[{"year":"2015","day":"18","publication":"Nucleic Acids Research","page":"1905-1917","doi":"10.1093/nar/gkv021","date_published":"2015-02-18T00:00:00Z","date_created":"2021-01-19T11:01:01Z","publisher":"Oxford University Press","quality_controlled":"1","citation":{"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.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Richet, Nicolas","last_name":"Richet","first_name":"Nicolas"},{"first_name":"Danni","last_name":"Liu","full_name":"Liu, Danni"},{"full_name":"Legrand, Pierre","last_name":"Legrand","first_name":"Pierre"},{"full_name":"Velours, Christophe","last_name":"Velours","first_name":"Christophe"},{"full_name":"Corpet, Armelle","last_name":"Corpet","first_name":"Armelle"},{"full_name":"Gaubert, Albane","last_name":"Gaubert","first_name":"Albane"},{"last_name":"Bakail","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E"},{"first_name":"Gwenaelle","last_name":"Moal-Raisin","full_name":"Moal-Raisin, Gwenaelle"},{"first_name":"Raphael","full_name":"Guerois, Raphael","last_name":"Guerois"},{"last_name":"Compper","full_name":"Compper, Christel","first_name":"Christel"},{"first_name":"Arthur","full_name":"Besle, Arthur","last_name":"Besle"},{"last_name":"Guichard","full_name":"Guichard, Berengère","first_name":"Berengère"},{"full_name":"Almouzni, Genevieve","last_name":"Almouzni","first_name":"Genevieve"},{"last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise","first_name":"Françoise"}],"article_processing_charge":"No","external_id":{"pmid":["25618846"]},"title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","publication_identifier":{"issn":["1362-4962","0305-1048"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":43,"issue":"3","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","month":"02","intvolume":" 43","date_updated":"2023-02-23T13:46:50Z","extern":"1","_id":"9017","article_type":"original","type":"journal_article","status":"public"},{"date_updated":"2021-01-12T08:21:56Z","citation":{"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.","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.","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","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","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.","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."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Riadh","last_name":"Boubaker","full_name":"Boubaker, Riadh"},{"first_name":"Vincent","last_name":"Platel","full_name":"Platel, Vincent"},{"first_name":"Alexis","full_name":"Bergès, Alexis","last_name":"Bergès"},{"first_name":"Mathieu","last_name":"Bancelin","full_name":"Bancelin, Mathieu"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"publist_id":"6514","article_processing_charge":"No","title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop","_id":"924","type":"journal_article","status":"public","year":"2015","publication_status":"published","day":"05","publication":"Applied Thermal Engineering","language":[{"iso":"eng"}],"page":"1 - 8","date_published":"2015-02-05T00:00:00Z","doi":"10.1016/j.applthermaleng.2014.10.009","volume":76,"date_created":"2018-12-11T11:49:13Z","abstract":[{"lang":"eng","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."}],"oa_version":"None","acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099).","publisher":"Elsevier","month":"02","intvolume":" 76"},{"publication":"PNAS","language":[{"iso":"eng"}],"day":"14","year":"2015","publication_status":"published","date_created":"2018-12-11T11:49:15Z","doi":"10.1073/pnas.1504762112","date_published":"2015-07-14T00:00:00Z","volume":112,"issue":"28","page":"8620 - 8625","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.","oa_version":"None","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"}],"intvolume":" 112","month":"07","publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","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","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","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.","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."},"date_updated":"2021-01-12T08:21:59Z","title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","article_processing_charge":"No","author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Bo","full_name":"Dong, Bo","last_name":"Dong"},{"full_name":"Recho, Pierre","last_name":"Recho","first_name":"Pierre"},{"last_name":"Joanny","full_name":"Joanny, Jean","first_name":"Jean"},{"first_name":"Shigeo","last_name":"Hayashi","full_name":"Hayashi, Shigeo"}],"publist_id":"6513","_id":"929","status":"public","type":"journal_article"},{"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","year":"2015","publication":"PNAS","day":"15","page":"15314 - 15319","date_created":"2018-12-11T11:49:16Z","date_published":"2015-12-15T00:00:00Z","doi":"10.1073/pnas.1510973112","citation":{"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.","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.","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.","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["26627719"]},"publist_id":"6511","author":[{"first_name":"Simón","last_name":"García","full_name":"García, Simón"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"},{"last_name":"Silberzan","full_name":"Silberzan, Pascal","first_name":"Pascal"},{"first_name":"Nir","full_name":"Gov, Nir","last_name":"Gov"}],"title":"Physics of active jamming during collective cellular motion in a monolayer","abstract":[{"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.","lang":"eng"}],"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","publication_status":"published","language":[{"iso":"eng"}],"volume":112,"issue":"50","_id":"933","type":"journal_article","status":"public","date_updated":"2021-01-12T08:22:01Z","extern":"1"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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.","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","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","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.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","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."},"title":"Evolution and function of genomic imprinting in plants","author":[{"first_name":"Jessica A.","full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"external_id":{"pmid":["26680300"]},"article_processing_charge":"No","day":"15","publication":"Genes and Development","has_accepted_license":"1","year":"2015","date_published":"2015-12-15T00:00:00Z","doi":"10.1101/gad.269902.115","date_created":"2021-06-08T09:56:24Z","page":"2517–2531","publisher":"Cold Spring Harbor Laboratory Press","quality_controlled":"1","oa":1,"extern":"1","ddc":["570"],"date_updated":"2021-12-14T07:58:15Z","department":[{"_id":"DaZi"}],"file_date_updated":"2021-06-08T09:55:10Z","_id":"9532","status":"public","article_type":"review","type":"journal_article","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)"},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"086a88cfca4677646da26ed960cb02e9","file_id":"9533","file_size":1116846,"date_updated":"2021-06-08T09:55:10Z","creator":"asandaue","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","date_created":"2021-06-08T09:55:10Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"publication_status":"published","volume":29,"issue":"24","license":"https://creativecommons.org/licenses/by-nc/4.0/","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"12","intvolume":" 29","scopus_import":"1"},{"status":"public","article_type":"original","type":"journal_article","article_number":"035001","_id":"9684","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","author":[{"first_name":"P S S","full_name":"Leung, P S S","last_name":"Leung"},{"first_name":"H S","last_name":"Leung","full_name":"Leung, H S"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"},{"first_name":"A H W","full_name":"Ngan, A H W","last_name":"Ngan"}],"article_processing_charge":"No","extern":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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.","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","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.","short":"P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015)."},"date_updated":"2023-02-23T14:04:54Z","month":"04","intvolume":" 23","scopus_import":"1","quality_controlled":"1","publisher":"IOP Publishing","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."}],"volume":23,"issue":"3","date_published":"2015-04-01T00:00:00Z","doi":"10.1088/0965-0393/23/3/035001","date_created":"2021-07-19T09:11:12Z","day":"01","publication":"Modelling and Simulation in Materials Science and Engineering","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1361-651X"],"issn":["0965-0393"]},"year":"2015","publication_status":"published"},{"article_number":"e1004541","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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).","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","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","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."},"title":"An exploration of the universe of polyglutamine structures","author":[{"last_name":"Gómez Sicilia","full_name":"Gómez Sicilia, Àngel","first_name":"Àngel"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"last_name":"Cieplak","full_name":"Cieplak, Marek","first_name":"Marek"},{"last_name":"Carrión Vázquez","full_name":"Carrión Vázquez, Mariano","first_name":"Mariano"}],"publist_id":"5605","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. ","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"day":"23","publication":"PLoS Computational Biology","has_accepted_license":"1","year":"2015","doi":"10.1371/journal.pcbi.1004541","date_published":"2015-10-23T00:00:00Z","date_created":"2018-12-11T11:52:45Z","_id":"1566","status":"public","pubrep_id":"478","type":"journal_article","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)"},"ddc":["570"],"date_updated":"2023-02-23T14:05:55Z","department":[{"_id":"CaHe"}],"file_date_updated":"2020-07-14T12:45:02Z","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."}],"month":"10","intvolume":" 11","scopus_import":1,"file":[{"file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","date_created":"2018-12-12T10:16:21Z","file_size":1412511,"date_updated":"2020-07-14T12:45:02Z","creator":"system","file_id":"5207","checksum":"8b67d729be663bfc9af04bfd94459655","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":11,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9714"}]},"issue":"10","license":"https://creativecommons.org/licenses/by/4.0/"},{"year":"2015","day":"06","doi":"10.1371/journal.pgen.1005639.s001","related_material":{"record":[{"id":"1666","status":"public","relation":"used_in_publication"}]},"date_published":"2015-11-06T00:00:00Z","date_created":"2021-07-23T12:00:37Z","oa_version":"Published Version","publisher":"Public Library of Science","month":"11","citation":{"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.","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","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015.","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.","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."},"date_updated":"2023-02-23T10:09:08Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758"},{"last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Other fitness models for comparison & for interacting TFBSs","_id":"9712","type":"research_data_reference","status":"public"},{"_id":"9714","type":"research_data_reference","status":"public","citation":{"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.","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.","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.","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","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","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."},"date_updated":"2023-02-23T10:04:35Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Àngel","full_name":"Gómez Sicilia, Àngel","last_name":"Gómez Sicilia"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K"},{"full_name":"Cieplak, Marek","last_name":"Cieplak","first_name":"Marek"},{"full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez","first_name":"Mariano"}],"department":[{"_id":"CaHe"}],"title":"An exploration of the universe of polyglutamine structures - submission to PLOS journals","oa_version":"Published Version","publisher":"Public Library of Science ","month":"10","year":"2015","day":"23","date_created":"2021-07-23T12:05:28Z","related_material":{"record":[{"relation":"used_in_publication","id":"1566","status":"public"}]},"doi":"10.1371/journal.pcbi.1004541.s001","date_published":"2015-10-23T00:00:00Z"},{"day":"18","year":"2015","date_created":"2021-07-23T12:11:30Z","date_published":"2015-05-18T00:00:00Z","doi":"10.1371/journal.pone.0126907.s001","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1809"}]},"oa_version":"Published Version","month":"05","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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.","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","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.","mla":"Trubenova, Barbora, et al. Mathematical Inference of the Results. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001."},"date_updated":"2023-02-23T10:15:25Z","department":[{"_id":"NiBa"}],"title":"Mathematical inference of the results","article_processing_charge":"No","author":[{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova"},{"last_name":"Novak","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"first_name":"Reinmar","full_name":"Hager, Reinmar","last_name":"Hager"}],"_id":"9715","status":"public","type":"research_data_reference"},{"ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9740"}]},"issue":"1799","volume":282,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"intvolume":" 282","month":"01","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"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. ","lang":"eng"}],"department":[{"_id":"SyCr"}],"date_updated":"2023-02-23T14:06:41Z","status":"public","article_type":"original","type":"journal_article","_id":"1993","date_created":"2018-12-11T11:55:06Z","doi":"10.1098/rspb.2014.1976","date_published":"2015-01-22T00:00:00Z","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"22","year":"2015","oa":1,"quality_controlled":"1","publisher":"The Royal Society","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.","title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","external_id":{"pmid":["25473011"]},"article_processing_charge":"No","author":[{"last_name":"Konrad","full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"full_name":"Tragust, Simon","last_name":"Tragust","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"publist_id":"5090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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."},"project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}],"article_number":"20141976"},{"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","last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883"},{"full_name":"Tourdot, Edouard","last_name":"Tourdot","first_name":"Edouard"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"},{"first_name":"Claudie","last_name":"Doums","full_name":"Doums, Claudie"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T10:30:52Z","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.","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","short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).","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.","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."},"status":"public","type":"research_data_reference","_id":"9742","doi":"10.5061/dryad.7kc79","related_material":{"record":[{"id":"2161","status":"public","relation":"used_in_publication"}]},"date_published":"2015-07-09T00:00:00Z","date_created":"2021-07-28T08:52:53Z","day":"09","year":"2015","month":"07","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7kc79"}],"oa":1,"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."}]},{"title":"Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs","department":[{"_id":"ToBo"}],"article_processing_charge":"No","author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87"},{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","last_name":"Lukacisinova","orcid":"0000-0002-2519-8004","full_name":"Lukacisinova, Marta"},{"first_name":"Tugce","full_name":"Batur, Tugce","last_name":"Batur"},{"last_name":"Guvenek","full_name":"Guvenek, Aysegul","first_name":"Aysegul"},{"full_name":"Ayhan, Dilay Hazal","last_name":"Ayhan","first_name":"Dilay Hazal"},{"first_name":"Erdal","last_name":"Toprak","full_name":"Toprak, Erdal"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","ieee":"G. Chevereau et al., “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 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","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."},"date_updated":"2023-02-23T10:07:02Z","status":"public","type":"research_data_reference","_id":"9765","date_created":"2021-08-03T07:05:16Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1619"}]},"date_published":"2015-11-18T00:00:00Z","doi":"10.1371/journal.pbio.1002299.s008","day":"18","year":"2015","month":"11","publisher":"Public Library of Science","oa_version":"Published Version"},{"year":"2015","day":"01","publication":"Advances in Water Resources","page":"94-111","doi":"10.1016/j.advwatres.2015.01.013","date_published":"2015-04-01T00:00:00Z","date_created":"2023-02-20T08:16:21Z","publisher":"Elsevier","quality_controlled":"1","citation":{"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","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","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ragettli","full_name":"Ragettli, S.","first_name":"S."},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"},{"first_name":"W.W.","full_name":"Immerzeel, W.W.","last_name":"Immerzeel"},{"full_name":"Miles, E.S.","last_name":"Miles","first_name":"E.S."},{"last_name":"Petersen","full_name":"Petersen, L.","first_name":"L."},{"full_name":"Heynen, M.","last_name":"Heynen","first_name":"M."},{"first_name":"J.M.","full_name":"Shea, J.M.","last_name":"Shea"},{"last_name":"Stumm","full_name":"Stumm, D.","first_name":"D."},{"first_name":"S.","full_name":"Joshi, S.","last_name":"Joshi"},{"last_name":"Shrestha","full_name":"Shrestha, A.","first_name":"A."}],"article_processing_charge":"No","title":"Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model","publication_identifier":{"issn":["0309-1708"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":78,"abstract":[{"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","lang":"eng"}],"oa_version":"None","scopus_import":"1","month":"04","intvolume":" 78","date_updated":"2023-02-24T09:28:04Z","extern":"1","_id":"12630","type":"journal_article","article_type":"original","status":"public","keyword":["Water Science and Technology"]},{"article_type":"original","type":"journal_article","keyword":["Earth-Surface Processes"],"status":"public","_id":"12628","date_updated":"2023-02-24T09:35:21Z","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3189/2015JoG13J237"}],"scopus_import":"1","intvolume":" 61","month":"03","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."}],"oa_version":"Published Version","issue":"226","volume":61,"publication_status":"published","publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"full_name":"Stephan, Christa","last_name":"Stephan","first_name":"Christa"},{"full_name":"Miles, Evan","last_name":"Miles","first_name":"Evan"},{"first_name":"Sam","last_name":"Herreid","full_name":"Herreid, Sam"},{"first_name":"Walter W.","full_name":"Immerzeel, Walter W.","last_name":"Immerzeel"},{"first_name":"Tobias","full_name":"Bolch, Tobias","last_name":"Bolch"}],"title":"Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999","citation":{"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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"International Glaciological Society","page":"373-386","date_created":"2023-02-20T08:16:11Z","doi":"10.3189/2015jog13j237","date_published":"2015-03-01T00:00:00Z","year":"2015","publication":"Journal of Glaciology","day":"01"},{"day":"18","publication":"Journal of Geophysical Research: Atmospheres","year":"2015","doi":"10.1002/2015jd023137","date_published":"2015-04-18T00:00:00Z","date_created":"2023-02-20T08:16:28Z","page":"3139-3157","publisher":"American Geophysical Union","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. Ayala, F. Pellicciotti, and J. M. Shea, “Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming,” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8. American Geophysical Union, pp. 3139–3157, 2015.","short":"A. Ayala, F. Pellicciotti, J.M. Shea, Journal of Geophysical Research: Atmospheres 120 (2015) 3139–3157.","apa":"Ayala, A., Pellicciotti, F., & Shea, J. M. (2015). Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1002/2015jd023137","ama":"Ayala A, Pellicciotti F, Shea JM. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 2015;120(8):3139-3157. doi:10.1002/2015jd023137","mla":"Ayala, A., et al. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8, American Geophysical Union, 2015, pp. 3139–57, doi:10.1002/2015jd023137.","ista":"Ayala A, Pellicciotti F, Shea JM. 2015. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 120(8), 3139–3157.","chicago":"Ayala, A., Francesca Pellicciotti, and J. M. Shea. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres. American Geophysical Union, 2015. https://doi.org/10.1002/2015jd023137."},"title":"Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming","author":[{"first_name":"A.","last_name":"Ayala","full_name":"Ayala, A."},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"full_name":"Shea, J. M.","last_name":"Shea","first_name":"J. M."}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2169-897X"],"eissn":["2169-8996"]},"publication_status":"published","issue":"8","volume":120,"oa_version":"Published Version","abstract":[{"text":"Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines.","lang":"eng"}],"month":"04","intvolume":" 120","scopus_import":"1","extern":"1","date_updated":"2023-02-24T09:16:26Z","_id":"12631","status":"public","keyword":["Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Geophysics"],"type":"journal_article","article_type":"original"},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1080/07900627.2015.1020417","open_access":"1"}],"month":"04","intvolume":" 31","abstract":[{"lang":"eng","text":"Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region."}],"oa_version":"Published Version","issue":"2","volume":31,"publication_identifier":{"issn":["0790-0627"],"eissn":["1360-0648"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","keyword":["Water Science and Technology","Development"],"_id":"12629","date_updated":"2023-02-24T09:30:42Z","extern":"1","publisher":"Taylor & Francis","quality_controlled":"1","oa":1,"page":"174-200","doi":"10.1080/07900627.2015.1020417","date_published":"2015-04-18T00:00:00Z","date_created":"2023-02-20T08:16:17Z","year":"2015","day":"18","publication":"International Journal of Water Resources Development","author":[{"first_name":"J.M.","last_name":"Shea","full_name":"Shea, J.M."},{"first_name":"P.","full_name":"Wagnon, P.","last_name":"Wagnon"},{"first_name":"W.W.","last_name":"Immerzeel","full_name":"Immerzeel, W.W."},{"last_name":"Biron","full_name":"Biron, R.","first_name":"R."},{"full_name":"Brun, F.","last_name":"Brun","first_name":"F."},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"}],"article_processing_charge":"No","title":"A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya","citation":{"chicago":"Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development. Taylor & Francis, 2015. https://doi.org/10.1080/07900627.2015.1020417.","ista":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 31(2), 174–200.","mla":"Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development, vol. 31, no. 2, Taylor & Francis, 2015, pp. 174–200, doi:10.1080/07900627.2015.1020417.","ieee":"J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti, “A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya,” International Journal of Water Resources Development, vol. 31, no. 2. Taylor & Francis, pp. 174–200, 2015.","short":"J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti, International Journal of Water Resources Development 31 (2015) 174–200.","apa":"Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., & Pellicciotti, F. (2015). A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. Taylor & Francis. https://doi.org/10.1080/07900627.2015.1020417","ama":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 2015;31(2):174-200. doi:10.1080/07900627.2015.1020417"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","abstract":[{"text":"Ice cliffs have been identified as a reason for higher ablation rates on debris-covered glaciers than are implied by the insulation effects of the debris. This study aims to improve our understanding of cliff backwasting, and the role of radiative fluxes in particular. An energy-balance model is forced with new data gathered in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show substantial variability in melt between cliffs, between locations on any cliff and between seasons. Using a high-resolution digital elevation model we calculate longwave fluxes incident to the cliff from surrounding terrain and include the effect of local shading on shortwave radiation. This is an advance over previous studies, that made simplified assumptions on cliff geometry and radiative fluxes. Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34 cm d−1 in October. Model results reproduce the strong variability in space and time, suggesting considerable differences in radiative fluxes over one cliff. In October the model fails to reproduce stake readings, probably due to the lack of a refreezing component. Disregarding local topography can lead to overestimation of melt at the point scale by up to ∼9%.","lang":"eng"}],"intvolume":" 61","month":"07","main_file_link":[{"url":"https://doi.org/10.3189/2015JoG14J194","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"volume":61,"issue":"229","_id":"12626","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-02-24T09:43:14Z","oa":1,"publisher":"International Glaciological Society","quality_controlled":"1","publication":"Journal of Glaciology","day":"01","year":"2015","date_created":"2023-02-20T08:16:01Z","doi":"10.3189/2015jog14j194","date_published":"2015-07-01T00:00:00Z","page":"889-907","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Steiner, Jakob F., et al. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology, vol. 61, no. 229, International Glaciological Society, 2015, pp. 889–907, doi:10.3189/2015jog14j194.","short":"J.F. Steiner, F. Pellicciotti, P. Buri, E.S. Miles, W.W. Immerzeel, T.D. Reid, Journal of Glaciology 61 (2015) 889–907.","ieee":"J. F. Steiner, F. Pellicciotti, P. Buri, E. S. Miles, W. W. Immerzeel, and T. D. Reid, “Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya,” Journal of Glaciology, vol. 61, no. 229. International Glaciological Society, pp. 889–907, 2015.","ama":"Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 2015;61(229):889-907. doi:10.3189/2015jog14j194","apa":"Steiner, J. F., Pellicciotti, F., Buri, P., Miles, E. S., Immerzeel, W. W., & Reid, T. D. (2015). Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j194","chicago":"Steiner, Jakob F., Francesca Pellicciotti, Pascal Buri, Evan S. Miles, Walter W. Immerzeel, and Tim D. Reid. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j194.","ista":"Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. 2015. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 61(229), 889–907."},"title":"Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya","article_processing_charge":"No","author":[{"full_name":"Steiner, Jakob F.","last_name":"Steiner","first_name":"Jakob F."},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"first_name":"Pascal","last_name":"Buri","full_name":"Buri, Pascal"},{"first_name":"Evan S.","last_name":"Miles","full_name":"Miles, Evan S."},{"last_name":"Immerzeel","full_name":"Immerzeel, Walter W.","first_name":"Walter W."},{"full_name":"Reid, Tim D.","last_name":"Reid","first_name":"Tim D."}]},{"year":"2015","publication":"Journal of Glaciology","day":"01","page":"524-536","date_created":"2023-02-20T08:16:06Z","doi":"10.3189/2015jog14j227","date_published":"2015-05-01T00:00:00Z","oa":1,"publisher":"International Glaciological Society","quality_controlled":"1","citation":{"ista":"Herreid S, Pellicciotti F, Ayala A, Chesnokova A, Kienholz C, Shea J, Shrestha A. 2015. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 61(227), 524–536.","chicago":"Herreid, Sam, Francesca Pellicciotti, Alvaro Ayala, Anna Chesnokova, Christian Kienholz, Joseph Shea, and Arun Shrestha. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j227.","apa":"Herreid, S., Pellicciotti, F., Ayala, A., Chesnokova, A., Kienholz, C., Shea, J., & Shrestha, A. (2015). Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j227","ama":"Herreid S, Pellicciotti F, Ayala A, et al. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 2015;61(227):524-536. doi:10.3189/2015jog14j227","ieee":"S. Herreid et al., “Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014,” Journal of Glaciology, vol. 61, no. 227. International Glaciological Society, pp. 524–536, 2015.","short":"S. Herreid, F. Pellicciotti, A. Ayala, A. Chesnokova, C. Kienholz, J. Shea, A. Shrestha, Journal of Glaciology 61 (2015) 524–536.","mla":"Herreid, Sam, et al. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology, vol. 61, no. 227, International Glaciological Society, 2015, pp. 524–36, doi:10.3189/2015jog14j227."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Sam","last_name":"Herreid","full_name":"Herreid, Sam"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"full_name":"Ayala, Alvaro","last_name":"Ayala","first_name":"Alvaro"},{"full_name":"Chesnokova, Anna","last_name":"Chesnokova","first_name":"Anna"},{"first_name":"Christian","full_name":"Kienholz, Christian","last_name":"Kienholz"},{"last_name":"Shea","full_name":"Shea, Joseph","first_name":"Joseph"},{"first_name":"Arun","full_name":"Shrestha, Arun","last_name":"Shrestha"}],"title":"Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014","publication_status":"published","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"language":[{"iso":"eng"}],"volume":61,"issue":"227","abstract":[{"text":"Spatial evolution of supraglacial debris cover on mountain glaciers is a largely unmonitored and poorly understood phenomenon that directly affects glacier melt. Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan, was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type glaciers occupy 41% of the study area and were considered separately. The time series of debris-covered surface area change shows a mean value of zero or near-zero change for both surging and non-surging glaciers. An increase in debris-covered area is often associated with negative regional mass balances. We extend this logic to suggest that the stable regional mass balances in the Karakoram explain the zero or near-zero change in debris-covered area. This coupling of trends combined with our 37 year time series of data suggests the Karakoram anomaly extends further back in time than previously known.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3189/2015JoG14J227"}],"scopus_import":"1","intvolume":" 61","month":"05","date_updated":"2023-02-24T09:40:30Z","extern":"1","_id":"12627","type":"journal_article","article_type":"original","status":"public"},{"oa":1,"publisher":"American Chemical Society","quality_controlled":"1","publication":"Biochemistry","day":"26","year":"2015","date_created":"2018-12-11T11:53:03Z","doi":"10.1021/acs.biochem.5b00560","date_published":"2015-06-26T00:00:00Z","page":"4163 - 4166","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560.","ista":"Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166.","mla":"Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560.","ama":"Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560","apa":"Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical Society. https://doi.org/10.1021/acs.biochem.5b00560","ieee":"C. Veldkamp et al., “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015.","short":"C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166."},"title":"Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites","article_processing_charge":"No","external_id":{"pmid":["26115234"]},"author":[{"last_name":"Veldkamp","full_name":"Veldkamp, Christopher","first_name":"Christopher"},{"first_name":"Eva","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6165-5738","full_name":"Kiermaier, Eva","last_name":"Kiermaier"},{"first_name":"Skylar","full_name":"Gabel Eissens, Skylar","last_name":"Gabel Eissens"},{"first_name":"Miranda","full_name":"Gillitzer, Miranda","last_name":"Gillitzer"},{"first_name":"David","last_name":"Lippner","full_name":"Lippner, David"},{"full_name":"Disilvio, Frank","last_name":"Disilvio","first_name":"Frank"},{"first_name":"Casey","full_name":"Mueller, Casey","last_name":"Mueller"},{"last_name":"Wantuch","full_name":"Wantuch, Paeton","first_name":"Paeton"},{"first_name":"Gary","full_name":"Chaffee, Gary","last_name":"Chaffee"},{"full_name":"Famiglietti, Michael","last_name":"Famiglietti","first_name":"Michael"},{"first_name":"Danielle","last_name":"Zgoba","full_name":"Zgoba, Danielle"},{"last_name":"Bailey","full_name":"Bailey, Asha","first_name":"Asha"},{"full_name":"Bah, Yaya","last_name":"Bah","first_name":"Yaya"},{"first_name":"Samantha","full_name":"Engebretson, Samantha","last_name":"Engebretson"},{"last_name":"Graupner","full_name":"Graupner, David","first_name":"David"},{"first_name":"Emily","full_name":"Lackner, Emily","last_name":"Lackner"},{"last_name":"Larosa","full_name":"Larosa, Vincent","first_name":"Vincent"},{"full_name":"Medeiros, Tysha","last_name":"Medeiros","first_name":"Tysha"},{"first_name":"Michael","last_name":"Olson","full_name":"Olson, Michael"},{"last_name":"Phillips","full_name":"Phillips, Andrew","first_name":"Andrew"},{"full_name":"Pyles, Harley","last_name":"Pyles","first_name":"Harley"},{"first_name":"Amanda","full_name":"Richard, Amanda","last_name":"Richard"},{"first_name":"Scott","last_name":"Schoeller","full_name":"Schoeller, Scott"},{"last_name":"Touzeau","full_name":"Touzeau, Boris","first_name":"Boris"},{"last_name":"Williams","full_name":"Williams, Larry","first_name":"Larry"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Peterson, Francis","last_name":"Peterson","first_name":"Francis"}],"publist_id":"5548","oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed."}],"intvolume":" 54","month":"06","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"27","volume":54,"_id":"1618","status":"public","type":"journal_article","date_updated":"2023-03-30T11:32:57Z","department":[{"_id":"MiSi"}]},{"language":[{"iso":"eng"}],"file":[{"checksum":"880eabe59c9df12f06a882aa1bc4e600","file_id":"12882","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-05-02T07:02:59Z","file_name":"2015_ECAL_Martius.pdf","date_updated":"2023-05-02T07:02:59Z","file_size":1674241,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"isbn":["9780262330275"]},"ec_funded":1,"oa_version":"Published Version","month":"07","scopus_import":"1","ddc":["000"],"date_updated":"2023-05-02T07:06:21Z","file_date_updated":"2023-05-02T07:02:59Z","department":[{"_id":"ChLa"}],"_id":"12881","status":"public","conference":{"start_date":"2015-07-20","end_date":"2015-07-24","location":"York, United Kingdom","name":"ECAL: European Conference on Artificial Life"},"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":"conference","publication":"Proceedings of the 13th European Conference on Artificial Life","day":"01","year":"2015","has_accepted_license":"1","date_created":"2023-04-30T22:01:07Z","date_published":"2015-07-01T00:00:00Z","doi":"10.7551/978-0-262-33027-5-ch018","page":"78","acknowledgement":"This work was supported by the DFG (SPP 1527) and the EU (FP7, REA grant no 291734).","oa":1,"publisher":"MIT Press","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” In Proceedings of the 13th European Conference on Artificial Life, 78. MIT Press, 2015. https://doi.org/10.7551/978-0-262-33027-5-ch018.","ista":"Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous robots. Proceedings of the 13th European Conference on Artificial Life. ECAL: European Conference on Artificial Life, 78.","mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78, doi:10.7551/978-0-262-33027-5-ch018.","ieee":"G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous robots,” in Proceedings of the 13th European Conference on Artificial Life, York, United Kingdom, 2015, p. 78.","short":"G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78.","apa":"Martius, G. S., & Olbrich, E. (2015). Quantifying self-organizing behavior of autonomous robots. In Proceedings of the 13th European Conference on Artificial Life (p. 78). York, United Kingdom: MIT Press. https://doi.org/10.7551/978-0-262-33027-5-ch018","ama":"Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous robots. In: Proceedings of the 13th European Conference on Artificial Life. MIT Press; 2015:78. doi:10.7551/978-0-262-33027-5-ch018"},"title":"Quantifying self-organizing behavior of autonomous robots","article_processing_charge":"No","author":[{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Olbrich, Eckehard","last_name":"Olbrich","first_name":"Eckehard"}],"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}]},{"acknowledgement":"This work was supported by the National Sciences and Engineering Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles Copeland for critical reading of the manuscript.","publisher":"Oxford University Press","quality_controlled":"1","publication":"Plant and Cell Physiology","year":"2015","date_published":"2015-08-01T00:00:00Z","doi":"10.1093/pcp/pcv087","date_created":"2023-01-16T09:20:22Z","page":"1616-1623","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623. doi:10.1093/pcp/pcv087","apa":"Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcv087","ieee":"K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology, vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.","short":"K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015) 1616–1623.","mla":"Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087.","ista":"Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.","chicago":"Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087."},"title":"The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity","author":[{"last_name":"Johnson","full_name":"Johnson, Kaeli C.M.","first_name":"Kaeli C.M."},{"full_name":"Xia, Shitou","last_name":"Xia","first_name":"Shitou"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"},{"last_name":"Li","full_name":"Li, Xin","first_name":"Xin"}],"article_processing_charge":"No","external_id":{"pmid":["26063389"]},"pmid":1,"oa_version":"None","abstract":[{"text":"SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity.","lang":"eng"}],"month":"08","intvolume":" 56","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0032-0781","1471-9053"]},"publication_status":"published","volume":56,"issue":"8","_id":"12196","status":"public","keyword":["Cell Biology","Plant Science","Physiology","General Medicine"],"article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-05-08T11:03:23Z","department":[{"_id":"XiFe"}]},{"citation":{"short":"H. Zhao, S. Sen, T. Udayabhaskararao, M. Sawczyk, K. Kučanda, D. Manna, P.K. Kundu, J.-W. Lee, P. Král, R. Klajn, Nature Nanotechnology 11 (2015) 82–88.","ieee":"H. Zhao et al., “Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks,” Nature Nanotechnology, vol. 11. Springer Nature, pp. 82–88, 2015.","apa":"Zhao, H., Sen, S., Udayabhaskararao, T., Sawczyk, M., Kučanda, K., Manna, D., … Klajn, R. (2015). Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/nnano.2015.256","ama":"Zhao H, Sen S, Udayabhaskararao T, et al. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 2015;11:82-88. doi:10.1038/nnano.2015.256","mla":"Zhao, Hui, et al. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” Nature Nanotechnology, vol. 11, Springer Nature, 2015, pp. 82–88, doi:10.1038/nnano.2015.256.","ista":"Zhao H, Sen S, Udayabhaskararao T, Sawczyk M, Kučanda K, Manna D, Kundu PK, Lee J-W, Král P, Klajn R. 2015. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 11, 82–88.","chicago":"Zhao, Hui, Soumyo Sen, T. Udayabhaskararao, Michał Sawczyk, Kristina Kučanda, Debasish Manna, Pintu K. Kundu, Ji-Woong Lee, Petr Král, and Rafal Klajn. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” Nature Nanotechnology. Springer Nature, 2015. https://doi.org/10.1038/nnano.2015.256."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Hui","full_name":"Zhao, Hui","last_name":"Zhao"},{"first_name":"Soumyo","last_name":"Sen","full_name":"Sen, Soumyo"},{"full_name":"Udayabhaskararao, T.","last_name":"Udayabhaskararao","first_name":"T."},{"first_name":"Michał","full_name":"Sawczyk, Michał","last_name":"Sawczyk"},{"last_name":"Kučanda","full_name":"Kučanda, Kristina","first_name":"Kristina"},{"last_name":"Manna","full_name":"Manna, Debasish","first_name":"Debasish"},{"first_name":"Pintu K.","last_name":"Kundu","full_name":"Kundu, Pintu K."},{"first_name":"Ji-Woong","last_name":"Lee","full_name":"Lee, Ji-Woong"},{"last_name":"Král","full_name":"Král, Petr","first_name":"Petr"},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"external_id":{"pmid":["26595335"]},"article_processing_charge":"No","title":"Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks","publisher":"Springer Nature","quality_controlled":"1","year":"2015","day":"23","publication":"Nature Nanotechnology","page":"82-88","date_published":"2015-11-23T00:00:00Z","doi":"10.1038/nnano.2015.256","date_created":"2023-08-01T09:44:04Z","_id":"13392","article_type":"original","type":"journal_article","status":"public","keyword":["Electrical and Electronic Engineering","Condensed Matter Physics","General Materials Science","Biomedical Engineering","Atomic and Molecular Physics","and Optics","Bioengineering"],"date_updated":"2023-08-07T12:55:46Z","extern":"1","abstract":[{"text":"The chemical behaviour of molecules can be significantly modified by confinement to volumes comparable to the dimensions of the molecules. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of molecules in and out of these materials has greatly hampered studying the effect of confinement on their physicochemical properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various molecules from the surrounding bulk solution. Once trapped, these molecules can undergo chemical reactions with increased rates and with stereoselectivities significantly different from those in bulk solution. Illumination with visible light disassembles these nanoflasks, releasing the product in solution and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chemical reactivities in confined environments and for synthesizing molecules that are otherwise hard to achieve in bulk solution.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","month":"11","intvolume":" 11","publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":11},{"scopus_import":"1","intvolume":" 7","month":"07","abstract":[{"lang":"eng","text":"The ability to guide the assembly of nanosized objects reversibly with external stimuli, in particular light, is of fundamental importance, and it contributes to the development of applications as diverse as nanofabrication and controlled drug delivery. However, all the systems described to date are based on nanoparticles (NPs) that are inherently photoresponsive, which makes their preparation cumbersome and can markedly hamper their performance. Here we describe a conceptually new methodology to assemble NPs reversibly using light that does not require the particles to be functionalized with light-responsive ligands. Our strategy is based on the use of a photoswitchable medium that responds to light in such a way that it modulates the interparticle interactions. NP assembly proceeds quantitatively and without apparent fatigue, both in solution and in gels. Exposing the gels to light in a spatially controlled manner allowed us to draw images that spontaneously disappeared after a specific period of time."}],"pmid":1,"oa_version":"None","volume":7,"publication_status":"published","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","keyword":["General Chemical Engineering","General Chemistry"],"status":"public","_id":"13394","date_updated":"2023-08-07T13:00:15Z","extern":"1","quality_controlled":"1","publisher":"Springer Nature","page":"646-652","date_created":"2023-08-01T09:44:33Z","doi":"10.1038/nchem.2303","date_published":"2015-07-20T00:00:00Z","year":"2015","publication":"Nature Chemistry","day":"20","article_processing_charge":"No","external_id":{"pmid":["26201741"]},"author":[{"last_name":"Kundu","full_name":"Kundu, Pintu K.","first_name":"Pintu K."},{"first_name":"Dipak","last_name":"Samanta","full_name":"Samanta, Dipak"},{"last_name":"Leizrowice","full_name":"Leizrowice, Ron","first_name":"Ron"},{"full_name":"Margulis, Baruch","last_name":"Margulis","first_name":"Baruch"},{"full_name":"Zhao, Hui","last_name":"Zhao","first_name":"Hui"},{"first_name":"Martin","last_name":"Börner","full_name":"Börner, Martin"},{"last_name":"Udayabhaskararao","full_name":"Udayabhaskararao, T.","first_name":"T."},{"full_name":"Manna, Debasish","last_name":"Manna","first_name":"Debasish"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"}],"title":"Light-controlled self-assembly of non-photoresponsive nanoparticles","citation":{"ista":"Kundu PK, Samanta D, Leizrowice R, Margulis B, Zhao H, Börner M, Udayabhaskararao T, Manna D, Klajn R. 2015. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 7, 646–652.","chicago":"Kundu, Pintu K., Dipak Samanta, Ron Leizrowice, Baruch Margulis, Hui Zhao, Martin Börner, T. Udayabhaskararao, Debasish Manna, and Rafal Klajn. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry. Springer Nature, 2015. https://doi.org/10.1038/nchem.2303.","short":"P.K. Kundu, D. Samanta, R. Leizrowice, B. Margulis, H. Zhao, M. Börner, T. Udayabhaskararao, D. Manna, R. Klajn, Nature Chemistry 7 (2015) 646–652.","ieee":"P. K. Kundu et al., “Light-controlled self-assembly of non-photoresponsive nanoparticles,” Nature Chemistry, vol. 7. Springer Nature, pp. 646–652, 2015.","ama":"Kundu PK, Samanta D, Leizrowice R, et al. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 2015;7:646-652. doi:10.1038/nchem.2303","apa":"Kundu, P. K., Samanta, D., Leizrowice, R., Margulis, B., Zhao, H., Börner, M., … Klajn, R. (2015). Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2303","mla":"Kundu, Pintu K., et al. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry, vol. 7, Springer Nature, 2015, pp. 646–52, doi:10.1038/nchem.2303."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Wiley","quality_controlled":"1","date_published":"2015-10-01T00:00:00Z","doi":"10.1002/anie.201502419","date_created":"2023-08-01T09:44:19Z","page":"12394-12397","day":"01","publication":"Angewandte Chemie International Edition","year":"2015","title":"Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes","author":[{"full_name":"Manna, Debasish","last_name":"Manna","first_name":"Debasish"},{"last_name":"Udayabhaskararao","full_name":"Udayabhaskararao, Thumu","first_name":"Thumu"},{"first_name":"Hui","full_name":"Zhao, Hui","last_name":"Zhao"},{"last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"external_id":{"pmid":["25959725"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Manna, Debasish, Thumu Udayabhaskararao, Hui Zhao, and Rafal Klajn. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition. Wiley, 2015. https://doi.org/10.1002/anie.201502419.","ista":"Manna D, Udayabhaskararao T, Zhao H, Klajn R. 2015. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 54(42), 12394–12397.","mla":"Manna, Debasish, et al. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition, vol. 54, no. 42, Wiley, 2015, pp. 12394–97, doi:10.1002/anie.201502419.","ama":"Manna D, Udayabhaskararao T, Zhao H, Klajn R. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 2015;54(42):12394-12397. doi:10.1002/anie.201502419","apa":"Manna, D., Udayabhaskararao, T., Zhao, H., & Klajn, R. (2015). Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201502419","ieee":"D. Manna, T. Udayabhaskararao, H. Zhao, and R. Klajn, “Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes,” Angewandte Chemie International Edition, vol. 54, no. 42. Wiley, pp. 12394–12397, 2015.","short":"D. Manna, T. Udayabhaskararao, H. Zhao, R. Klajn, Angewandte Chemie International Edition 54 (2015) 12394–12397."},"month":"10","intvolume":" 54","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"Precise control of the self-assembly of selected components within complex mixtures is a challenging goal whose realization is important for fabricating novel nanomaterials. Herein we show that by decorating the surfaces of metallic nanoparticles with differently substituted azobenzenes, it is possible to modulate the wavelength of light at which the self-assembly of these nanoparticles is induced. Exposing a mixture of two types of nanoparticles, each functionalized with a different azobenzene, to UV or blue light induces the selective self-assembly of only one type of nanoparticles. Irradiation with the other wavelength triggers the disassembly of the aggregates, and the simultaneous self-assembly of nanoparticles of the other type. By placing both types of azobenzenes on the same nanoparticles, we created unique materials (“frustrated” nanoparticles) whose self-assembly is induced irrespective of the wavelength of the incident light."}],"volume":54,"issue":"42","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"publication_status":"published","status":"public","keyword":["General Chemistry","Catalysis"],"type":"journal_article","article_type":"original","_id":"13393","extern":"1","date_updated":"2023-08-07T12:58:29Z"},{"citation":{"apa":"Lee, J.-W., & Klajn, R. (2015). Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/c4cc08541h","ama":"Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 2015;51(11):2036-2039. doi:10.1039/c4cc08541h","ieee":"J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2,” Chemical Communications, vol. 51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015.","short":"J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039.","mla":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications, vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:10.1039/c4cc08541h.","ista":"Lee J-W, Klajn R. 2015. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 51(11), 2036–2039.","chicago":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4cc08541h."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Lee, Ji-Woong","last_name":"Lee","first_name":"Ji-Woong"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"article_processing_charge":"No","external_id":{"pmid":["25417754"]},"title":"Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2","year":"2015","day":"18","publication":"Chemical Communications","page":"2036-2039","date_published":"2015-11-18T00:00:00Z","doi":"10.1039/c4cc08541h","date_created":"2023-08-01T09:44:48Z","publisher":"Royal Society of Chemistry","quality_controlled":"1","oa":1,"date_updated":"2023-08-07T13:01:53Z","extern":"1","_id":"13395","type":"journal_article","article_type":"original","status":"public","keyword":["Materials Chemistry","Metals and Alloys","Surfaces","Coatings and Films","General Chemistry","Ceramics and Composites","Electronic","Optical and Magnetic Materials","Catalysis"],"publication_identifier":{"issn":["1359-7345"],"eissn":["1364-548X"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":51,"issue":"11","abstract":[{"lang":"eng","text":"Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive ligands were prepared and shown to respond to these two types of stimuli reversibly and in an orthogonal fashion. The composition of the coating could be tailored to yield nanoparticles capable of aggregating exclusively when both UV and CO2 were applied at the same time, analogously to the behaviour of an AND logic gate."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/C4CC08541H"}],"month":"11","intvolume":" 51"},{"publisher":"American Chemical Society","quality_controlled":"1","publication":"Langmuir","day":"27","year":"2015","date_created":"2023-08-01T09:45:02Z","date_published":"2015-01-27T00:00:00Z","doi":"10.1021/la504291n","page":"1048-1057","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Moldt, Thomas, Daniel Brete, Daniel Przyrembel, Sanjib Das, Joel R. Goldman, Pintu K. Kundu, Cornelius Gahl, Rafal Klajn, and Martin Weinelt. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504291n.","ista":"Moldt T, Brete D, Przyrembel D, Das S, Goldman JR, Kundu PK, Gahl C, Klajn R, Weinelt M. 2015. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 31(3), 1048–1057.","mla":"Moldt, Thomas, et al. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” Langmuir, vol. 31, no. 3, American Chemical Society, 2015, pp. 1048–57, doi:10.1021/la504291n.","ieee":"T. Moldt et al., “Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature,” Langmuir, vol. 31, no. 3. American Chemical Society, pp. 1048–1057, 2015.","short":"T. Moldt, D. Brete, D. Przyrembel, S. Das, J.R. Goldman, P.K. Kundu, C. Gahl, R. Klajn, M. Weinelt, Langmuir 31 (2015) 1048–1057.","ama":"Moldt T, Brete D, Przyrembel D, et al. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 2015;31(3):1048-1057. doi:10.1021/la504291n","apa":"Moldt, T., Brete, D., Przyrembel, D., Das, S., Goldman, J. R., Kundu, P. K., … Weinelt, M. (2015). Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. American Chemical Society. https://doi.org/10.1021/la504291n"},"title":"Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature","article_processing_charge":"No","external_id":{"pmid":["25544061"]},"author":[{"first_name":"Thomas","full_name":"Moldt, Thomas","last_name":"Moldt"},{"first_name":"Daniel","full_name":"Brete, Daniel","last_name":"Brete"},{"last_name":"Przyrembel","full_name":"Przyrembel, Daniel","first_name":"Daniel"},{"full_name":"Das, Sanjib","last_name":"Das","first_name":"Sanjib"},{"first_name":"Joel R.","last_name":"Goldman","full_name":"Goldman, Joel R."},{"first_name":"Pintu K.","last_name":"Kundu","full_name":"Kundu, Pintu K."},{"first_name":"Cornelius","last_name":"Gahl","full_name":"Gahl, Cornelius"},{"full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"},{"first_name":"Martin","full_name":"Weinelt, Martin","last_name":"Weinelt"}],"pmid":1,"oa_version":"None","abstract":[{"text":"Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs) is strongly affected by steric constraints and excitonic coupling between neighboring chromophores. Therefore, control of the chromophore density is essential for enhancing and manipulating the photoisomerization yield. We systematically compare two methods to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual decrease of the chromophore density and enable efficient photoswitching with low-power light sources. X-ray spectroscopy reveals that coadsorption from solution yields mixtures with tunable composition. The orientation of the chromophores with respect to the surface normal changes from a tilted to an upright position with increasing azobenzene density. For both systems, optical spectroscopy reveals a pronounced excitonic shift that increases with the chromophore density. In spite of exciting the optical transition of the monomer, the main spectral change in mixed SAMs occurs in the excitonic band. In addition, the photoisomerization yield decreases only slightly by increasing the azobenzene–alkanethiolate density, and we observed photoswitching even with minor dilutions. Unlike in solution, azobenzene in the planar SAM can be switched back almost completely by optical excitation from the cis to the original trans state within a short time scale. These observations indicate cooperativity in the photoswitching process of mixed SAMs.","lang":"eng"}],"intvolume":" 31","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0743-7463"],"eissn":["1520-5827"]},"volume":31,"issue":"3","_id":"13396","keyword":["Electrochemistry","Spectroscopy","Surfaces and Interfaces","Condensed Matter Physics","General Materials Science"],"status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-08-07T13:05:04Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Singh, Gurvinder, Henry Chan, T. Udayabhaskararao, Elijah Gelman, Davide Peddis, Artem Baskin, Gregory Leitus, Petr Král, and Rafal Klajn. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4fd00265b.","ista":"Singh G, Chan H, Udayabhaskararao T, Gelman E, Peddis D, Baskin A, Leitus G, Král P, Klajn R. 2015. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 181, 403–421.","mla":"Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 403–21, doi:10.1039/c4fd00265b.","ama":"Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 2015;181:403-421. doi:10.1039/c4fd00265b","apa":"Singh, G., Chan, H., Udayabhaskararao, T., Gelman, E., Peddis, D., Baskin, A., … Klajn, R. (2015). Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00265b","ieee":"G. Singh et al., “Magnetic field-induced self-assembly of iron oxide nanocubes,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 403–421, 2015.","short":"G. Singh, H. Chan, T. Udayabhaskararao, E. Gelman, D. Peddis, A. Baskin, G. Leitus, P. Král, R. Klajn, Faraday Discussions 181 (2015) 403–421."},"title":"Magnetic field-induced self-assembly of iron oxide nanocubes","author":[{"first_name":"Gurvinder","last_name":"Singh","full_name":"Singh, Gurvinder"},{"full_name":"Chan, Henry","last_name":"Chan","first_name":"Henry"},{"first_name":"T.","last_name":"Udayabhaskararao","full_name":"Udayabhaskararao, T."},{"full_name":"Gelman, Elijah","last_name":"Gelman","first_name":"Elijah"},{"first_name":"Davide","full_name":"Peddis, Davide","last_name":"Peddis"},{"first_name":"Artem","last_name":"Baskin","full_name":"Baskin, Artem"},{"first_name":"Gregory","last_name":"Leitus","full_name":"Leitus, Gregory"},{"last_name":"Král","full_name":"Král, Petr","first_name":"Petr"},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"article_processing_charge":"No","external_id":{"pmid":["25920522"]},"day":"02","publication":"Faraday Discussions","year":"2015","doi":"10.1039/c4fd00265b","date_published":"2015-01-02T00:00:00Z","date_created":"2023-08-01T09:45:17Z","page":"403-421","publisher":"Royal Society of Chemistry","quality_controlled":"1","oa":1,"extern":"1","date_updated":"2023-08-07T13:06:23Z","_id":"13397","status":"public","keyword":["Physical and Theoretical Chemistry"],"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"publication_status":"published","volume":181,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Self-assembly of inorganic nanoparticles has been studied extensively for particles having different sizes and compositions. However, relatively little attention has been devoted to how the shape and surface chemistry of magnetic nanoparticles affects their self-assembly properties. Here, we undertook a combined experiment–theory study aimed at better understanding of the self-assembly of cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental parameters, such as the direction of the magnetic field and nanoparticle density, a variety of superstructures can be obtained, including one-dimensional filaments and helices, as well as C-shaped assemblies described here for the first time. Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive ligands. Using these modified nanoparticles, we were able to achieve orthogonal control of self-assembly using a magnetic field and light."}],"month":"01","intvolume":" 181","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1039/C4FD00265B","open_access":"1"}]},{"_id":"13398","article_type":"letter_note","type":"journal_article","keyword":["Physical and Theoretical Chemistry"],"status":"public","date_updated":"2023-08-08T07:16:20Z","extern":"1","pmid":1,"oa_version":"None","scopus_import":"1","intvolume":" 181","month":"07","publication_status":"published","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"language":[{"iso":"eng"}],"volume":181,"citation":{"chicago":"Sun, Yugang, Leonardo Scarabelli, Nicholas Kotov, Moritz Tebbe, Xiao-Min Lin, Ward Brullot, Lucio Isa, et al. “Field-Assisted Self-Assembly Process: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c5fd90041g.","ista":"Sun Y, Scarabelli L, Kotov N, Tebbe M, Lin X-M, Brullot W, Isa L, Schurtenberger P, Moehwald H, Fedin I, Velev O, Faivre D, Sorensen C, Perzynski R, Chanana M, Li Z, Bresme F, Král P, Firlar E, Schiffrin D, Souza Junior JB, Fery A, Shevchenko E, Tarhan O, Alivisatos AP, Disch S, Klajn R, Ghosh S. 2015. Field-assisted self-assembly process: General discussion. Faraday Discussions. 181, 463–479.","mla":"Sun, Yugang, et al. “Field-Assisted Self-Assembly Process: General Discussion.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 463–79, doi:10.1039/c5fd90041g.","short":"Y. Sun, L. Scarabelli, N. Kotov, M. Tebbe, X.-M. Lin, W. Brullot, L. Isa, P. Schurtenberger, H. Moehwald, I. Fedin, O. Velev, D. Faivre, C. Sorensen, R. Perzynski, M. Chanana, Z. Li, F. Bresme, P. Král, E. Firlar, D. Schiffrin, J.B. Souza Junior, A. Fery, E. Shevchenko, O. Tarhan, A.P. Alivisatos, S. Disch, R. Klajn, S. Ghosh, Faraday Discussions 181 (2015) 463–479.","ieee":"Y. Sun et al., “Field-assisted self-assembly process: General discussion,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 463–479, 2015.","apa":"Sun, Y., Scarabelli, L., Kotov, N., Tebbe, M., Lin, X.-M., Brullot, W., … Ghosh, S. (2015). Field-assisted self-assembly process: General discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c5fd90041g","ama":"Sun Y, Scarabelli L, Kotov N, et al. Field-assisted self-assembly process: General discussion. Faraday Discussions. 2015;181:463-479. doi:10.1039/c5fd90041g"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["26149295"]},"author":[{"last_name":"Sun","full_name":"Sun, Yugang","first_name":"Yugang"},{"first_name":"Leonardo","full_name":"Scarabelli, Leonardo","last_name":"Scarabelli"},{"first_name":"Nicholas","last_name":"Kotov","full_name":"Kotov, Nicholas"},{"full_name":"Tebbe, Moritz","last_name":"Tebbe","first_name":"Moritz"},{"first_name":"Xiao-Min","last_name":"Lin","full_name":"Lin, Xiao-Min"},{"first_name":"Ward","last_name":"Brullot","full_name":"Brullot, Ward"},{"first_name":"Lucio","full_name":"Isa, Lucio","last_name":"Isa"},{"first_name":"Peter","full_name":"Schurtenberger, Peter","last_name":"Schurtenberger"},{"first_name":"Helmuth","full_name":"Moehwald, Helmuth","last_name":"Moehwald"},{"first_name":"Igor","last_name":"Fedin","full_name":"Fedin, Igor"},{"full_name":"Velev, Orlin","last_name":"Velev","first_name":"Orlin"},{"last_name":"Faivre","full_name":"Faivre, Damien","first_name":"Damien"},{"last_name":"Sorensen","full_name":"Sorensen, Christopher","first_name":"Christopher"},{"last_name":"Perzynski","full_name":"Perzynski, Régine","first_name":"Régine"},{"last_name":"Chanana","full_name":"Chanana, Munish","first_name":"Munish"},{"first_name":"Zhihai","last_name":"Li","full_name":"Li, Zhihai"},{"first_name":"Fernando","last_name":"Bresme","full_name":"Bresme, Fernando"},{"full_name":"Král, Petr","last_name":"Král","first_name":"Petr"},{"last_name":"Firlar","full_name":"Firlar, Emre","first_name":"Emre"},{"first_name":"David","full_name":"Schiffrin, David","last_name":"Schiffrin"},{"first_name":"Joao Batista","full_name":"Souza Junior, Joao Batista","last_name":"Souza Junior"},{"first_name":"Andreas","full_name":"Fery, Andreas","last_name":"Fery"},{"first_name":"Elena","last_name":"Shevchenko","full_name":"Shevchenko, Elena"},{"full_name":"Tarhan, Ozgur","last_name":"Tarhan","first_name":"Ozgur"},{"last_name":"Alivisatos","full_name":"Alivisatos, Armand Paul","first_name":"Armand Paul"},{"last_name":"Disch","full_name":"Disch, Sabrina","first_name":"Sabrina"},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"first_name":"Suvojit","full_name":"Ghosh, Suvojit","last_name":"Ghosh"}],"title":"Field-assisted self-assembly process: General discussion","quality_controlled":"1","publisher":"Royal Society of Chemistry","year":"2015","publication":"Faraday Discussions","day":"07","page":"463-479","date_created":"2023-08-01T09:45:29Z","date_published":"2015-07-07T00:00:00Z","doi":"10.1039/c5fd90041g"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review A","day":"19","year":"2015","date_created":"2023-08-10T06:38:10Z","doi":"10.1103/physreva.91.023421","date_published":"2015-02-19T00:00:00Z","article_number":"023421","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. 2015. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 91(2), 023421.","chicago":"Zhang, Song Bin, Denitsa Rangelova Baykusheva, Peter M. Kraus, Hans Jakob Wörner, and Nina Rohringer. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/physreva.91.023421.","apa":"Zhang, S. B., Baykusheva, D. R., Kraus, P. M., Wörner, H. J., & Rohringer, N. (2015). Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.91.023421","ama":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 2015;91(2). doi:10.1103/physreva.91.023421","ieee":"S. B. Zhang, D. R. Baykusheva, P. M. Kraus, H. J. Wörner, and N. Rohringer, “Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation,” Physical Review A, vol. 91, no. 2. American Physical Society, 2015.","short":"S.B. Zhang, D.R. Baykusheva, P.M. Kraus, H.J. Wörner, N. Rohringer, Physical Review A 91 (2015).","mla":"Zhang, Song Bin, et al. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A, vol. 91, no. 2, 023421, American Physical Society, 2015, doi:10.1103/physreva.91.023421."},"title":"Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation","article_processing_charge":"No","external_id":{"arxiv":["1504.03933"]},"author":[{"full_name":"Zhang, Song Bin","last_name":"Zhang","first_name":"Song Bin"},{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"first_name":"Peter M.","full_name":"Kraus, Peter M.","last_name":"Kraus"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"},{"first_name":"Nina","full_name":"Rohringer, Nina","last_name":"Rohringer"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The detection of electron motion and electronic wave-packet dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide molecule as an example, we have introduced and demonstrated an experimental approach to measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the theory in detail, which is based on a generalized density-matrix approach that describes the pump process and the subsequent probing of the wave packets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wave packets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented that facilitates interpretation of the results."}],"intvolume":" 91","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.03933"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1094-1622"],"issn":["1050-2947"]},"issue":"2","volume":91,"_id":"14017","keyword":["Atomic and Molecular Physics","and Optics"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-22T08:56:34Z"},{"publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_published":"2015-05-05T00:00:00Z","doi":"10.1038/ncomms8039","date_created":"2023-08-10T06:38:01Z","day":"05","publication":"Nature Communications","year":"2015","article_number":"7039","title":"Observation of laser-induced electronic structure in oriented polyatomic molecules","author":[{"first_name":"P. M.","last_name":"Kraus","full_name":"Kraus, P. M."},{"first_name":"O. I.","full_name":"Tolstikhin, O. I.","last_name":"Tolstikhin"},{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"first_name":"A.","full_name":"Rupenyan, A.","last_name":"Rupenyan"},{"last_name":"Schneider","full_name":"Schneider, J.","first_name":"J."},{"last_name":"Bisgaard","full_name":"Bisgaard, C. Z.","first_name":"C. Z."},{"first_name":"T.","full_name":"Morishita, T.","last_name":"Morishita"},{"last_name":"Jensen","full_name":"Jensen, F.","first_name":"F."},{"last_name":"Madsen","full_name":"Madsen, L. B.","first_name":"L. B."},{"full_name":"Wörner, H. J.","last_name":"Wörner","first_name":"H. J."}],"article_processing_charge":"No","external_id":{"pmid":["25940229"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 6, 7039.","chicago":"Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan, J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J. Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039.","ama":"Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 2015;6. doi:10.1038/ncomms8039","apa":"Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider, J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms8039","ieee":"P. M. Kraus et al., “Observation of laser-induced electronic structure in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer Nature, 2015.","short":"P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider, C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications 6 (2015).","mla":"Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer Nature, 2015, doi:10.1038/ncomms8039."},"month":"05","intvolume":" 6","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms8039"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies."}],"volume":6,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","status":"public","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"article_type":"original","type":"journal_article","_id":"14016","extern":"1","date_updated":"2023-08-22T08:52:56Z"},{"scopus_import":"1","intvolume":" 350","month":"10","abstract":[{"lang":"eng","text":"The ultrafast motion of electrons and holes after light-matter interaction is fundamental to a broad range of chemical and biophysical processes. We advanced high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately after ionization of iodoacetylene while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement and accurate theoretical description of both even and odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~100 attoseconds. We separately reconstructed quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determined the shape of the hole created by ionization. Our technique opens the prospect of laser control over electronic primary processes."}],"pmid":1,"oa_version":"None","issue":"6262","volume":350,"publication_status":"published","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","keyword":["Multidisciplinary"],"status":"public","_id":"14013","date_updated":"2023-08-22T08:47:39Z","extern":"1","publisher":"American Association for the Advancement of Science","quality_controlled":"1","page":"790-795","date_created":"2023-08-10T06:37:35Z","doi":"10.1126/science.aab2160","date_published":"2015-10-22T00:00:00Z","year":"2015","publication":"Science","day":"22","article_processing_charge":"No","external_id":{"pmid":["26494175"]},"author":[{"full_name":"Kraus, P. M.","last_name":"Kraus","first_name":"P. M."},{"first_name":"B.","last_name":"Mignolet","full_name":"Mignolet, B."},{"full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"first_name":"A.","last_name":"Rupenyan","full_name":"Rupenyan, A."},{"first_name":"L.","full_name":"Horný, L.","last_name":"Horný"},{"last_name":"Penka","full_name":"Penka, E. F.","first_name":"E. F."},{"full_name":"Grassi, G.","last_name":"Grassi","first_name":"G."},{"last_name":"Tolstikhin","full_name":"Tolstikhin, O. I.","first_name":"O. I."},{"first_name":"J.","full_name":"Schneider, J.","last_name":"Schneider"},{"first_name":"F.","last_name":"Jensen","full_name":"Jensen, F."},{"full_name":"Madsen, L. B.","last_name":"Madsen","first_name":"L. B."},{"last_name":"Bandrauk","full_name":"Bandrauk, A. D.","first_name":"A. D."},{"full_name":"Remacle, F.","last_name":"Remacle","first_name":"F."},{"first_name":"H. J.","full_name":"Wörner, H. J.","last_name":"Wörner"}],"title":"Measurement and laser control of attosecond charge migration in ionized iodoacetylene","citation":{"mla":"Kraus, P. M., et al. “Measurement and Laser Control of Attosecond Charge Migration in Ionized Iodoacetylene.” Science, vol. 350, no. 6262, American Association for the Advancement of Science, 2015, pp. 790–95, doi:10.1126/science.aab2160.","ama":"Kraus PM, Mignolet B, Baykusheva DR, et al. Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. 2015;350(6262):790-795. doi:10.1126/science.aab2160","apa":"Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka, E. F., … Wörner, H. J. (2015). Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aab2160","short":"P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, G. Grassi, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle, H.J. Wörner, Science 350 (2015) 790–795.","ieee":"P. M. Kraus et al., “Measurement and laser control of attosecond charge migration in ionized iodoacetylene,” Science, vol. 350, no. 6262. American Association for the Advancement of Science, pp. 790–795, 2015.","chicago":"Kraus, P. M., B. Mignolet, Denitsa Rangelova Baykusheva, A. Rupenyan, L. Horný, E. F. Penka, G. Grassi, et al. “Measurement and Laser Control of Attosecond Charge Migration in Ionized Iodoacetylene.” Science. American Association for the Advancement of Science, 2015. https://doi.org/10.1126/science.aab2160.","ista":"Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Grassi G, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015. Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. 350(6262), 790–795."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We advance high-harmonic spectroscopy to resolve molecular charge migration in time and space and simultaneously demonstrate extensive control over the process. A multidimensional approach enables us to reconstruct both quantum amplitudes and phases with a resolution of better than 100 attoseconds and to separately reconstruct field-free and laser- driven charge migration. Our techniques make charge migration in molecules measurable on the attosecond time scale and open new avenues for laser control of electronic primary processes."}],"intvolume":" 635","month":"07","main_file_link":[{"url":"https://doi.org/10.1088/1742-6596/635/11/112136","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1742-6588"],"eissn":["1742-6596"]},"volume":635,"issue":"11","_id":"14015","keyword":["General Physics and Astronomy"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-22T08:49:14Z","oa":1,"publisher":"IOP Publishing","quality_controlled":"1","publication":"Journal of Physics: Conference Series","day":"01","year":"2015","date_created":"2023-08-10T06:37:53Z","doi":"10.1088/1742-6596/635/11/112136","date_published":"2015-07-01T00:00:00Z","article_number":"112136","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015. Attosecond charge migration and its laser control. Journal of Physics: Conference Series. 635(11), 112136.","chicago":"Kraus, P M, B Mignolet, Denitsa Rangelova Baykusheva, A Rupenyan, L Horný, E F Penka, O I Tolstikhin, et al. “Attosecond Charge Migration and Its Laser Control.” Journal of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112136.","ama":"Kraus PM, Mignolet B, Baykusheva DR, et al. Attosecond charge migration and its laser control. Journal of Physics: Conference Series. 2015;635(11). doi:10.1088/1742-6596/635/11/112136","apa":"Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka, E. F., … Wörner, H. J. (2015). Attosecond charge migration and its laser control. Journal of Physics: Conference Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112136","ieee":"P. M. Kraus et al., “Attosecond charge migration and its laser control,” Journal of Physics: Conference Series, vol. 635, no. 11. IOP Publishing, 2015.","short":"P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle, H.J. Wörner, Journal of Physics: Conference Series 635 (2015).","mla":"Kraus, P. M., et al. “Attosecond Charge Migration and Its Laser Control.” Journal of Physics: Conference Series, vol. 635, no. 11, 112136, IOP Publishing, 2015, doi:10.1088/1742-6596/635/11/112136."},"title":"Attosecond charge migration and its laser control","article_processing_charge":"No","author":[{"first_name":"P M","full_name":"Kraus, P M","last_name":"Kraus"},{"first_name":"B","last_name":"Mignolet","full_name":"Mignolet, B"},{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"full_name":"Rupenyan, A","last_name":"Rupenyan","first_name":"A"},{"full_name":"Horný, L","last_name":"Horný","first_name":"L"},{"first_name":"E F","last_name":"Penka","full_name":"Penka, E F"},{"last_name":"Tolstikhin","full_name":"Tolstikhin, O I","first_name":"O I"},{"full_name":"Schneider, J","last_name":"Schneider","first_name":"J"},{"full_name":"Jensen, F","last_name":"Jensen","first_name":"F"},{"first_name":"L B","last_name":"Madsen","full_name":"Madsen, L B"},{"last_name":"Bandrauk","full_name":"Bandrauk, A D","first_name":"A D"},{"first_name":"F","last_name":"Remacle","full_name":"Remacle, F"},{"first_name":"H J","full_name":"Wörner, H J","last_name":"Wörner"}]},{"issue":"11","volume":635,"publication_status":"published","publication_identifier":{"eissn":["1742-6596"],"issn":["1742-6588"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/1742-6596/635/11/112135"}],"scopus_import":"1","intvolume":" 635","month":"11","abstract":[{"lang":"eng","text":"We have studied a coupled electronic-nuclear wave packet in nitric oxide using time-resolved strong-field photoelectron holography and rescattering. We show that the electronic dynamics mainly appears in the holographic structures whereas nuclear motion strongly modulates the angular distribution of the rescattered photoelectrons."}],"oa_version":"Published Version","date_updated":"2023-08-22T08:51:33Z","extern":"1","article_type":"original","type":"journal_article","keyword":["General Physics and Astronomy"],"status":"public","_id":"14014","date_created":"2023-08-10T06:37:44Z","date_published":"2015-11-01T00:00:00Z","doi":"10.1088/1742-6596/635/11/112135","year":"2015","publication":"Journal of Physics: Conference Series","day":"01","oa":1,"publisher":"IOP Publishing","quality_controlled":"1","article_processing_charge":"No","author":[{"first_name":"Samuel G","last_name":"Walt","full_name":"Walt, Samuel G"},{"full_name":"Ram, N Bhargava","last_name":"Ram","first_name":"N Bhargava"},{"first_name":"Aaron","last_name":"von Conta","full_name":"von Conta, Aaron"},{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"full_name":"Atala, Marcos","last_name":"Atala","first_name":"Marcos"},{"full_name":"Wörner, Hans Jakob","last_name":"Wörner","first_name":"Hans Jakob"}],"title":"Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography","citation":{"ista":"Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. 2015. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. 635(11), 112135.","chicago":"Walt, Samuel G, N Bhargava Ram, Aaron von Conta, Denitsa Rangelova Baykusheva, Marcos Atala, and Hans Jakob Wörner. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” Journal of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112135.","ama":"Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. 2015;635(11). doi:10.1088/1742-6596/635/11/112135","apa":"Walt, S. G., Ram, N. B., von Conta, A., Baykusheva, D. R., Atala, M., & Wörner, H. J. (2015). Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112135","ieee":"S. G. Walt, N. B. Ram, A. von Conta, D. R. Baykusheva, M. Atala, and H. J. Wörner, “Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography,” Journal of Physics: Conference Series, vol. 635, no. 11. IOP Publishing, 2015.","short":"S.G. Walt, N.B. Ram, A. von Conta, D.R. Baykusheva, M. Atala, H.J. Wörner, Journal of Physics: Conference Series 635 (2015).","mla":"Walt, Samuel G., et al. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” Journal of Physics: Conference Series, vol. 635, no. 11, 112135, IOP Publishing, 2015, doi:10.1088/1742-6596/635/11/112135."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"112135"},{"year":"2015","day":"21","date_created":"2021-07-26T08:44:04Z","related_material":{"record":[{"relation":"used_in_publication","id":"5749","status":"public"}]},"doi":"10.5061/dryad.cj910","date_published":"2015-12-21T00:00:00Z","abstract":[{"text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.","lang":"eng"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cj910"}],"publisher":"Dryad","month":"12","citation":{"apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., & Hall, A. R. (2015). Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. Dryad. https://doi.org/10.5061/dryad.cj910","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. 2015. doi:10.5061/dryad.cj910","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, (2015).","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria.” Dryad, 2015.","mla":"Wielgoss, Sébastien, et al. Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria. Dryad, 2015, doi:10.5061/dryad.cj910.","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2015. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria, Dryad, 10.5061/dryad.cj910.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria.” Dryad, 2015. https://doi.org/10.5061/dryad.cj910."},"date_updated":"2023-09-05T13:46:04Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Sébastien","full_name":"Wielgoss, Sébastien","last_name":"Wielgoss"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bischofberger, Anna M.","last_name":"Bischofberger","first_name":"Anna M."},{"last_name":"Hall","full_name":"Hall, Alex R.","first_name":"Alex R."}],"department":[{"_id":"CaGu"}],"title":"Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria","_id":"9719","type":"research_data_reference","status":"public"},{"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_created":"2021-02-22T11:33:17Z","file_name":"2015_Thesis_Sharmanska.pdf","creator":"dernst","date_updated":"2021-02-22T11:33:17Z","file_size":7964342,"file_id":"9177","checksum":"3605b402bb6934e09ae4cf672c84baf7","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_id":"10297","checksum":"e37593b3ee75bf3180629df2d6ca8f4e","content_type":"application/pdf","access_level":"closed","relation":"main_file","date_created":"2021-11-16T14:40:45Z","file_name":"2015_Thesis_Sharmanska_pdfa.pdf","date_updated":"2021-11-17T13:47:24Z","file_size":7372241,"creator":"cchlebak"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"main_file_link":[{"url":"http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf"}],"month":"04","supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"date_updated":"2023-09-07T11:40:11Z","ddc":["000"],"file_date_updated":"2021-11-17T13:47:24Z","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"_id":"1401","type":"dissertation","status":"public","has_accepted_license":"1","year":"2015","day":"01","page":"144","date_published":"2015-04-01T00:00:00Z","doi":"10.15479/at:ista:1401","date_created":"2018-12-11T11:51:48Z","acknowledgement":"I would like to thank my supervisor, Christoph Lampert, for guidance throughout my studies and for patience in transforming me into a scientist, and my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice. \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative needs and was always nice and friendly to me, and the campus team for making the IST Austria campus my second home. \r\nI was honored to collaborate with brilliant researchers and to learn from their experience. Undoubtedly, I learned most of all from Novi Quadrianto: brainstorming our projects and getting exciting results was the most enjoyable part of my work – thank you! I am also grateful to David Knowles, Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina for the fantastic projects we worked on together, and to Kristen Grauman and Adriana Kovashka for the exceptional experience working with user studies. I would like to thank my colleagues at IST Austria and my office mates who shared their happy moods, scientific breakthroughs and thought-provoking conversations with me: Chao, Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina, Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael, Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games of table soccer we played together and the tournaments we teamed up for: we will definitely win next time:) A very warm hug to Asya for always being so inspiring and supportive to me, and for helping me to increase the proportion of female computer scientists in our group. ","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"ista":"Sharmanska V. 2015. Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria.","chicago":"Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/at:ista:1401.","short":"V. Sharmanska, Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.","ieee":"V. Sharmanska, “Learning with attributes for object recognition: Parametric and non-parametrics views,” Institute of Science and Technology Austria, 2015.","ama":"Sharmanska V. Learning with attributes for object recognition: Parametric and non-parametrics views. 2015. doi:10.15479/at:ista:1401","apa":"Sharmanska, V. (2015). Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1401","mla":"Sharmanska, Viktoriia. Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views. Institute of Science and Technology Austria, 2015, doi:10.15479/at:ista:1401."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Sharmanska","orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","first_name":"Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5806","article_processing_charge":"No","title":"Learning with attributes for object recognition: Parametric and non-parametrics views"},{"day":"15","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","year":"2015","date_published":"2015-07-15T00:00:00Z","doi":"10.1098/rspb.2015.1041","date_created":"2018-12-11T11:53:35Z","acknowledgement":"This work was supported by grants from the John Templeton Foundation, ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE), FWF Grant (No P23499N23) and a Microsoft faculty fellows award.","publisher":"Royal Society","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812, Royal Society, 2015, doi:10.1098/rspb.2015.1041.","apa":"Reiter, J., Kanodia, A., Gupta, R., Nowak, M., & Chatterjee, K. (2015). Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society. https://doi.org/10.1098/rspb.2015.1041","ama":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 2015;282(1812). doi:10.1098/rspb.2015.1041","ieee":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological auctions with multiple rewards,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812. Royal Society, 2015.","short":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","chicago":"Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu Chatterjee. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rspb.2015.1041.","ista":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1812)."},"title":"Biological auctions with multiple rewards","author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"},{"full_name":"Gupta, Raghav","last_name":"Gupta","first_name":"Raghav"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"publist_id":"5425","article_processing_charge":"No","external_id":{"pmid":["26180069"]},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":282,"issue":"1812","related_material":{"record":[{"status":"public","id":"1400","relation":"dissertation_contains"}]},"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards."}],"month":"07","intvolume":" 282","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/"}],"date_updated":"2023-09-07T11:40:43Z","department":[{"_id":"KrCh"}],"_id":"1709","status":"public","article_type":"original","type":"journal_article"},{"page":"183","date_created":"2018-12-11T11:51:48Z","date_published":"2015-04-01T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"1709","status":"public"},{"status":"public","id":"2000","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2247"},{"id":"2816","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"2858","relation":"part_of_dissertation"},{"status":"public","id":"3157","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"3260","status":"public"}]},"degree_awarded":"PhD","year":"2015","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"day":"01","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"month":"04","abstract":[{"lang":"eng","text":"Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease."}],"oa_version":"None","article_processing_charge":"No","publist_id":"5807","author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter"}],"department":[{"_id":"KrCh"}],"title":"The subclonal evolution of cancer","date_updated":"2023-09-07T11:40:44Z","citation":{"mla":"Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science and Technology Austria, 2015.","ama":"Reiter J. The subclonal evolution of cancer. 2015.","apa":"Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science and Technology Austria.","short":"J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology Austria, 2015.","ieee":"J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015.","chicago":"Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015.","ista":"Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria."},"supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","status":"public","_id":"1400"},{"status":"public","type":"journal_article","_id":"1792","title":"A Koksma-Hlawka inequality for general discrepancy systems","department":[{"_id":"HeEd"}],"publist_id":"5320","author":[{"last_name":"Pausinger","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Svane","full_name":"Svane, Anne","first_name":"Anne"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T11:41:25Z","citation":{"ista":"Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 31(6), 773–797.","chicago":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity. Academic Press, 2015. https://doi.org/10.1016/j.jco.2015.06.002.","ama":"Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 2015;31(6):773-797. doi:10.1016/j.jco.2015.06.002","apa":"Pausinger, F., & Svane, A. (2015). A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.06.002","ieee":"F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy systems,” Journal of Complexity, vol. 31, no. 6. Academic Press, pp. 773–797, 2015.","short":"F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797.","mla":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity, vol. 31, no. 6, Academic Press, 2015, pp. 773–97, doi:10.1016/j.jco.2015.06.002."},"month":"12","intvolume":" 31","quality_controlled":"1","publisher":"Academic Press","scopus_import":1,"oa_version":"None","acknowledgement":"F.P. is supported by the Graduate School of IST Austria, A.M.S is supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by a grant from the Villum Foundation.","abstract":[{"lang":"eng","text":"Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology."}],"related_material":{"record":[{"status":"public","id":"1399","relation":"dissertation_contains"}]},"volume":31,"doi":"10.1016/j.jco.2015.06.002","date_published":"2015-12-01T00:00:00Z","issue":"6","date_created":"2018-12-11T11:54:02Z","page":"773 - 797","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Complexity","year":"2015","publication_status":"published"},{"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","month":"06","abstract":[{"lang":"eng","text":"This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold."}],"oa_version":"None","page":"144","date_created":"2018-12-11T11:51:48Z","date_published":"2015-06-01T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"1662","status":"public"},{"status":"public","id":"1792","relation":"part_of_dissertation"},{"id":"2255","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","degree_awarded":"PhD","year":"2015","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"day":"01","type":"dissertation","status":"public","_id":"1399","article_processing_charge":"No","author":[{"first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768"}],"publist_id":"5808","title":"On the approximation of intrinsic volumes","department":[{"_id":"HeEd"}],"date_updated":"2023-09-07T11:41:25Z","citation":{"short":"F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015.","ieee":"F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science and Technology Austria, 2015.","apa":"Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","ama":"Pausinger F. On the approximation of intrinsic volumes. 2015.","mla":"Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute of Science and Technology Austria, 2015.","ista":"Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","chicago":"Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute of Science and Technology Austria, 2015."},"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"month":"11","intvolume":" 11","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.","lang":"eng"}],"issue":"11","volume":11,"related_material":{"record":[{"id":"9712","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"1131","status":"public"}]},"ec_funded":1,"file":[{"date_created":"2018-12-12T10:07:58Z","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","date_updated":"2020-07-14T12:45:10Z","file_size":2580778,"creator":"system","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","file_id":"4657","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"463","type":"journal_article","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)"},"_id":"1666","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:10Z","ddc":["576"],"date_updated":"2023-09-07T11:53:49Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"date_published":"2015-11-06T00:00:00Z","doi":"10.1371/journal.pgen.1005639","date_created":"2018-12-11T11:53:21Z","day":"06","publication":"PLoS Genetics","has_accepted_license":"1","year":"2015","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"title":"Dynamics of transcription factor binding site evolution","author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","last_name":"Tugrul"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5483","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11)."}},{"_id":"1502","conference":{"name":"CBSE: Component-Based Software Engineering ","end_date":"2015-05-08","location":"Montreal, QC, Canada","start_date":"2015-05-04"},"type":"conference","pubrep_id":"625","status":"public","date_updated":"2023-09-07T11:58:33Z","ddc":["000"],"file_date_updated":"2020-07-14T12:44:59Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system."}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering "],"month":"05","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-3471-6"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf","date_created":"2018-12-12T10:17:46Z","file_size":467561,"date_updated":"2020-07-14T12:44:59Z","creator":"system","checksum":"c6ce681035c163a158751f240cb7d389","file_id":"5303","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1155"}]},"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Beneš, Nikola, et al. Complete Composition Operators for IOCO-Testing Theory. ACM, 2015, pp. 101–10, doi:10.1145/2737166.2737175.","ama":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:10.1145/2737166.2737175","apa":"Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., & Nickovic, D. (2015). Complete composition operators for IOCO-testing theory (pp. 101–110). Presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM. https://doi.org/10.1145/2737166.2737175","ieee":"N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.","short":"N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015, pp. 101–110.","chicago":"Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10. ACM, 2015. https://doi.org/10.1145/2737166.2737175.","ista":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition operators for IOCO-testing theory. CBSE: Component-Based Software Engineering , Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering , , 101–110."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Nikola","full_name":"Beneš, Nikola","last_name":"Beneš"},{"id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","last_name":"Daca"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"publist_id":"5676","title":"Complete composition operators for IOCO-testing theory","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373 (nSafeCer). Jan Křetínský has been partially supported by the Czech Science Foundation, grant No. P202/12/G061. Nikola Beneš has been supported by the\r\nMEYS project No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for Scientific Excellence.","oa":1,"quality_controlled":"1","publisher":"ACM","year":"2015","has_accepted_license":"1","day":"01","page":"101 - 110","date_created":"2018-12-11T11:52:24Z","date_published":"2015-05-01T00:00:00Z","doi":"10.1145/2737166.2737175"},{"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE), and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).","date_created":"2018-12-11T11:52:23Z","doi":"10.1007/s10703-015-0235-2","date_published":"2015-10-01T00:00:00Z","page":"230 - 264","publication":"Formal Methods in System Design","day":"01","year":"2015","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","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"title":"CEGAR for compositional analysis of qualitative properties in Markov decision processes","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","full_name":"Daca, Przemyslaw"}],"publist_id":"5677","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 47(2), 230–264.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design. Springer, 2015. https://doi.org/10.1007/s10703-015-0235-2.","short":"K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015) 230–264.","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis of qualitative properties in Markov decision processes,” Formal Methods in System Design, vol. 47, no. 2. Springer, pp. 230–264, 2015.","apa":"Chatterjee, K., Chmelik, M., & Daca, P. (2015). CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-015-0235-2","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 2015;47(2):230-264. doi:10.1007/s10703-015-0235-2","mla":"Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design, vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:10.1007/s10703-015-0235-2."},"intvolume":" 47","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1405.0835"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. ","lang":"eng"}],"ec_funded":1,"issue":"2","related_material":{"record":[{"id":"1155","status":"public","relation":"dissertation_contains"}]},"volume":47,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"1501","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-07T11:58:33Z"},{"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices, vol. 50, no. 1, ACM, 2015, pp. 97–109, doi:10.1145/2676726.2676979.","apa":"Chatterjee, K., Ibsen-Jensen, R., Pavlogiannis, A., & Goyal, P. (2015). Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676979","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 2015;50(1):97-109. doi:10.1145/2676726.2676979","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, and P. Goyal, “Faster algorithms for algebraic path properties in recursive state machines with constant treewidth,” ACM SIGPLAN Notices, vol. 50, no. 1. ACM, pp. 97–109, 2015.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, P. Goyal, ACM SIGPLAN Notices 50 (2015) 97–109.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Andreas Pavlogiannis, and Prateesh Goyal. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices. ACM, 2015. https://doi.org/10.1145/2676726.2676979.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. 2015. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 50(1), 97–109."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Prateesh","full_name":"Goyal, Prateesh","last_name":"Goyal"}],"publist_id":"5565","external_id":{"arxiv":["1410.7724"]},"title":"Faster algorithms for algebraic path properties in recursive state machines with constant treewidth","acknowledgement":"We thank anonymous reviewers for helpful comments to improve the presentation of the paper.","publisher":"ACM","quality_controlled":"1","oa":1,"year":"2015","day":"01","publication":"ACM SIGPLAN Notices","page":"97 - 109","doi":"10.1145/2676726.2676979","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:52:58Z","_id":"1602","type":"journal_article","conference":{"name":"SIGPLAN: Symposium on Principles of Programming Languages","start_date":"2015-01-15","location":"Mumbai, India","end_date":"2015-01-17"},"status":"public","date_updated":"2023-09-07T12:01:58Z","department":[{"_id":"KrCh"}],"abstract":[{"text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, etc. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring, and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, etc. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in a very important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect that we consider is that the control flow graphs for most programs have constant treewidth. Our main contributions are simple and implementable algorithms that supportmultiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing, but can answer subsequent queries significantly faster as compared to the current best-known solutions for several important problems, such as interprocedural reachability and shortest path. We provide a prototype implementation for interprocedural reachability and intraprocedural shortest path that gives a significant speed-up on several benchmarks.","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1410.7724","open_access":"1"}],"month":"01","intvolume":" 50","publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":50,"related_material":{"record":[{"status":"public","id":"821","relation":"dissertation_contains"}]},"ec_funded":1},{"related_material":{"record":[{"relation":"earlier_version","id":"5445","status":"public"},{"status":"public","id":"821","relation":"dissertation_contains"}]},"volume":50,"issue":"1","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-3300-9"]},"publication_status":"published","month":"01","intvolume":" 50","scopus_import":1,"oa_version":"None","abstract":[{"text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs.","lang":"eng"}],"department":[{"_id":"KrCh"}],"date_updated":"2023-09-07T12:01:59Z","status":"public","pubrep_id":"523","type":"journal_article","conference":{"name":"SIGPLAN: Symposium on Principles of Programming Languages","location":"Mumbai, India","end_date":"2015-01-17","start_date":"2015-01-15"},"_id":"1604","date_published":"2015-01-01T00:00:00Z","doi":"10.1145/2676726.2676968","date_created":"2018-12-11T11:52:59Z","page":"539 - 551","day":"01","publication":"Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT ","year":"2015","quality_controlled":"1","publisher":"ACM","title":"Quantitative interprocedural analysis","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"publist_id":"5563","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . ACM, 2015. https://doi.org/10.1145/2676726.2676968.","apa":"Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2015). Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676968","ama":"Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 2015;50(1):539-551. doi:10.1145/2676726.2676968","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural analysis,” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1. ACM, pp. 539–551, 2015.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT 50 (2015) 539–551.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1, ACM, 2015, pp. 539–51, doi:10.1145/2676726.2676968."},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}]},{"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","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in constant treewidth graphs,” presented at the CAV: Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp. 140–157.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157. doi:10.1007/978-3-319-21690-4_9","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157). Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer. https://doi.org/10.1007/978-3-319-21690-4_9","mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification, LNCS, vol. 9206, 140–157.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,” 9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9."},"title":"Faster algorithms for quantitative verification in constant treewidth graphs","publist_id":"5560","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","oa":1,"publisher":"Springer","quality_controlled":"1","day":"16","year":"2015","date_created":"2018-12-11T11:52:59Z","date_published":"2015-07-16T00:00:00Z","doi":"10.1007/978-3-319-21690-4_9","page":"140 - 157","_id":"1607","status":"public","conference":{"name":"CAV: Computer Aided Verification","location":"San Francisco, CA, USA","end_date":"2015-07-24","start_date":"2015-07-18"},"type":"conference","date_updated":"2023-09-07T12:01:59Z","department":[{"_id":"KrCh"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W)) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks."}],"intvolume":" 9206","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.07384"}],"alternative_title":["LNCS"],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"status":"public","id":"5430","relation":"earlier_version"},{"id":"5437","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"821"}]},"volume":9206},{"publication":"Real-Time Systems Symposium","day":"15","year":"2015","date_created":"2018-12-11T11:53:37Z","date_published":"2015-01-15T00:00:00Z","doi":"10.1109/RTSS.2014.9","page":"118 - 127","quality_controlled":"1","publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” Real-Time Systems Symposium, vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:10.1109/RTSS.2014.9.","short":"K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems Symposium, IEEE, 2015, pp. 118–127.","ieee":"K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks,” in Real-Time Systems Symposium, Rome, Italy, 2015, vol. 2015, no. January, pp. 118–127.","ama":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In: Real-Time Systems Symposium. Vol 2015. IEEE; 2015:118-127. doi:10.1109/RTSS.2014.9","apa":"Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2015). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In Real-Time Systems Symposium (Vol. 2015, pp. 118–127). Rome, Italy: IEEE. https://doi.org/10.1109/RTSS.2014.9","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” In Real-Time Systems Symposium, 2015:118–27. IEEE, 2015. https://doi.org/10.1109/RTSS.2014.9.","ista":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127."},"title":"A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks","article_processing_charge":"No","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"first_name":"Alexander","last_name":"Kößler","full_name":"Kößler, Alexander"},{"full_name":"Schmid, Ulrich","last_name":"Schmid","first_name":"Ulrich"}],"publist_id":"5417","language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"id":"5423","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"821"}]},"issue":"January","volume":2015,"oa_version":"None","abstract":[{"lang":"eng","text":"We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application."}],"intvolume":" 2015","month":"01","scopus_import":1,"date_updated":"2023-09-07T12:01:59Z","department":[{"_id":"KrCh"}],"_id":"1714","status":"public","conference":{"name":"RTSS: Real-Time Systems Symposium","end_date":"2014-12-05","location":"Rome, Italy","start_date":"2014-12-02"},"type":"conference"},{"intvolume":" 34","month":"07","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix.","lang":"eng"}],"ec_funded":1,"related_material":{"record":[{"id":"839","status":"public","relation":"dissertation_contains"}]},"volume":34,"issue":"4","language":[{"iso":"eng"}],"file":[{"file_id":"5131","checksum":"955aee971983f6b6152bcc1c9b4a7c20","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:15:13Z","file_name":"IST-2016-609-v1+1_FractureBEM.pdf","creator":"system","date_updated":"2020-07-14T12:45:07Z","file_size":20154270}],"publication_status":"published","pubrep_id":"609","status":"public","conference":{"start_date":"2015-08-09","location":"Los Angeles, CA, United States","end_date":"2015-08-13","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"type":"conference","_id":"1633","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:07Z","ddc":["000"],"date_updated":"2023-09-07T12:02:56Z","oa":1,"publisher":"ACM","quality_controlled":"1","date_created":"2018-12-11T11:53:09Z","date_published":"2015-07-27T00:00:00Z","doi":"10.1145/2766896","day":"27","year":"2015","has_accepted_license":"1","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"151","title":"High-resolution brittle fracture simulation with boundary elements","publist_id":"5522","author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Hahn, David","last_name":"Hahn"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 151.","chicago":"Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.","short":"D. Hahn, C. Wojtan, in:, ACM, 2015.","ieee":"D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","ama":"Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896","apa":"Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766896","mla":"Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896."}},{"acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","publisher":"Cell Press","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"12","publication":"Cell","page":"673 - 685","date_published":"2015-02-12T00:00:00Z","doi":"10.1016/j.cell.2015.01.008","date_created":"2018-12-11T11:52:35Z","project":[{"call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","grant_number":"I 812-B12","call_identifier":"FWF","_id":"2527D5CC-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:10.1016/j.cell.2015.01.008.","short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685.","ieee":"V. Ruprecht et al., “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” Cell, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.008","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 2015;160(4):673-685. doi:10.1016/j.cell.2015.01.008","chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.008.","ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ruprecht","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Wieser","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan"},{"full_name":"Callan Jones, Andrew","last_name":"Callan Jones","first_name":"Andrew"},{"first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090","last_name":"Smutny"},{"full_name":"Morita, Hitoshi","last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi"},{"last_name":"Sako","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","first_name":"Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barone","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"first_name":"Monika","full_name":"Ritsch Marte, Monika","last_name":"Ritsch Marte"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"publist_id":"5634","title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","abstract":[{"lang":"eng","text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype."}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","scopus_import":1,"month":"02","intvolume":" 160","publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:01Z","file_size":4362653,"creator":"system","date_created":"2018-12-12T10:13:21Z","file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"228d3edf40627d897b3875088a0ac51f","file_id":"5003"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"961","status":"public","relation":"dissertation_contains"}]},"volume":160,"issue":"4","_id":"1537","type":"journal_article","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)"},"status":"public","pubrep_id":"484","date_updated":"2023-09-07T12:05:08Z","ddc":["570"],"department":[{"_id":"CaHe"},{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:01Z"},{"department":[{"_id":"JiFr"}],"date_updated":"2023-09-07T12:06:09Z","type":"journal_article","status":"public","_id":"1591","volume":27,"issue":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"938","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/"}],"month":"01","intvolume":" 27","abstract":[{"text":"Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","author":[{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5580","external_id":{"pmid":["25604445"]},"title":"PIN-dependent auxin transport: Action, regulation, and evolution","citation":{"mla":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874.","apa":"Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.134874","ama":"Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874","ieee":"M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation, and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists, pp. 20–32, 2015.","short":"M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.","chicago":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists, 2015. https://doi.org/10.1105/tpc.114.134874.","ista":"Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 27(1), 20–32."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"20 - 32","date_published":"2015-01-20T00:00:00Z","doi":"10.1105/tpc.114.134874","date_created":"2018-12-11T11:52:54Z","year":"2015","day":"20","publication":"Plant Cell","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1}]