[{"date_created":"2018-12-11T11:49:32Z","date_published":"2015-01-01T00:00:00Z","issue":"4","doi":"10.1103/PhysRevX.5.041047","volume":5,"publication":"Physical Review X","day":"01","year":"2015","publication_status":"published","intvolume":" 5","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1507.01635","open_access":"1"}],"oa":1,"quality_controlled":0,"publisher":"American Physical Society","acknowledgement":"We acknowledge helpful discussions with Sid Parameswaran, Andrew Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor library. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. This research was supported by Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation, NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester.","abstract":[{"lang":"eng","text":"We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions."}],"title":"Criterion for many-body localization-delocalization phase transition","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"},{"first_name":"Dmitry","last_name":"Abanin","full_name":"Abanin, Dmitry A"}],"publist_id":"6418","extern":1,"citation":{"mla":"Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical Society, 2015, doi:10.1103/PhysRevX.5.041047.","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” Physical Review X, vol. 5, no. 4. American Physical Society, 2015.","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).","apa":"Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047","ama":"Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X. American Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047.","ista":"Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4)."},"date_updated":"2021-01-12T08:22:25Z","status":"public","type":"journal_article","_id":"982"},{"citation":{"mla":"Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 1017–21, doi:10.1038/nphys3461.","short":"A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P. Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11 (2015) 1017–1021.","ieee":"A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing Group, pp. 1017–1021, 2015.","apa":"Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth, F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461","ama":"Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021. doi:10.1038/nphys3461","chicago":"Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg, and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461.","ista":"Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1501.05155"]},"publist_id":"7955","author":[{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham"},{"first_name":"S M","full_name":"Albrecht, S M","last_name":"Albrecht"},{"first_name":"Gediminas","full_name":"Kiršanskas, Gediminas","last_name":"Kiršanskas"},{"first_name":"W","full_name":"Chang, W","last_name":"Chang"},{"last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand"},{"first_name":"Peter","full_name":"Krogstrup, Peter","last_name":"Krogstrup"},{"first_name":"Thomas","last_name":"Jespersen","full_name":"Jespersen, Thomas"},{"last_name":"Nygård","full_name":"Nygård, Jesper","first_name":"Jesper"},{"first_name":"Karsten","full_name":"Flensberg, Karsten","last_name":"Flensberg"},{"first_name":"Charles","full_name":"Marcus, Charles","last_name":"Marcus"}],"title":"Parity lifetime of bound states in a proximitized semiconductor nanowire","year":"2015","publication":"Nature Physics","day":"14","page":"1017 - 1021","date_created":"2018-12-11T11:44:37Z","doi":"10.1038/nphys3461","date_published":"2015-09-14T00:00:00Z","acknowledgement":"Research support by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M. acknowledges support from the Villum Foundation.","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","date_updated":"2021-01-12T08:22:28Z","extern":"1","_id":"99","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":11,"issue":"12","abstract":[{"lang":"eng","text":"Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1501.05155","open_access":"1"}],"intvolume":" 11","month":"09"},{"page":"1553-1560","date_created":"2020-09-18T10:46:14Z","date_published":"2015-12-21T00:00:00Z","volume":144,"doi":"10.1090/proc/12796","issue":"4","publication_status":"published","year":"2015","publication_identifier":{"issn":["0002-9939","1088-6826"]},"language":[{"iso":"eng"}],"publication":"Proceedings of the American Mathematical Society","day":"21","quality_controlled":"1","publisher":"American Mathematical Society","intvolume":" 144","month":"12","abstract":[{"lang":"eng","text":"In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \\sqrt {\\varepsilon }$, after a time of order $ \\sqrt {\\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting."}],"oa_version":"None","article_processing_charge":"No","author":[{"first_name":"Abed","last_name":"Bounemoura","full_name":"Bounemoura, Abed"},{"last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim"}],"title":"A note on micro-instability for Hamiltonian systems close to integrable","date_updated":"2021-01-12T08:19:40Z","citation":{"ista":"Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560.","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796.","ieee":"A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.","short":"A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560.","apa":"Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12796","ama":"Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 2015;144(4):1553-1560. doi:10.1090/proc/12796","mla":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_type":"letter_note","type":"journal_article","status":"public","_id":"8495"},{"type":"journal_article","status":"public","_id":"866","publist_id":"6783","author":[{"first_name":"Colin","full_name":"Kretz, Colin A","last_name":"Kretz"},{"last_name":"Dai","full_name":"Dai, Manhong","first_name":"Manhong"},{"last_name":"Soylemez","full_name":"Soylemez, Onuralp","first_name":"Onuralp"},{"first_name":"Andrew","last_name":"Yee","full_name":"Yee, Andrew"},{"first_name":"Karl","last_name":"Desch","full_name":"Desch, Karl C"},{"last_name":"Siemieniak","full_name":"Siemieniak, David R","first_name":"David"},{"full_name":"Tomberg, Kärt","last_name":"Tomberg","first_name":"Kärt"},{"last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Fan","last_name":"Meng","full_name":"Meng, Fan"},{"last_name":"Ginsburg","full_name":"Ginsburg, David B","first_name":"David"}],"title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","citation":{"short":"C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.","ieee":"C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015.","apa":"Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511328112","ama":"Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 2015;112(30):9328-9333. doi:10.1073/pnas.1511328112","mla":"Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.","ista":"Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.","chicago":"Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112."},"date_updated":"2021-01-12T08:20:26Z","extern":1,"publisher":"National Academy of Sciences","quality_controlled":0,"intvolume":" 112","month":"07","abstract":[{"lang":"eng","text":"Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF."}],"acknowledgement":"We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.\n","page":"9328 - 9333","date_created":"2018-12-11T11:48:55Z","issue":"30","date_published":"2015-07-28T00:00:00Z","volume":112,"doi":"10.1073/pnas.1511328112","publication_status":"published","year":"2015","publication":"PNAS","day":"28"},{"type":"journal_article","status":"public","_id":"886","author":[{"full_name":"Kondrashov, Dmitry A","last_name":"Kondrashov","first_name":"Dmitry"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov"}],"publist_id":"6764","title":"Topological features of rugged fitness landscapes in sequence space","date_updated":"2021-01-12T08:21:16Z","citation":{"ista":"Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33.","chicago":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015. https://doi.org/10.1016/j.tig.2014.09.009.","ieee":"D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33, 2015.","short":"D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.","apa":"Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009","ama":"Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009","mla":"Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009."},"extern":1,"publisher":"Elsevier","quality_controlled":0,"intvolume":" 31","month":"01","abstract":[{"text":"The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.","lang":"eng"}],"acknowledgement":"This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.","page":"24 - 33","date_created":"2018-12-11T11:49:01Z","doi":"10.1016/j.tig.2014.09.009","volume":31,"date_published":"2015-01-01T00:00:00Z","issue":"1","publication_status":"published","year":"2015","publication":"Trends in Genetics","day":"01"},{"_id":"9017","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-02-23T13:46:50Z","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway."}],"month":"02","intvolume":" 43","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1362-4962","0305-1048"]},"publication_status":"published","volume":43,"issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research, vol. 43, no. 3, Oxford University Press, 2015, pp. 1905–17, doi:10.1093/nar/gkv021.","ieee":"N. Richet et al., “Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork,” Nucleic Acids Research, vol. 43, no. 3. Oxford University Press, pp. 1905–1917, 2015.","short":"N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail, G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F. Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.","apa":"Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein, F. (2015). Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv021","ama":"Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 2015;43(3):1905-1917. doi:10.1093/nar/gkv021","chicago":"Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv021.","ista":"Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 43(3), 1905–1917."},"title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","author":[{"last_name":"Richet","full_name":"Richet, Nicolas","first_name":"Nicolas"},{"last_name":"Liu","full_name":"Liu, Danni","first_name":"Danni"},{"first_name":"Pierre","full_name":"Legrand, Pierre","last_name":"Legrand"},{"first_name":"Christophe","last_name":"Velours","full_name":"Velours, Christophe"},{"full_name":"Corpet, Armelle","last_name":"Corpet","first_name":"Armelle"},{"first_name":"Albane","full_name":"Gaubert, Albane","last_name":"Gaubert"},{"first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","last_name":"Bakail"},{"last_name":"Moal-Raisin","full_name":"Moal-Raisin, Gwenaelle","first_name":"Gwenaelle"},{"last_name":"Guerois","full_name":"Guerois, Raphael","first_name":"Raphael"},{"first_name":"Christel","last_name":"Compper","full_name":"Compper, Christel"},{"first_name":"Arthur","last_name":"Besle","full_name":"Besle, Arthur"},{"full_name":"Guichard, Berengère","last_name":"Guichard","first_name":"Berengère"},{"full_name":"Almouzni, Genevieve","last_name":"Almouzni","first_name":"Genevieve"},{"first_name":"Françoise","full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein"}],"external_id":{"pmid":["25618846"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Oxford University Press","day":"18","publication":"Nucleic Acids Research","year":"2015","date_published":"2015-02-18T00:00:00Z","doi":"10.1093/nar/gkv021","date_created":"2021-01-19T11:01:01Z","page":"1905-1917"},{"title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop","publist_id":"6514","author":[{"first_name":"Riadh","last_name":"Boubaker","full_name":"Boubaker, Riadh"},{"first_name":"Vincent","full_name":"Platel, Vincent","last_name":"Platel"},{"full_name":"Bergès, Alexis","last_name":"Bergès","first_name":"Alexis"},{"last_name":"Bancelin","full_name":"Bancelin, Mathieu","first_name":"Mathieu"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:21:56Z","citation":{"short":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8.","ieee":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015.","ama":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009","apa":"Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015). Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009","mla":"Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol. 76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009.","ista":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 76, 1–8.","chicago":"Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015. https://doi.org/10.1016/j.applthermaleng.2014.10.009."},"status":"public","type":"journal_article","_id":"924","date_published":"2015-02-05T00:00:00Z","volume":76,"doi":"10.1016/j.applthermaleng.2014.10.009","date_created":"2018-12-11T11:49:13Z","page":"1 - 8","day":"05","publication":"Applied Thermal Engineering","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","month":"02","intvolume":" 76","publisher":"Elsevier","oa_version":"None","acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099).","abstract":[{"text":"This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper.","lang":"eng"}]},{"publication_status":"published","year":"2015","day":"14","language":[{"iso":"eng"}],"publication":"PNAS","page":"8620 - 8625","volume":112,"doi":"10.1073/pnas.1504762112","date_published":"2015-07-14T00:00:00Z","issue":"28","date_created":"2018-12-11T11:49:15Z","abstract":[{"text":"An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. ","lang":"eng"}],"oa_version":"None","acknowledgement":"We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro, Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto), and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions and discussion. This work was supported by the Taishan Scholar Program of Shandong and the Fundamental Research Funds for the Central Universities in China (3005000-841412019) (to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.","publisher":"National Academy of Sciences","month":"07","intvolume":" 112","date_updated":"2021-01-12T08:21:59Z","citation":{"ista":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 112(28), 8620–8625.","chicago":"Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112.","apa":"Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112","ama":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 2015;112(28):8620-8625. doi:10.1073/pnas.1504762112","ieee":"E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015.","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","mla":"Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6513","author":[{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Bo","last_name":"Dong","full_name":"Dong, Bo"},{"first_name":"Pierre","full_name":"Recho, Pierre","last_name":"Recho"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"},{"last_name":"Hayashi","full_name":"Hayashi, Shigeo","first_name":"Shigeo"}],"article_processing_charge":"No","title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","_id":"929","type":"journal_article","status":"public"},{"year":"2015","publication":"PNAS","day":"15","page":"15314 - 15319","date_created":"2018-12-11T11:49:16Z","doi":"10.1073/pnas.1510973112","date_published":"2015-12-15T00:00:00Z","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","citation":{"mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:10.1073/pnas.1510973112.","apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112","ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319. doi:10.1073/pnas.1510973112","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","ieee":"S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015.","chicago":"García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112.","ista":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["26627719"]},"author":[{"last_name":"García","full_name":"García, Simón","first_name":"Simón"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Elgeti, Jens","last_name":"Elgeti","first_name":"Jens"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"},{"last_name":"Silberzan","full_name":"Silberzan, Pascal","first_name":"Pascal"},{"first_name":"Nir","last_name":"Gov","full_name":"Gov, Nir"}],"publist_id":"6511","title":"Physics of active jamming during collective cellular motion in a monolayer","publication_status":"published","language":[{"iso":"eng"}],"issue":"50","volume":112,"abstract":[{"lang":"eng","text":"Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data."}],"oa_version":"None","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf"}],"intvolume":" 112","month":"12","date_updated":"2021-01-12T08:22:01Z","extern":"1","_id":"933","type":"journal_article","status":"public"},{"citation":{"ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115","apa":"Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.269902.115","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"pmid":["26680300"]},"author":[{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"title":"Evolution and function of genomic imprinting in plants","oa":1,"publisher":"Cold Spring Harbor Laboratory Press","quality_controlled":"1","year":"2015","has_accepted_license":"1","publication":"Genes and Development","day":"15","page":"2517–2531","date_created":"2021-06-08T09:56:24Z","doi":"10.1101/gad.269902.115","date_published":"2015-12-15T00:00:00Z","_id":"9532","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","article_type":"review","status":"public","date_updated":"2021-12-14T07:58:15Z","ddc":["570"],"extern":"1","department":[{"_id":"DaZi"}],"file_date_updated":"2021-06-08T09:55:10Z","abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 29","month":"12","publication_status":"published","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"9533","checksum":"086a88cfca4677646da26ed960cb02e9","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","date_created":"2021-06-08T09:55:10Z","file_size":1116846,"date_updated":"2021-06-08T09:55:10Z","creator":"asandaue"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"24","volume":29},{"language":[{"iso":"eng"}],"publication":"Modelling and Simulation in Materials Science and Engineering","day":"01","year":"2015","publication_status":"published","publication_identifier":{"issn":["0965-0393"],"eissn":["1361-651X"]},"date_created":"2021-07-19T09:11:12Z","issue":"3","volume":23,"date_published":"2015-04-01T00:00:00Z","doi":"10.1088/0965-0393/23/3/035001","oa_version":"None","abstract":[{"lang":"eng","text":"The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept."}],"intvolume":" 23","month":"04","quality_controlled":"1","scopus_import":"1","publisher":"IOP Publishing","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","extern":"1","citation":{"mla":"Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001.","ama":"Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001","apa":"Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001","short":"P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015).","ieee":"P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3. IOP Publishing, 2015.","chicago":"Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering. IOP Publishing, 2015. https://doi.org/10.1088/0965-0393/23/3/035001.","ista":"Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001."},"date_updated":"2023-02-23T14:04:54Z","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","article_processing_charge":"No","author":[{"full_name":"Leung, P S S","last_name":"Leung","first_name":"P S S"},{"last_name":"Leung","full_name":"Leung, H S","first_name":"H S"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"A H W","full_name":"Ngan, A H W","last_name":"Ngan"}],"article_number":"035001","_id":"9684","status":"public","article_type":"original","type":"journal_article"},{"title":"An exploration of the universe of polyglutamine structures","publist_id":"5605","author":[{"last_name":"Gómez Sicilia","full_name":"Gómez Sicilia, Àngel","first_name":"Àngel"},{"first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K","last_name":"Sikora"},{"first_name":"Marek","last_name":"Cieplak","full_name":"Cieplak, Marek"},{"first_name":"Mariano","full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10). doi:10.1371/journal.pcbi.1004541","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures,” PLoS Computational Biology, vol. 11, no. 10. Public Library of Science, 2015.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015).","mla":"Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 11(10), e1004541.","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541."},"article_number":"e1004541","date_created":"2018-12-11T11:52:45Z","doi":"10.1371/journal.pcbi.1004541","date_published":"2015-10-23T00:00:00Z","publication":"PLoS Computational Biology","day":"23","year":"2015","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","acknowledgement":"We acknowledge the support by the EU Joint Programme in Neurodegenerative Diseases (JPND AC14/00037) project. The project is supported through the following funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland, National Science Centre; and Spain, ISCIII. ","file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"CaHe"}],"ddc":["570"],"date_updated":"2023-02-23T14:05:55Z","pubrep_id":"478","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1566","license":"https://creativecommons.org/licenses/by/4.0/","related_material":{"record":[{"relation":"research_data","status":"public","id":"9714"}]},"volume":11,"issue":"10","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5207","checksum":"8b67d729be663bfc9af04bfd94459655","date_updated":"2020-07-14T12:45:02Z","file_size":1412511,"creator":"system","date_created":"2018-12-12T10:16:21Z","file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf"}],"publication_status":"published","intvolume":" 11","month":"10","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease."}]},{"_id":"9712","type":"research_data_reference","status":"public","date_updated":"2023-02-23T10:09:08Z","citation":{"ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","mla":"Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","last_name":"Tugrul"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Other fitness models for comparison & for interacting TFBSs","oa_version":"Published Version","publisher":"Public Library of Science","month":"11","year":"2015","day":"06","date_created":"2021-07-23T12:00:37Z","doi":"10.1371/journal.pgen.1005639.s001","date_published":"2015-11-06T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"1666","status":"public"}]}},{"status":"public","type":"research_data_reference","_id":"9714","department":[{"_id":"CaHe"}],"title":"An exploration of the universe of polyglutamine structures - submission to PLOS journals","article_processing_charge":"No","author":[{"first_name":"Àngel","full_name":"Gómez Sicilia, Àngel","last_name":"Gómez Sicilia"},{"first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K","last_name":"Sikora"},{"full_name":"Cieplak, Marek","last_name":"Cieplak","first_name":"Marek"},{"full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez","first_name":"Mariano"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:04:35Z","citation":{"ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures - submission to PLOS journals, Public Library of Science , 10.1371/journal.pcbi.1004541.s001.","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals.” Public Library of Science , 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures - submission to PLOS journals. Public Library of Science . https://doi.org/10.1371/journal.pcbi.1004541.s001","ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures - submission to PLOS journals. 2015. doi:10.1371/journal.pcbi.1004541.s001","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures - submission to PLOS journals.” Public Library of Science , 2015.","mla":"Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals. Public Library of Science , 2015, doi:10.1371/journal.pcbi.1004541.s001."},"month":"10","publisher":"Public Library of Science ","oa_version":"Published Version","date_created":"2021-07-23T12:05:28Z","doi":"10.1371/journal.pcbi.1004541.s001","related_material":{"record":[{"relation":"used_in_publication","id":"1566","status":"public"}]},"date_published":"2015-10-23T00:00:00Z","day":"23","year":"2015"},{"month":"05","publisher":"Public Library of Science","oa_version":"Published Version","date_created":"2021-07-23T12:11:30Z","date_published":"2015-05-18T00:00:00Z","related_material":{"record":[{"status":"public","id":"1809","relation":"used_in_publication"}]},"doi":"10.1371/journal.pone.0126907.s001","day":"18","year":"2015","status":"public","type":"research_data_reference","_id":"9715","department":[{"_id":"NiBa"}],"title":"Mathematical inference of the results","article_processing_charge":"No","author":[{"orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak"},{"last_name":"Hager","full_name":"Hager, Reinmar","first_name":"Reinmar"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"B. Trubenova, S. Novak, R. Hager, (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:10.1371/journal.pone.0126907.s001","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001","mla":"Trubenova, Barbora, et al. Mathematical Inference of the Results. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001.","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, 10.1371/journal.pone.0126907.s001.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001."},"date_updated":"2023-02-23T10:15:25Z"},{"_id":"1993","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-02-23T14:06:41Z","department":[{"_id":"SyCr"}],"pmid":1,"oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. "}],"month":"01","intvolume":" 282","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"publication_status":"published","volume":282,"related_material":{"record":[{"relation":"research_data","id":"9740","status":"public"}]},"issue":"1799","ec_funded":1,"article_number":"20141976","project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2014.1976","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1799. The Royal Society, 2015.","mla":"Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:10.1098/rspb.2014.1976.","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1799), 20141976.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976."},"title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","publist_id":"5090","author":[{"last_name":"Konrad","full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V","last_name":"Grasse"},{"last_name":"Tragust","full_name":"Tragust, Simon","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"article_processing_charge":"No","external_id":{"pmid":["25473011"]},"acknowledgement":"Funding was obtained by the German Research Foundation (CR 118–2) and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank Line V. Ugelvig for help with ant collection and statistical discussion, Xavier Espadaler for detailed information on the ant collection site, Birgit Lautenschläger for the electron microscopy images and Eva Sixt for ant drawings. We further thank Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization and immune gene primer development, Paul Schmid-Hempel for discussion, and Line V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript. S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments; M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with intense contributions of A.V.G. and S.T.; all authors approved the manuscript.","publisher":"The Royal Society","quality_controlled":"1","oa":1,"day":"22","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","year":"2015","date_published":"2015-01-22T00:00:00Z","doi":"10.1098/rspb.2014.1976","date_created":"2018-12-11T11:55:06Z"},{"day":"09","year":"2015","date_published":"2015-07-09T00:00:00Z","doi":"10.5061/dryad.7kc79","related_material":{"record":[{"id":"2161","status":"public","relation":"used_in_publication"}]},"date_created":"2021-07-28T08:52:53Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects."}],"month":"07","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7kc79"}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant, Dryad, 10.5061/dryad.7kc79.","chicago":"Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. https://doi.org/10.5061/dryad.7kc79.","ieee":"C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant.” Dryad, 2015.","short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).","ama":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. 2015. doi:10.5061/dryad.7kc79","apa":"Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer, S. (2015). Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Dryad. https://doi.org/10.5061/dryad.7kc79","mla":"Westhus, Claudia, et al. Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant. Dryad, 2015, doi:10.5061/dryad.7kc79."},"date_updated":"2023-02-23T10:30:52Z","title":"Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","department":[{"_id":"SyCr"}],"author":[{"first_name":"Claudia","last_name":"Westhus","full_name":"Westhus, Claudia"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","last_name":"Ugelvig"},{"first_name":"Edouard","last_name":"Tourdot","full_name":"Tourdot, Edouard"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"first_name":"Claudie","last_name":"Doums","full_name":"Doums, Claudie"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"article_processing_charge":"No","_id":"9742","status":"public","type":"research_data_reference"},{"oa_version":"Published Version","publisher":"Public Library of Science","month":"11","year":"2015","day":"18","date_published":"2015-11-18T00:00:00Z","doi":"10.1371/journal.pbio.1002299.s008","related_material":{"record":[{"id":"1619","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-03T07:05:16Z","_id":"9765","type":"research_data_reference","status":"public","citation":{"chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s008.","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs, Public Library of Science, 10.1371/journal.pbio.1002299.s008.","mla":"Chevereau, Guillaume, et al. Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s008.","ieee":"G. Chevereau et al., “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s008","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. 2015. doi:10.1371/journal.pbio.1002299.s008"},"date_updated":"2023-02-23T10:07:02Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume","full_name":"Chevereau, Guillaume","last_name":"Chevereau"},{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004"},{"full_name":"Batur, Tugce","last_name":"Batur","first_name":"Tugce"},{"first_name":"Aysegul","full_name":"Guvenek, Aysegul","last_name":"Guvenek"},{"first_name":"Dilay Hazal","full_name":"Ayhan, Dilay Hazal","last_name":"Ayhan"},{"last_name":"Toprak","full_name":"Toprak, Erdal","first_name":"Erdal"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"article_processing_charge":"No","title":"Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs","department":[{"_id":"ToBo"}]},{"_id":"12630","keyword":["Water Science and Technology"],"status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-02-24T09:28:04Z","oa_version":"None","abstract":[{"lang":"eng","text":"The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region (HKH) is poorly known. The correct representation of internal states and process dynamics in glacio-hydrological models can often not be verified due to missing in situ measurements. We use a new set of detailed ground data from the upper Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological model through a parameter assigning process with the aim to understand the hydrology of the catchment and contribution of snow and ice processes to runoff. 14 parameters are directly calculated on the basis of local data, and 13 parameters are calibrated against 5 different datasets of in situ or remote sensing data. Spatial fields of debris thickness are reconstructed through a novel approach that employs data from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The advanced representation of processes allowed assessing the role played by avalanching for runoff for the first time for a Himalayan catchment (5% of annual water inputs to the hydrological system are due to snow redistribution) and to quantify the hydrological significance of sub-debris ice melt (9% of annual water inputs). Snowmelt is the most important contributor to total runoff during the hydrological year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and ice melt (26%). A sensitivity analysis is used to assess the efficiency of the monitoring network and identify the timing and location of field measurements that constrain model uncertainty. The methodology to set up a glacio-hydrological model in high-elevation regions presented in this study can be regarded as a benchmark for modelers in the HKH seeking to evaluate their calibration approach, their experimental setup and thus to reduce the predictive model uncertainty.\r\n\r\n"}],"intvolume":" 78","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0309-1708"]},"issue":"4","volume":78,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ragettli, S., Francesca Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, and A. Shrestha. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources. Elsevier, 2015. https://doi.org/10.1016/j.advwatres.2015.01.013.","ista":"Ragettli S, Pellicciotti F, Immerzeel WW, Miles ES, Petersen L, Heynen M, Shea JM, Stumm D, Joshi S, Shrestha A. 2015. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 78(4), 94–111.","mla":"Ragettli, S., et al. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources, vol. 78, no. 4, Elsevier, 2015, pp. 94–111, doi:10.1016/j.advwatres.2015.01.013.","apa":"Ragettli, S., Pellicciotti, F., Immerzeel, W. W., Miles, E. S., Petersen, L., Heynen, M., … Shrestha, A. (2015). Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. Elsevier. https://doi.org/10.1016/j.advwatres.2015.01.013","ama":"Ragettli S, Pellicciotti F, Immerzeel WW, et al. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 2015;78(4):94-111. doi:10.1016/j.advwatres.2015.01.013","short":"S. Ragettli, F. Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, A. Shrestha, Advances in Water Resources 78 (2015) 94–111.","ieee":"S. Ragettli et al., “Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model,” Advances in Water Resources, vol. 78, no. 4. Elsevier, pp. 94–111, 2015."},"title":"Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model","article_processing_charge":"No","author":[{"first_name":"S.","last_name":"Ragettli","full_name":"Ragettli, S."},{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"first_name":"W.W.","full_name":"Immerzeel, W.W.","last_name":"Immerzeel"},{"first_name":"E.S.","last_name":"Miles","full_name":"Miles, E.S."},{"first_name":"L.","full_name":"Petersen, L.","last_name":"Petersen"},{"last_name":"Heynen","full_name":"Heynen, M.","first_name":"M."},{"last_name":"Shea","full_name":"Shea, J.M.","first_name":"J.M."},{"first_name":"D.","full_name":"Stumm, D.","last_name":"Stumm"},{"first_name":"S.","full_name":"Joshi, S.","last_name":"Joshi"},{"last_name":"Shrestha","full_name":"Shrestha, A.","first_name":"A."}],"quality_controlled":"1","publisher":"Elsevier","publication":"Advances in Water Resources","day":"01","year":"2015","date_created":"2023-02-20T08:16:21Z","doi":"10.1016/j.advwatres.2015.01.013","date_published":"2015-04-01T00:00:00Z","page":"94-111"},{"issue":"226","volume":61,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"intvolume":" 61","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3189/2015JoG13J237"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Thick debris cover on glaciers can significantly reduce ice melt. However, several studies have suggested that debris-covered glaciers in the Himalaya might have lost mass at a rate similar to debris-free glaciers. We reconstruct elevation and mass changes for the debris-covered glaciers of the upper Langtang valley, Nepalese Himalaya, using a digital elevation model (DEM) from 1974 stereo Hexagon satellite data and the 2000 SRTM (Shuttle Radar Topography Mission) DEM. Uncertainties are high in the accumulation areas, due to data gaps in the SRTM and difficulties with delineation of the glacier borders. Even with these uncertainties, we obtain thinning rates comparable to those of several other studies in the Himalaya. In particular, we obtain a total mass balance for the investigated debris-covered glaciers of the basin of –0.32 ± 0.18 m w.e. a−1. However, there are major spatial differences both between glaciers and within any single glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation. Through analysis of surface velocities derived from Landsat ETM+ imagery, we show that thinning occurs in areas of low velocity and low slope. These areas are prone to a general, dynamic decay of surface features and to the development of supraglacial lakes and ice cliffs, which may be responsible for a considerable increase in overall glacier ablation."}],"extern":"1","date_updated":"2023-02-24T09:35:21Z","keyword":["Earth-Surface Processes"],"status":"public","type":"journal_article","article_type":"original","_id":"12628","date_created":"2023-02-20T08:16:11Z","doi":"10.3189/2015jog13j237","date_published":"2015-03-01T00:00:00Z","page":"373-386","publication":"Journal of Glaciology","day":"01","year":"2015","oa":1,"publisher":"International Glaciological Society","quality_controlled":"1","title":"Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999","article_processing_charge":"No","author":[{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"},{"first_name":"Christa","last_name":"Stephan","full_name":"Stephan, Christa"},{"first_name":"Evan","last_name":"Miles","full_name":"Miles, Evan"},{"last_name":"Herreid","full_name":"Herreid, Sam","first_name":"Sam"},{"first_name":"Walter W.","full_name":"Immerzeel, Walter W.","last_name":"Immerzeel"},{"first_name":"Tobias","last_name":"Bolch","full_name":"Bolch, Tobias"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W.W. Immerzeel, T. Bolch, Journal of Glaciology 61 (2015) 373–386.","ieee":"F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W. W. Immerzeel, and T. Bolch, “Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999,” Journal of Glaciology, vol. 61, no. 226. International Glaciological Society, pp. 373–386, 2015.","apa":"Pellicciotti, F., Stephan, C., Miles, E., Herreid, S., Immerzeel, W. W., & Bolch, T. (2015). Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog13j237","ama":"Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 2015;61(226):373-386. doi:10.3189/2015jog13j237","mla":"Pellicciotti, Francesca, et al. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology, vol. 61, no. 226, International Glaciological Society, 2015, pp. 373–86, doi:10.3189/2015jog13j237.","ista":"Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. 2015. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 61(226), 373–386.","chicago":"Pellicciotti, Francesca, Christa Stephan, Evan Miles, Sam Herreid, Walter W. Immerzeel, and Tobias Bolch. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog13j237."}}]