a>.","mla":"Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.” <i>Nano Letters</i>, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">10.1021/acs.nanolett.8b00786</a>."},"day":"18","article_type":"original","extern":"1","page":"5350-5356","volume":18,"publication":"Nano Letters","article_processing_charge":"No","author":[{"first_name":"Tine","last_name":"Curk","full_name":"Curk, Tine"},{"first_name":"Peter","last_name":"Wirnsberger","full_name":"Wirnsberger, Peter"},{"full_name":"Dobnikar, Jure","first_name":"Jure","last_name":"Dobnikar"},{"full_name":"Frenkel, Daan","last_name":"Frenkel","first_name":"Daan"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"}],"title":"Controlling cargo trafficking in multicomponent membranes","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-11-26T15:14:08Z","oa_version":"Preprint"},{"publication":"Nature Chemistry","volume":10,"article_processing_charge":"No","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide","author":[{"last_name":"Cohen","first_name":"Samuel I. A.","full_name":"Cohen, Samuel I. A."},{"last_name":"Cukalevski","first_name":"Risto","full_name":"Cukalevski, Risto"},{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"full_name":"Törnquist, Mattias","first_name":"Mattias","last_name":"Törnquist"},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"full_name":"Buell, Alexander K.","first_name":"Alexander K.","last_name":"Buell"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."},{"last_name":"Linse","first_name":"Sara","full_name":"Linse, Sara"}],"date_updated":"2021-11-26T15:14:00Z","oa_version":"None","intvolume":"        10","quality_controlled":"1","doi":"10.1038/s41557-018-0023-x","keyword":["general chemical engineering","general chemistry"],"citation":{"apa":"Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist, M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-018-0023-x\">https://doi.org/10.1038/s41557-018-0023-x</a>","ama":"Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. <i>Nature Chemistry</i>. 2018;10(5):523-531. doi:<a href=\"https://doi.org/10.1038/s41557-018-0023-x\">10.1038/s41557-018-0023-x</a>","ista":"Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 10(5), 523–531.","chicago":"Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić, Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell, Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” <i>Nature Chemistry</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41557-018-0023-x\">https://doi.org/10.1038/s41557-018-0023-x</a>.","short":"S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M. Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry 10 (2018) 523–531.","mla":"Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” <i>Nature Chemistry</i>, vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:<a href=\"https://doi.org/10.1038/s41557-018-0023-x\">10.1038/s41557-018-0023-x</a>.","ieee":"S. I. A. Cohen <i>et al.</i>, “Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide,” <i>Nature Chemistry</i>, vol. 10, no. 5. Springer Nature, pp. 523–531, 2018."},"day":"26","page":"523-531","article_type":"original","extern":"1","date_created":"2021-11-26T12:41:38Z","abstract":[{"text":"Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.","lang":"eng"}],"year":"2018","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"month":"03","_id":"10360","publication_status":"published","external_id":{"pmid":["29581486"]},"publisher":"Springer Nature","issue":"5","fulldoi":"https://doi.org/10.1038/s41557-018-0023-x","pmid":1,"acknowledgement":"We thank B. Jönsson and I. André for helpful discussions. We acknowledge financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge (S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden (S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust (A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases (C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).","date_published":"2018-03-26T00:00:00Z","scopus_import":"1","language":[{"iso":"eng"}],"status":"public"},{"_id":"10361","month":"02","publisher":"Annual Reviews","external_id":{"pmid":["29490200"]},"publication_status":"published","year":"2018","abstract":[{"text":"Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.","lang":"eng"}],"date_created":"2021-11-26T12:52:12Z","publication_identifier":{"issn":["0066-426X"],"eissn":["1545-1593"]},"scopus_import":"1","date_published":"2018-02-28T00:00:00Z","acknowledgement":"We acknowledge support from the Swiss National Science Foundation (T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.); the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt (337969).","status":"public","language":[{"iso":"eng"}],"pmid":1,"fulldoi":"https://doi.org/10.1146/annurev-physchem-050317-021322","issue":"1","date_updated":"2021-11-26T15:58:19Z","oa_version":"None","volume":69,"publication":"Annual Review of Physical Chemistry","author":[{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Habchi","first_name":"Johnny","full_name":"Habchi, Johnny"},{"last_name":"Chia","first_name":"Sean","full_name":"Chia, Sean"},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"last_name":"Knowles","first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J."}],"title":"Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","citation":{"ieee":"T. C. T. Michaels <i>et al.</i>, “Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation,” <i>Annual Review of Physical Chemistry</i>, vol. 69, no. 1. Annual Reviews, pp. 273–298, 2018.","mla":"Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” <i>Annual Review of Physical Chemistry</i>, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:<a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">10.1146/annurev-physchem-050317-021322</a>.","short":"T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.","chicago":"Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” <i>Annual Review of Physical Chemistry</i>. Annual Reviews, 2018. <a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">https://doi.org/10.1146/annurev-physchem-050317-021322</a>.","ista":"Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 69(1), 273–298.","ama":"Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. <i>Annual Review of Physical Chemistry</i>. 2018;69(1):273-298. doi:<a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">10.1146/annurev-physchem-050317-021322</a>","apa":"Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo, M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. <i>Annual Review of Physical Chemistry</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">https://doi.org/10.1146/annurev-physchem-050317-021322</a>"},"extern":"1","article_type":"original","page":"273-298","day":"28","quality_controlled":"1","intvolume":"        69","doi":"10.1146/annurev-physchem-050317-021322","keyword":["physical and theoretical chemistry"]},{"intvolume":"        12","quality_controlled":"1","doi":"10.1021/acsnano.7b08044","keyword":["general physics and astronomy"],"citation":{"ieee":"P. D. E. Fisher <i>et al.</i>, “A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement,” <i>ACS Nano</i>, vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.","short":"P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley, A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518.","chicago":"Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” <i>ACS Nano</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acsnano.7b08044\">https://doi.org/10.1021/acsnano.7b08044</a>.","mla":"Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” <i>ACS Nano</i>, vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:<a href=\"https://doi.org/10.1021/acsnano.7b08044\">10.1021/acsnano.7b08044</a>.","ista":"Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 12(2), 1508–1518.","apa":"Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley, D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.7b08044\">https://doi.org/10.1021/acsnano.7b08044</a>","ama":"Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. <i>ACS Nano</i>. 2018;12(2):1508-1518. doi:<a href=\"https://doi.org/10.1021/acsnano.7b08044\">10.1021/acsnano.7b08044</a>"},"day":"19","extern":"1","article_type":"original","page":"1508-1518","volume":12,"publication":"ACS Nano","article_processing_charge":"No","author":[{"first_name":"Patrick D. Ellis","last_name":"Fisher","full_name":"Fisher, Patrick D. Ellis"},{"first_name":"Qi","last_name":"Shen","full_name":"Shen, Qi"},{"first_name":"Bernice","last_name":"Akpinar","full_name":"Akpinar, Bernice"},{"last_name":"Davis","first_name":"Luke K.","full_name":"Davis, Luke K."},{"full_name":"Chung, Kenny Kwok Hin","last_name":"Chung","first_name":"Kenny Kwok Hin"},{"last_name":"Baddeley","first_name":"David","full_name":"Baddeley, David"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"last_name":"Melia","first_name":"Thomas J.","full_name":"Melia, Thomas J."},{"full_name":"Hoogenboom, Bart W.","last_name":"Hoogenboom","first_name":"Bart W."},{"last_name":"Lin","first_name":"Chenxiang","full_name":"Lin, Chenxiang"},{"full_name":"Lusk, C. Patrick","last_name":"Lusk","first_name":"C. Patrick"}],"title":"A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-11-26T15:57:02Z","oa_version":"None","issue":"2","pmid":1,"fulldoi":"https://doi.org/10.1021/acsnano.7b08044","date_published":"2018-01-19T00:00:00Z","acknowledgement":"We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1, and EP/M028100/1).","scopus_import":"1","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.","lang":"eng"}],"date_created":"2021-11-26T15:15:00Z","year":"2018","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"month":"01","_id":"10362","publication_status":"published","publisher":"American Chemical Society","external_id":{"pmid":["29350911"]}},{"oa_version":"Published Version","date_updated":"2023-09-19T10:06:42Z","file_date_updated":"2018-12-18T09:46:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","author":[{"last_name":"Seitner","first_name":"Denise","full_name":"Seitner, Denise"},{"full_name":"Uhse, Simon","first_name":"Simon","last_name":"Uhse"},{"first_name":"Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368"},{"full_name":"Djamei, Armin","last_name":"Djamei","first_name":"Armin"}],"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","article_processing_charge":"No","ddc":["580"],"publication":"Molecular Plant Pathology","volume":19,"page":"2277 - 2287","day":"01","citation":{"ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287.","apa":"Seitner, D., Uhse, S., Gallei, M. C., &#38; Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. Wiley. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>","ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. 2018;19(10):2277-2287. doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>","ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” <i>Molecular Plant Pathology</i>, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.","chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>.","short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>."},"doi":"10.1111/mpp.12698","quality_controlled":"1","oa":1,"intvolume":"        19","external_id":{"isi":["000445624100006"]},"publisher":"Wiley","file":[{"access_level":"open_access","file_id":"5740","file_name":"2018_MolecPlantPath_Seitner.pdf","success":1,"date_created":"2018-12-18T09:46:00Z","creator":"dernst","content_type":"application/pdf","date_updated":"2018-12-18T09:46:00Z","relation":"main_file","file_size":682335}],"has_accepted_license":"1","publication_status":"published","month":"10","_id":"104","year":"2018","date_created":"2018-12-11T11:44:39Z","abstract":[{"lang":"eng","text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host."}],"status":"public","publist_id":"7950","language":[{"iso":"eng"}],"scopus_import":"1","department":[{"_id":"GradSch"}],"acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","date_published":"2018-10-01T00:00:00Z","fulldoi":"https://doi.org/10.1111/mpp.12698","issue":"10","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"}},{"oa":1,"intvolume":"         2","quality_controlled":"1","doi":"10.1145/3158119","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2018. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. <i>Proceedings of the ACM on Programming Languages</i>. 2018;2(POPL). doi:<a href=\"https://doi.org/10.1145/3158119\">10.1145/3158119</a>","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., &#38; Vaidya, K. (2018). Data-centric dynamic partial order reduction. <i>Proceedings of the ACM on Programming Languages</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3158119\">https://doi.org/10.1145/3158119</a>","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL. Association for Computing Machinery, 2018.","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL, 31, Association for Computing Machinery, 2018, doi:<a href=\"https://doi.org/10.1145/3158119\">10.1145/3158119</a>.","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2018. <a href=\"https://doi.org/10.1145/3158119\">https://doi.org/10.1145/3158119</a>.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2018)."},"day":"01","article_type":"original","publication":"Proceedings of the ACM on Programming Languages","volume":2,"ddc":["000"],"article_processing_charge":"No","conference":{"start_date":"2018-01-07","name":"POPL: Programming Languages","location":"Los Angeles, CA, United States","end_date":"2018-01-13"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","title":"Data-centric dynamic partial order reduction","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"full_name":"Sinha, Nishant","first_name":"Nishant","last_name":"Sinha"},{"first_name":"Kapil","last_name":"Vaidya","full_name":"Vaidya, Kapil"}],"related_material":{"record":[{"id":"5448","relation":"earlier_version","status":"public"},{"id":"5456","relation":"earlier_version","status":"public"}]},"OA_place":"publisher","file_date_updated":"2025-05-20T09:44:47Z","date_updated":"2025-05-20T09:45:10Z","oa_version":"Published Version","ec_funded":1,"issue":"POPL","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"fulldoi":"https://doi.org/10.1145/3158119","arxiv":1,"article_number":"31","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","date_published":"2018-01-01T00:00:00Z","scopus_import":"1","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"status":"public","OA_type":"hybrid","date_created":"2021-12-05T23:01:49Z","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence."}],"year":"2018","publication_identifier":{"eissn":["2475-1421"]},"month":"01","_id":"10417","has_accepted_license":"1","publication_status":"published","external_id":{"arxiv":["1610.01188"]},"file":[{"date_created":"2025-05-20T09:44:47Z","success":1,"creator":"dernst","access_level":"open_access","file_id":"19716","file_name":"2018_ACM_Chalupa.pdf","relation":"main_file","checksum":"b27ab1745f6dba2387deb785798a657c","file_size":388891,"content_type":"application/pdf","date_updated":"2025-05-20T09:44:47Z"}],"publisher":"Association for Computing Machinery"},{"date_published":"2018-09-01T00:00:00Z","scopus_import":"1","department":[{"_id":"HeEd"}],"publist_id":"7948","language":[{"iso":"eng"}],"status":"public","issue":"3","isi":1,"fulldoi":"https://doi.org/10.1007/s00283-018-9795-5","arxiv":1,"month":"09","_id":"106","publication_status":"published","external_id":{"isi":["000444141200005"],"arxiv":["1702.05172"]},"publisher":"Springer","date_created":"2018-12-11T11:44:40Z","abstract":[{"lang":"eng","text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below."}],"year":"2018","citation":{"ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” <i>Mathematical Intelligencer</i>, vol. 40, no. 3. Springer, pp. 26–31, 2018.","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>.","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31.","apa":"Akopyan, A., &#38; Petrunin, A. (2018). Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. Springer. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. 2018;40(3):26-31. doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>"},"day":"01","page":"26 - 31","oa":1,"intvolume":"        40","quality_controlled":"1","doi":"10.1007/s00283-018-9795-5","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.05172"}],"date_updated":"2023-09-13T08:49:16Z","oa_version":"Preprint","publication":"Mathematical Intelligencer","volume":40,"article_processing_charge":"No","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"full_name":"Petrunin, Anton","first_name":"Anton","last_name":"Petrunin"}],"title":"Long geodesics on convex surfaces"},{"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"date_created":"2022-01-14T12:15:47Z","abstract":[{"lang":"eng","text":"Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4."}],"year":"2018","publication_status":"published","external_id":{"arxiv":["1805.04199"]},"publisher":"American Physical Society","_id":"10626","month":"11","arxiv":1,"issue":"22","fulldoi":"https://doi.org/10.1103/physrevlett.121.226801","language":[{"iso":"eng"}],"status":"public","article_number":"226801","acknowledgement":"We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for discussing their unpublished data and for sharing the stack inversion technique. The authors acknowledge further discussions of the results with I. Sodemann, M. Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Prize Fellowship in Science of the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard Foundation.","date_published":"2018-11-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","first_name":"Hryhoriy"},{"first_name":"H.","last_name":"Zhou","full_name":"Zhou, H."},{"full_name":"Spanton, E. M.","first_name":"E. M.","last_name":"Spanton"},{"full_name":"Taniguchi, T.","first_name":"T.","last_name":"Taniguchi"},{"last_name":"Watanabe","first_name":"K.","full_name":"Watanabe, K."},{"full_name":"Young, A. F.","last_name":"Young","first_name":"A. F."}],"title":"Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices","publication":"Physical Review Letters","volume":121,"date_updated":"2022-01-14T13:48:35Z","oa_version":"Preprint","doi":"10.1103/physrevlett.121.226801","keyword":["general physics and astronomy"],"main_file_link":[{"url":"https://arxiv.org/abs/1805.04199","open_access":"1"}],"oa":1,"intvolume":"       121","quality_controlled":"1","day":"28","extern":"1","article_type":"original","citation":{"ista":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 121(22), 226801.","apa":"Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., &#38; Young, A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.121.226801\">https://doi.org/10.1103/physrevlett.121.226801</a>","ama":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. <i>Physical Review Letters</i>. 2018;121(22). doi:<a href=\"https://doi.org/10.1103/physrevlett.121.226801\">10.1103/physrevlett.121.226801</a>","ieee":"H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young, “Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices,” <i>Physical Review Letters</i>, vol. 121, no. 22. American Physical Society, 2018.","chicago":"Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevlett.121.226801\">https://doi.org/10.1103/physrevlett.121.226801</a>.","short":"H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young, Physical Review Letters 121 (2018).","mla":"Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” <i>Physical Review Letters</i>, vol. 121, no. 22, 226801, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevlett.121.226801\">10.1103/physrevlett.121.226801</a>."}},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.08184"}],"doi":"10.1103/physrevb.97.184501","quality_controlled":"1","oa":1,"intvolume":"        97","article_type":"original","extern":"1","day":"08","citation":{"ista":"Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 97(18), 184501.","ama":"Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size superconducting rings. <i>Physical Review B</i>. 2018;97(18). doi:<a href=\"https://doi.org/10.1103/physrevb.97.184501\">10.1103/physrevb.97.184501</a>","apa":"Polshyn, H., Naibert, T. R., &#38; Budakian, R. (2018). Imaging phase slip dynamics in micron-size superconducting rings. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.97.184501\">https://doi.org/10.1103/physrevb.97.184501</a>","ieee":"H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in micron-size superconducting rings,” <i>Physical Review B</i>, vol. 97, no. 18. American Physical Society, 2018.","mla":"Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” <i>Physical Review B</i>, vol. 97, no. 18, 184501, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevb.97.184501\">10.1103/physrevb.97.184501</a>.","short":"H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).","chicago":"Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevb.97.184501\">https://doi.org/10.1103/physrevb.97.184501</a>."},"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Imaging phase slip dynamics in micron-size superconducting rings","author":[{"orcid":"0000-0001-8223-8896","last_name":"Polshyn","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"last_name":"Naibert","first_name":"Tyler R.","full_name":"Naibert, Tyler R."},{"first_name":"Raffi","last_name":"Budakian","full_name":"Budakian, Raffi"}],"article_processing_charge":"No","publication":"Physical Review B","volume":97,"date_updated":"2022-01-14T13:58:24Z","oa_version":"Preprint","arxiv":1,"fulldoi":"https://doi.org/10.1103/physrevb.97.184501","issue":"18","status":"public","language":[{"iso":"eng"}],"scopus_import":"1","acknowledgement":"We are grateful to Nadya Mason for useful discussions. This work was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649, the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.\r\n","article_number":"184501","date_published":"2018-05-08T00:00:00Z","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"year":"2018","date_created":"2022-01-14T13:48:47Z","abstract":[{"lang":"eng","text":"We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures."}],"external_id":{"arxiv":["1703.08184"]},"publisher":"American Physical Society","publication_status":"published","month":"05","_id":"10627"},{"intvolume":"        59","oa":1,"quality_controlled":"1","doi":"10.1007/s00454-017-9883-x","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"citation":{"ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete &#38; Computational Geometry. 59(4), 1001–1009.","ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. 2018;59(4):1001-1009. doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>","apa":"Akopyan, A., Balitskiy, A., &#38; Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4. Springer, pp. 1001–1009, 2018.","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>.","short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete &#38; Computational Geometry 59 (2018) 1001–1009.","chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>."},"day":"01","article_type":"original","page":"1001-1009","volume":59,"publication":"Discrete & Computational Geometry","ddc":["516","000"],"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"full_name":"Balitskiy, Alexey","last_name":"Balitskiy","first_name":"Alexey"},{"full_name":"Grigorev, Mikhail","first_name":"Mikhail","last_name":"Grigorev"}],"title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2019-01-18T09:27:36Z","oa_version":"Published Version","date_updated":"2026-05-20T10:19:33Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"isi":1,"ec_funded":1,"issue":"4","fulldoi":"https://doi.org/10.1007/s00454-017-9883-x","date_published":"2018-06-01T00:00:00Z","corr_author":"1","scopus_import":"1","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"publist_id":"6324","status":"public","abstract":[{"lang":"eng","text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets."}],"date_created":"2018-12-11T11:49:57Z","year":"2018","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"06","_id":"1064","publication_status":"published","has_accepted_license":"1","publisher":"Springer","file":[{"date_created":"2019-01-18T09:27:36Z","success":1,"creator":"dernst","access_level":"open_access","file_id":"5844","file_name":"2018_DiscreteComp_Akopyan.pdf","relation":"main_file","file_size":482518,"content_type":"application/pdf","date_updated":"2019-01-18T09:27:36Z"}],"external_id":{"isi":["000432205500011"]}},{"date_updated":"2025-04-14T07:22:06Z","oa_version":"Preprint","volume":65,"publication":"Journal of the ACM","article_processing_charge":"No","author":[{"full_name":"Dziembowski, Stefan","first_name":"Stefan","last_name":"Dziembowski"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"title":"Non-malleable codes","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. <i>Journal of the ACM</i>. 2018;65(4). doi:<a href=\"https://doi.org/10.1145/3178432\">10.1145/3178432</a>","apa":"Dziembowski, S., Pietrzak, K. Z., &#38; Wichs, D. (2018). Non-malleable codes. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3178432\">https://doi.org/10.1145/3178432</a>","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” <i>Journal of the ACM</i>, vol. 65, no. 4. ACM, 2018.","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” <i>Journal of the ACM</i>, vol. 65, no. 4, 20, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3178432\">10.1145/3178432</a>.","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” <i>Journal of the ACM</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3178432\">https://doi.org/10.1145/3178432</a>."},"day":"01","article_type":"original","intvolume":"        65","oa":1,"quality_controlled":"1","doi":"10.1145/3178432","main_file_link":[{"url":"https://eprint.iacr.org/2009/608","open_access":"1"}],"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"},{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"month":"08","_id":"107","publication_status":"published","publisher":"ACM","external_id":{"isi":["000442938200004"]},"abstract":[{"lang":"eng","text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory."}],"date_created":"2018-12-11T11:44:40Z","year":"2018","date_published":"2018-08-01T00:00:00Z","article_number":"20","scopus_import":"1","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"publist_id":"7947","status":"public","isi":1,"ec_funded":1,"issue":"4","fulldoi":"https://doi.org/10.1145/3178432"},{"citation":{"mla":"Obremski, Marciej, and Maciej Skórski. <i>Inverted Leftover Hash Lemma</i>. Vol. 2018, IEEE, 2018, doi:<a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">10.1109/ISIT.2018.8437654</a>.","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. <a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">https://doi.org/10.1109/ISIT.2018.8437654</a>.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:<a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">10.1109/ISIT.2018.8437654</a>","apa":"Obremski, M., &#38; Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. <a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">https://doi.org/10.1109/ISIT.2018.8437654</a>","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018."},"day":"16","quality_controlled":"1","oa":1,"intvolume":"      2018","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"doi":"10.1109/ISIT.2018.8437654","date_updated":"2023-09-13T08:23:18Z","oa_version":"Submitted Version","alternative_title":["ISIT Proceedings"],"volume":2018,"conference":{"name":"ISIT: International Symposium on Information Theory","start_date":"2018-06-17 ","end_date":"2018-06-22","location":"Vail, CO, USA"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"conference","author":[{"full_name":"Obremski, Marciej","last_name":"Obremski","first_name":"Marciej"},{"first_name":"Maciej","last_name":"Skorski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skorski, Maciej"}],"title":"Inverted leftover hash lemma","article_processing_charge":"No","department":[{"_id":"KrPi"}],"scopus_import":"1","date_published":"2018-08-16T00:00:00Z","status":"public","publist_id":"7946","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1109/ISIT.2018.8437654","isi":1,"month":"08","_id":"108","external_id":{"isi":["000448139300368"]},"publisher":"IEEE","publication_status":"published","year":"2018","date_created":"2018-12-11T11:44:40Z","abstract":[{"text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes.","lang":"eng"}]},{"status":"public","publist_id":"7978","language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","department":[{"_id":"DaAl"}],"date_published":"2018-09-12T00:00:00Z","fulldoi":"https://doi.org/10.1007/s00446-018-0342-6","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"external_id":{"isi":["000475627800005"]},"file":[{"date_updated":"2020-07-14T12:48:01Z","content_type":"application/pdf","checksum":"872db70bba9b401500abe3c6ae2f1a61","file_size":799337,"relation":"main_file","file_name":"2018_DistributedComputing_Lenzen.pdf","access_level":"open_access","file_id":"5711","creator":"dernst","date_created":"2018-12-17T14:21:22Z"}],"publisher":"Springer","has_accepted_license":"1","publication_status":"published","month":"09","_id":"76","year":"2018","date_created":"2018-12-11T11:44:30Z","abstract":[{"text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C&gt;1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f&lt;n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.","lang":"eng"}],"day":"12","citation":{"ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” <i>Distributed Computing</i>. Springer, 2018.","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” <i>Distributed Computing</i>, Springer, 2018, doi:<a href=\"https://doi.org/10.1007/s00446-018-0342-6\">10.1007/s00446-018-0342-6</a>.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” <i>Distributed Computing</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00446-018-0342-6\">https://doi.org/10.1007/s00446-018-0342-6</a>.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing.","ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. <i>Distributed Computing</i>. 2018. doi:<a href=\"https://doi.org/10.1007/s00446-018-0342-6\">10.1007/s00446-018-0342-6</a>","apa":"Lenzen, C., &#38; Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. <i>Distributed Computing</i>. Springer. <a href=\"https://doi.org/10.1007/s00446-018-0342-6\">https://doi.org/10.1007/s00446-018-0342-6</a>"},"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"doi":"10.1007/s00446-018-0342-6","quality_controlled":"1","oa":1,"oa_version":"Published Version","date_updated":"2025-04-15T06:53:15Z","file_date_updated":"2020-07-14T12:48:01Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","title":"Near-optimal self-stabilising counting and firing squads","author":[{"full_name":"Lenzen, Christoph","first_name":"Christoph","last_name":"Lenzen"},{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646"}],"article_processing_charge":"Yes (via OA deal)","ddc":["000"],"publication":"Distributed Computing"},{"date_published":"2018-01-04T00:00:00Z","citation":{"ista":"Sweeney LB, Bikoff JB, Gabitto MI, Brenner-Morton S, Baek M, Yang JH, Tabak EG, Dasen JS, Kintner CR, Jessell TM. 2018. Origin and segmental diversity of spinal inhibitory interneurons. Neuron. 97(2), 341–355.e3.","ama":"Sweeney LB, Bikoff JB, Gabitto MI, et al. Origin and segmental diversity of spinal inhibitory interneurons. <i>Neuron</i>. 2018;97(2):341-355.e3. doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.12.029\">10.1016/j.neuron.2017.12.029</a>","apa":"Sweeney, L. B., Bikoff, J. B., Gabitto, M. I., Brenner-Morton, S., Baek, M., Yang, J. H., … Jessell, T. M. (2018). Origin and segmental diversity of spinal inhibitory interneurons. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2017.12.029\">https://doi.org/10.1016/j.neuron.2017.12.029</a>","ieee":"L. B. Sweeney <i>et al.</i>, “Origin and segmental diversity of spinal inhibitory interneurons,” <i>Neuron</i>, vol. 97, no. 2. Elsevier, p. 341–355.e3, 2018.","mla":"Sweeney, Lora B., et al. “Origin and Segmental Diversity of Spinal Inhibitory Interneurons.” <i>Neuron</i>, vol. 97, no. 2, Elsevier, 2018, p. 341–355.e3, doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.12.029\">10.1016/j.neuron.2017.12.029</a>.","chicago":"Sweeney, Lora B., Jay B. Bikoff, Mariano I. Gabitto, Susan Brenner-Morton, Myungin Baek, Jerry H. Yang, Esteban G. Tabak, Jeremy S. Dasen, Christopher R. Kintner, and Thomas M. Jessell. “Origin and Segmental Diversity of Spinal Inhibitory Interneurons.” <i>Neuron</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.neuron.2017.12.029\">https://doi.org/10.1016/j.neuron.2017.12.029</a>.","short":"L.B. Sweeney, J.B. Bikoff, M.I. Gabitto, S. Brenner-Morton, M. Baek, J.H. Yang, E.G. Tabak, J.S. Dasen, C.R. Kintner, T.M. Jessell, Neuron 97 (2018) 341–355.e3."},"language":[{"iso":"eng"}],"day":"04","article_type":"original","extern":"1","page":"341-355.e3","status":"public","intvolume":"        97","issue":"2","quality_controlled":"1","fulldoi":"https://doi.org/10.1016/j.neuron.2017.12.029","doi":"10.1016/j.neuron.2017.12.029","_id":"7698","month":"01","publication_status":"published","publisher":"Elsevier","oa_version":"None","date_updated":"2024-01-31T10:13:54Z","volume":97,"abstract":[{"text":"Motor output varies along the rostro-caudal axis of the tetrapod spinal cord. At limb levels, ∼60 motor pools control the alternation of flexor and extensor muscles about each joint, whereas at thoracic levels as few as 10 motor pools supply muscle groups that support posture, inspiration, and expiration. Whether such differences in motor neuron identity and muscle number are associated with segmental distinctions in interneuron diversity has not been resolved. We show that select combinations of nineteen transcription factors that specify lumbar V1 inhibitory interneurons generate subpopulations enriched at limb and thoracic levels. Specification of limb and thoracic V1 interneurons involves the Hox gene Hoxc9 independently of motor neurons. Thus, early Hox patterning of the spinal cord determines the identity of V1 interneurons and motor neurons. These studies reveal a developmental program of V1 interneuron diversity, providing insight into the organization of inhibitory interneurons associated with differential motor output.","lang":"eng"}],"publication":"Neuron","date_created":"2020-04-30T10:35:13Z","year":"2018","publication_identifier":{"issn":["0896-6273"]},"article_processing_charge":"No","title":"Origin and segmental diversity of spinal inhibitory interneurons","author":[{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","full_name":"Sweeney, Lora Beatrice Jaeger","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601"},{"full_name":"Bikoff, Jay B.","last_name":"Bikoff","first_name":"Jay B."},{"last_name":"Gabitto","first_name":"Mariano I.","full_name":"Gabitto, Mariano I."},{"last_name":"Brenner-Morton","first_name":"Susan","full_name":"Brenner-Morton, Susan"},{"first_name":"Myungin","last_name":"Baek","full_name":"Baek, Myungin"},{"last_name":"Yang","first_name":"Jerry H.","full_name":"Yang, Jerry H."},{"full_name":"Tabak, Esteban G.","last_name":"Tabak","first_name":"Esteban G."},{"last_name":"Dasen","first_name":"Jeremy S.","full_name":"Dasen, Jeremy S."},{"full_name":"Kintner, Christopher R.","first_name":"Christopher R.","last_name":"Kintner"},{"full_name":"Jessell, Thomas M.","last_name":"Jessell","first_name":"Thomas M."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article"},{"date_updated":"2026-04-08T07:27:13Z","oa_version":"Published Version","related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","relation":"dissertation_contains","id":"7996"}]},"file_date_updated":"2020-07-14T12:48:02Z","article_processing_charge":"Yes","author":[{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes","first_name":"Hannes","last_name":"Watzinger"},{"first_name":"Josip","last_name":"Kukucka","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vukusic, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","last_name":"Vukusic","orcid":"0000-0003-2424-8636"},{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"first_name":"Ting","last_name":"Wang","full_name":"Wang, Ting"},{"last_name":"Schäffler","first_name":"Friedrich","full_name":"Schäffler, Friedrich"},{"last_name":"Zhang","first_name":"Jian","full_name":"Zhang, Jian"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X"}],"title":"A germanium hole spin qubit","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":9,"publication":"Nature Communications","ddc":["530"],"day":"25","article_type":"original","citation":{"ama":"Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. <i>Nature Communications</i>. 2018;9(3902). doi:<a href=\"https://doi.org/10.1038/s41467-018-06418-4\">10.1038/s41467-018-06418-4</a>","apa":"Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F., … Katsaros, G. (2018). A germanium hole spin qubit. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-018-06418-4\">https://doi.org/10.1038/s41467-018-06418-4</a>","ista":"Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902).","mla":"Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” <i>Nature Communications</i>, vol. 9, no. 3902, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-06418-4\">10.1038/s41467-018-06418-4</a>.","chicago":"Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-018-06418-4\">https://doi.org/10.1038/s41467-018-06418-4</a>.","short":"H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang, G. Katsaros, Nature Communications 9 (2018).","ieee":"H. Watzinger <i>et al.</i>, “A germanium hole spin qubit,” <i>Nature Communications</i>, vol. 9, no. 3902. Nature Publishing Group, 2018."},"doi":"10.1038/s41467-018-06418-4","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires","grant_number":"335497"},{"name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","grant_number":"Y00715","_id":"2552F888-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"intvolume":"         9","oa":1,"quality_controlled":"1","publication_status":"published","has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"file":[{"file_id":"5687","access_level":"open_access","file_name":"2018_NatureComm_Watzinger.pdf","date_created":"2018-12-17T10:28:30Z","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:48:02Z","relation":"main_file","checksum":"e7148c10a64497e279c4de570b6cc544","file_size":1063469}],"publisher":"Nature Publishing Group","external_id":{"isi":["000445560800010"]},"month":"09","_id":"77","abstract":[{"text":"Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices.","lang":"eng"}],"date_created":"2018-12-11T11:44:30Z","year":"2018","language":[{"iso":"eng"}],"status":"public","date_published":"2018-09-25T00:00:00Z","scopus_import":"1","department":[{"_id":"GeKa"}],"isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"issue":"3902 ","ec_funded":1,"fulldoi":"https://doi.org/10.1038/s41467-018-06418-4"},{"date_updated":"2021-01-12T08:15:02Z","oa_version":"Published Version","publication":"Nature Communications","volume":9,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Yap, Chloe X.","last_name":"Yap","first_name":"Chloe X."},{"full_name":"Sidorenko, Julia","last_name":"Sidorenko","first_name":"Julia"},{"full_name":"Wu, Yang","first_name":"Yang","last_name":"Wu"},{"full_name":"Kemper, Kathryn E.","last_name":"Kemper","first_name":"Kathryn E."},{"first_name":"Jian","last_name":"Yang","full_name":"Yang, Jian"},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813"},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"}],"title":"Dissection of genetic variation and evidence for pleiotropy in male pattern baldness","article_processing_charge":"No","citation":{"ieee":"C. X. Yap <i>et al.</i>, “Dissection of genetic variation and evidence for pleiotropy in male pattern baldness,” <i>Nature Communications</i>, vol. 9. Springer Nature, 2018.","short":"C.X. Yap, J. Sidorenko, Y. Wu, K.E. Kemper, J. Yang, N.R. Wray, M.R. Robinson, P.M. Visscher, Nature Communications 9 (2018).","chicago":"Yap, Chloe X., Julia Sidorenko, Yang Wu, Kathryn E. Kemper, Jian Yang, Naomi R. Wray, Matthew Richard Robinson, and Peter M. Visscher. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-07862-y\">https://doi.org/10.1038/s41467-018-07862-y</a>.","mla":"Yap, Chloe X., et al. “Dissection of Genetic Variation and Evidence for Pleiotropy in Male Pattern Baldness.” <i>Nature Communications</i>, vol. 9, 5407, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-07862-y\">10.1038/s41467-018-07862-y</a>.","ista":"Yap CX, Sidorenko J, Wu Y, Kemper KE, Yang J, Wray NR, Robinson MR, Visscher PM. 2018. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. Nature Communications. 9, 5407.","apa":"Yap, C. X., Sidorenko, J., Wu, Y., Kemper, K. E., Yang, J., Wray, N. R., … Visscher, P. M. (2018). Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-07862-y\">https://doi.org/10.1038/s41467-018-07862-y</a>","ama":"Yap CX, Sidorenko J, Wu Y, et al. Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. <i>Nature Communications</i>. 2018;9. doi:<a href=\"https://doi.org/10.1038/s41467-018-07862-y\">10.1038/s41467-018-07862-y</a>"},"article_type":"original","extern":"1","day":"20","quality_controlled":"1","oa":1,"intvolume":"         9","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-018-07862-y"}],"doi":"10.1038/s41467-018-07862-y","_id":"7712","month":"12","publisher":"Springer Nature","publication_status":"published","year":"2018","date_created":"2020-04-30T10:41:19Z","abstract":[{"text":"Male pattern baldness (MPB) is a sex-limited, age-related, complex trait. We study MPB genetics in 205,327 European males from the UK Biobank. Here we show that MPB is strongly heritable and polygenic, with pedigree-heritability of 0.62 (SE = 0.03) estimated from close relatives, and SNP-heritability of 0.39 (SE = 0.01) from conventionally-unrelated males. We detect 624 near-independent genome-wide loci, contributing SNP-heritability of 0.25 (SE = 0.01), of which 26 X-chromosome loci explain 11.6%. Autosomal genetic variance is enriched for common variants and regions of lower linkage disequilibrium. We identify plausible genetic correlations between MPB and multiple sex-limited markers of earlier puberty, increased bone mineral density (rg = 0.15) and pancreatic β-cell function (rg = 0.12). Correlations with reproductive traits imply an effect on fitness, consistent with an estimated linear selection gradient of -0.018 per MPB standard deviation. Overall, we provide genetic insights into MPB: a phenotype of interest in its own right, with value as a model sex-limited, complex trait.","lang":"eng"}],"publication_identifier":{"issn":["2041-1723"]},"article_number":"5407","date_published":"2018-12-20T00:00:00Z","status":"public","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41467-018-07862-y"}]