[{"date_updated":"2022-01-24T12:43:13Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2017","oa":1,"publication_identifier":{"issn":["0169-3298","1573-0956"]},"volume":38,"type":"journal_article","date_created":"2021-02-15T14:20:38Z","date_published":"2017-11-01T00:00:00Z","author":[{"last_name":"Holloway","full_name":"Holloway, Christopher E.","first_name":"Christopher E."},{"first_name":"Allison A.","full_name":"Wing, Allison A.","last_name":"Wing"},{"full_name":"Bony, Sandrine","first_name":"Sandrine","last_name":"Bony"},{"last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"},{"last_name":"Masunaga","first_name":"Hirohiko","full_name":"Masunaga, Hirohiko"},{"first_name":"Tristan S.","full_name":"L’Ecuyer, Tristan S.","last_name":"L’Ecuyer"},{"first_name":"David D.","full_name":"Turner, David D.","last_name":"Turner"},{"last_name":"Zuidema","first_name":"Paquita","full_name":"Zuidema, Paquita"}],"quality_controlled":"1","article_processing_charge":"No","publication_status":"published","intvolume":" 38","month":"11","language":[{"iso":"eng"}],"status":"public","_id":"9138","oa_version":"Published Version","article_type":"original","citation":{"chicago":"Holloway, Christopher E., Allison A. Wing, Sandrine Bony, Caroline J Muller, Hirohiko Masunaga, Tristan S. L’Ecuyer, David D. Turner, and Paquita Zuidema. “Observing Convective Aggregation.” Surveys in Geophysics. Springer Nature, 2017. https://doi.org/10.1007/s10712-017-9419-1.","apa":"Holloway, C. E., Wing, A. A., Bony, S., Muller, C. J., Masunaga, H., L’Ecuyer, T. S., … Zuidema, P. (2017). Observing convective aggregation. Surveys in Geophysics. Springer Nature. https://doi.org/10.1007/s10712-017-9419-1","mla":"Holloway, Christopher E., et al. “Observing Convective Aggregation.” Surveys in Geophysics, vol. 38, no. 6, Springer Nature, 2017, pp. 1199–236, doi:10.1007/s10712-017-9419-1.","short":"C.E. Holloway, A.A. Wing, S. Bony, C.J. Muller, H. Masunaga, T.S. L’Ecuyer, D.D. Turner, P. Zuidema, Surveys in Geophysics 38 (2017) 1199–1236.","ista":"Holloway CE, Wing AA, Bony S, Muller CJ, Masunaga H, L’Ecuyer TS, Turner DD, Zuidema P. 2017. Observing convective aggregation. Surveys in Geophysics. 38(6), 1199–1236.","ama":"Holloway CE, Wing AA, Bony S, et al. Observing convective aggregation. Surveys in Geophysics. 2017;38(6):1199-1236. doi:10.1007/s10712-017-9419-1","ieee":"C. E. Holloway et al., “Observing convective aggregation,” Surveys in Geophysics, vol. 38, no. 6. Springer Nature, pp. 1199–1236, 2017."},"title":"Observing convective aggregation","day":"01","publication":"Surveys in Geophysics","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1007/s10712-017-9419-1","open_access":"1"}],"extern":"1","doi":"10.1007/s10712-017-9419-1","keyword":["Geochemistry and Petrology","Geophysics"],"page":"1199-1236","abstract":[{"lang":"eng","text":"Convective self-aggregation, the spontaneous organization of initially scattered convection into isolated convective clusters despite spatially homogeneous boundary conditions and forcing, was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network."}],"issue":"6"},{"publication_identifier":{"issn":["0169-3298","1573-0956"]},"volume":38,"type":"journal_article","date_created":"2021-02-15T14:20:56Z","extern":"1","doi":"10.1007/s10712-017-9408-4","date_published":"2017-11-01T00:00:00Z","keyword":["Geochemistry and Petrology","Geophysics"],"date_updated":"2022-01-24T12:42:36Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Wing AA, Emanuel K, Holloway CE, Muller CJ. Convective self-aggregation in numerical simulations: A review. Surveys in Geophysics. 2017;38(6):1173-1197. doi:10.1007/s10712-017-9408-4","ieee":"A. A. Wing, K. Emanuel, C. E. Holloway, and C. J. Muller, “Convective self-aggregation in numerical simulations: A review,” Surveys in Geophysics, vol. 38, no. 6. Springer Nature, pp. 1173–1197, 2017.","ista":"Wing AA, Emanuel K, Holloway CE, Muller CJ. 2017. Convective self-aggregation in numerical simulations: A review. Surveys in Geophysics. 38(6), 1173–1197.","apa":"Wing, A. A., Emanuel, K., Holloway, C. E., & Muller, C. J. (2017). Convective self-aggregation in numerical simulations: A review. Surveys in Geophysics. Springer Nature. https://doi.org/10.1007/s10712-017-9408-4","short":"A.A. Wing, K. Emanuel, C.E. Holloway, C.J. Muller, Surveys in Geophysics 38 (2017) 1173–1197.","mla":"Wing, Allison A., et al. “Convective Self-Aggregation in Numerical Simulations: A Review.” Surveys in Geophysics, vol. 38, no. 6, Springer Nature, 2017, pp. 1173–97, doi:10.1007/s10712-017-9408-4.","chicago":"Wing, Allison A., Kerry Emanuel, Christopher E. Holloway, and Caroline J Muller. “Convective Self-Aggregation in Numerical Simulations: A Review.” Surveys in Geophysics. Springer Nature, 2017. https://doi.org/10.1007/s10712-017-9408-4."},"year":"2017","title":"Convective self-aggregation in numerical simulations: A review","day":"01","publication":"Surveys in Geophysics","publisher":"Springer Nature","publication_status":"published","month":"11","intvolume":" 38","language":[{"iso":"eng"}],"status":"public","oa_version":"None","_id":"9139","article_type":"original","issue":"6","author":[{"first_name":"Allison A.","full_name":"Wing, Allison A.","last_name":"Wing"},{"last_name":"Emanuel","full_name":"Emanuel, Kerry","first_name":"Kerry"},{"last_name":"Holloway","first_name":"Christopher E.","full_name":"Holloway, Christopher E."},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","first_name":"Caroline J"}],"page":"1173-1197","quality_controlled":"1","abstract":[{"text":"Organized convection in the tropics occurs across a range of spatial and temporal scales and strongly influences cloud cover and humidity. One mode of organization found is “self-aggregation,” in which moist convection spontaneously organizes into one or several isolated clusters despite spatially homogeneous boundary conditions and forcing. Self-aggregation is driven by interactions between clouds, moisture, radiation, surface fluxes, and circulation, and occurs in a wide variety of idealized simulations of radiative–convective equilibrium. Here we provide a review of convective self-aggregation in numerical simulations, including its character, causes, and effects. We describe the evolution of self-aggregation including its time and length scales and the physical mechanisms leading to its triggering and maintenance, and we also discuss possible links to climate and climate change.","lang":"eng"}],"article_processing_charge":"No"},{"year":"2017","date_updated":"2023-09-26T15:45:47Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","oa":1,"type":"journal_article","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:49:10Z","publication_identifier":{"issn":["20545703"]},"publist_id":"6527","volume":4,"date_published":"2017-07-05T00:00:00Z","has_accepted_license":"1","quality_controlled":"1","author":[{"last_name":"Giehr","first_name":"Julia","full_name":"Giehr, Julia"},{"full_name":"Grasse, Anna V","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"last_name":"Heinze","first_name":"Jürgen","full_name":"Heinze, Jürgen"},{"first_name":"Alexandra","full_name":"Schrempf, Alexandra","last_name":"Schrempf"}],"article_processing_charge":"No","acknowledgement":"We thank two anonymous reviewers for helpful suggestions on the manuscript.","file_date_updated":"2020-07-14T12:48:15Z","status":"public","_id":"914","oa_version":"Published Version","month":"07","external_id":{"isi":["000406670000025"]},"publication_status":"published","intvolume":" 4","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","title":"Ant queens increase their reproductive efforts after pathogen infection","related_material":{"record":[{"relation":"research_data","status":"public","id":"9853"}]},"citation":{"ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 4(7), 170547.","ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 2017;4(7). doi:10.1098/rsos.170547","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens increase their reproductive efforts after pathogen infection,” Royal Society Open Science, vol. 4, no. 7. Royal Society, The, 2017.","chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science. Royal Society, The, 2017. https://doi.org/10.1098/rsos.170547.","mla":"Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science, vol. 4, no. 7, 170547, Royal Society, The, 2017, doi:10.1098/rsos.170547.","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open Science 4 (2017).","apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017). Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.170547"},"publication":"Royal Society Open Science","publisher":"Royal Society, The","department":[{"_id":"SyCr"}],"day":"05","isi":1,"doi":"10.1098/rsos.170547","file":[{"checksum":"351ae5e7a37e6e7d9295cd41146c4190","relation":"main_file","creator":"system","access_level":"open_access","content_type":"application/pdf","file_size":530412,"file_id":"4684","date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf","date_created":"2018-12-12T10:08:24Z"}],"abstract":[{"text":"Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect.","lang":"eng"}],"ddc":["576","592"],"article_number":"170547","pubrep_id":"849","issue":"7"},{"ddc":["000"],"file":[{"date_created":"2019-01-18T12:52:46Z","file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf","date_updated":"2020-07-14T12:48:15Z","file_id":"5849","file_size":883264,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","checksum":"7e51dacefa693574581a32da3eff63dc"}],"page":"4990-4999","abstract":[{"text":"We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining.","lang":"eng"}],"isi":1,"doi":"10.1109/CVPR.2017.530","title":"A message passing algorithm for the minimum cost multicut problem","citation":{"apa":"Swoboda, P., & Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.530","mla":"Swoboda, Paul, and Bjoern Andres. A Message Passing Algorithm for the Minimum Cost Multicut Problem. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:10.1109/CVPR.2017.530.","short":"P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.","chicago":"Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.530.","ieee":"P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.","ama":"Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:10.1109/CVPR.2017.530","ista":"Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999."},"publisher":"IEEE","department":[{"_id":"VlKo"}],"day":"01","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:48:15Z","status":"public","_id":"915","oa_version":"Submitted Version","publication_status":"published","month":"07","external_id":{"isi":["000418371405009"]},"intvolume":" 2017","language":[{"iso":"eng"}],"conference":{"start_date":"2017-07-21","end_date":"2017-07-26","location":"Honolulu, HA, United States","name":"CVPR: Computer Vision and Pattern Recognition"},"quality_controlled":"1","author":[{"last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","full_name":"Swoboda, Paul"},{"full_name":"Andres, Bjoern","first_name":"Bjoern","last_name":"Andres"}],"article_processing_charge":"No","type":"conference","date_created":"2018-12-11T11:49:11Z","publication_identifier":{"isbn":["978-153860457-1"]},"volume":2017,"publist_id":"6526","date_published":"2017-07-01T00:00:00Z","has_accepted_license":"1","year":"2017","date_updated":"2023-09-26T15:43:27Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","ec_funded":1,"oa":1},{"keyword":["Oceanography"],"extern":"1","doi":"10.1175/jpo-d-16-0197.1","title":"Impact of a mean current on the internal tide energy dissipation at the critical latitude","citation":{"apa":"Richet, O., Muller, C. J., & Chomaz, J.-M. (2017). Impact of a mean current on the internal tide energy dissipation at the critical latitude. Journal of Physical Oceanography. American Meteorological Society. https://doi.org/10.1175/jpo-d-16-0197.1","short":"O. Richet, C.J. Muller, J.-M. Chomaz, Journal of Physical Oceanography 47 (2017) 1457–1472.","mla":"Richet, O., et al. “Impact of a Mean Current on the Internal Tide Energy Dissipation at the Critical Latitude.” Journal of Physical Oceanography, vol. 47, no. 6, American Meteorological Society, 2017, pp. 1457–72, doi:10.1175/jpo-d-16-0197.1.","chicago":"Richet, O., Caroline J Muller, and J.-M. Chomaz. “Impact of a Mean Current on the Internal Tide Energy Dissipation at the Critical Latitude.” Journal of Physical Oceanography. American Meteorological Society, 2017. https://doi.org/10.1175/jpo-d-16-0197.1.","ieee":"O. Richet, C. J. Muller, and J.-M. Chomaz, “Impact of a mean current on the internal tide energy dissipation at the critical latitude,” Journal of Physical Oceanography, vol. 47, no. 6. American Meteorological Society, pp. 1457–1472, 2017.","ama":"Richet O, Muller CJ, Chomaz J-M. Impact of a mean current on the internal tide energy dissipation at the critical latitude. Journal of Physical Oceanography. 2017;47(6):1457-1472. doi:10.1175/jpo-d-16-0197.1","ista":"Richet O, Muller CJ, Chomaz J-M. 2017. Impact of a mean current on the internal tide energy dissipation at the critical latitude. Journal of Physical Oceanography. 47(6), 1457–1472."},"publication":"Journal of Physical Oceanography","publisher":"American Meteorological Society","main_file_link":[{"url":"https://doi.org/10.1175/JPO-D-16-0197.1","open_access":"1"}],"day":"01","issue":"6","page":"1457-1472","abstract":[{"lang":"eng","text":"Previous numerical studies of the dissipation of internal tides in idealized settings suggest the existence of a critical latitude (~29°) where dissipation is enhanced. But observations only indicate a modest enhancement at this latitude. To resolve this difference between observational and numerical results, the authors study the latitudinal dependence of internal tides’ dissipation in more realistic conditions. In particular, the ocean is not a quiescent medium; the presence of large-scale currents or mesoscale eddies can impact the propagation and dissipation of internal tides. This paper investigates the impact of a weak background mean current in numerical simulations. The authors focus on the local dissipation of high spatial mode internal waves near their generation site. The vertical profile of dissipation and its variation with latitude without the mean current are consistent with earlier studies. But adding a weak mean current has a major impact on the latitudinal distribution of dissipation. The peak at the critical latitude disappears, and the dissipation is closer to a constant, albeit with two weak peaks at ~25° and ~35° latitude. This disappearance results from the Doppler shift of the internal tides’ frequency, which hinders the nonlinear transfer of energy to small-scale secondary waves via the parametric subharmonic instability (PSI). The new two weak peaks correspond to the Doppler-shifted critical latitudes of the left- and right-propagating waves. The results are confirmed in simulations with simple sinusoidal topography. Thus, although nonlinear transfers via PSI are efficient at dissipating internal tides, the exact location of the dissipation is sensitive to large-scale oceanic conditions."}],"type":"journal_article","date_created":"2021-02-15T15:11:04Z","publication_identifier":{"issn":["0022-3670","1520-0485"]},"volume":47,"date_published":"2017-06-01T00:00:00Z","year":"2017","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-01-24T13:36:31Z","oa":1,"status":"public","oa_version":"Published Version","_id":"9152","publication_status":"published","intvolume":" 47","month":"06","language":[{"iso":"eng"}],"article_type":"original","quality_controlled":"1","author":[{"full_name":"Richet, O.","first_name":"O.","last_name":"Richet"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","first_name":"Caroline J"},{"full_name":"Chomaz, J.-M.","first_name":"J.-M.","last_name":"Chomaz"}],"article_processing_charge":"No"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-26T15:41:40Z","scopus_import":"1","year":"2017","oa":1,"ec_funded":1,"publication_identifier":{"isbn":["978-153860457-1"]},"publist_id":"6525","volume":2017,"type":"conference","date_created":"2018-12-11T11:49:11Z","has_accepted_license":"1","date_published":"2017-01-01T00:00:00Z","author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul","first_name":"Paul"},{"last_name":"Rother","full_name":"Rother, Carsten","first_name":"Carsten"},{"last_name":"Abu Alhaija","full_name":"Abu Alhaija, Carsten","first_name":"Carsten"},{"full_name":"Kainmueller, Dagmar","first_name":"Dagmar","last_name":"Kainmueller"},{"last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan","first_name":"Bogdan"}],"quality_controlled":"1","article_processing_charge":"No","month":"01","external_id":{"isi":["000418371407018"]},"publication_status":"published","intvolume":" 2017","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:15Z","status":"public","oa_version":"Submitted Version","_id":"916","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","location":"Honolulu, HA, United States","end_date":"2017-07-26","start_date":"2017-07-21"},"citation":{"ieee":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy, “A study of lagrangean decompositions and dual ascent solvers for graph matching,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 7062–7071.","ama":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol 2017. IEEE; 2017:7062-7071. doi:10.1109/CVPR.2017.747","ista":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A study of lagrangean decompositions and dual ascent solvers for graph matching. CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.","apa":"Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., & Savchynskyy, B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.747","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","mla":"Swoboda, Paul, et al. A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:10.1109/CVPR.2017.747.","chicago":"Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller, and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.747."},"title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7"}],"day":"01","publisher":"IEEE","department":[{"_id":"VlKo"}],"isi":1,"doi":"10.1109/CVPR.2017.747","page":"7062-7071","file":[{"relation":"main_file","checksum":"e38a2740daad1ea178465843b5072906","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_id":"5848","file_size":944332,"date_updated":"2020-07-14T12:48:15Z","file_name":"2017_CVPR_Swoboda2.pdf","date_created":"2019-01-18T12:49:38Z"}],"abstract":[{"lang":"eng","text":"We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each."}],"ddc":["000"]},{"date_created":"2021-02-18T14:29:42Z","type":"journal_article","volume":30,"publication_identifier":{"issn":["1359-0294"]},"date_published":"2017-07-01T00:00:00Z","doi":"10.1016/j.cocis.2017.05.007","extern":"1","year":"2017","title":"Eppur si muove, and yet it moves: Patchy (phoretic) swimmers","scopus_import":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"chicago":"Aubret, A., S. Ramananarivo, and Jérémie A Palacci. “Eppur Si Muove, and yet It Moves: Patchy (Phoretic) Swimmers.” Current Opinion in Colloid & Interface Science. Elsevier, 2017. https://doi.org/10.1016/j.cocis.2017.05.007.","short":"A. Aubret, S. Ramananarivo, J.A. Palacci, Current Opinion in Colloid & Interface Science 30 (2017) 81–89.","mla":"Aubret, A., et al. “Eppur Si Muove, and yet It Moves: Patchy (Phoretic) Swimmers.” Current Opinion in Colloid & Interface Science, vol. 30, Elsevier, 2017, pp. 81–89, doi:10.1016/j.cocis.2017.05.007.","apa":"Aubret, A., Ramananarivo, S., & Palacci, J. A. (2017). Eppur si muove, and yet it moves: Patchy (phoretic) swimmers. Current Opinion in Colloid & Interface Science. Elsevier. https://doi.org/10.1016/j.cocis.2017.05.007","ista":"Aubret A, Ramananarivo S, Palacci JA. 2017. Eppur si muove, and yet it moves: Patchy (phoretic) swimmers. Current Opinion in Colloid & Interface Science. 30, 81–89.","ama":"Aubret A, Ramananarivo S, Palacci JA. Eppur si muove, and yet it moves: Patchy (phoretic) swimmers. Current Opinion in Colloid & Interface Science. 2017;30:81-89. doi:10.1016/j.cocis.2017.05.007","ieee":"A. Aubret, S. Ramananarivo, and J. A. Palacci, “Eppur si muove, and yet it moves: Patchy (phoretic) swimmers,” Current Opinion in Colloid & Interface Science, vol. 30. Elsevier, pp. 81–89, 2017."},"date_updated":"2021-02-22T09:32:11Z","publication":"Current Opinion in Colloid & Interface Science","publisher":"Elsevier","day":"01","_id":"9165","oa_version":"None","status":"public","language":[{"iso":"eng"}],"month":"07","intvolume":" 30","publication_status":"published","article_type":"original","quality_controlled":"1","page":"81-89","author":[{"full_name":"Aubret, A.","first_name":"A.","last_name":"Aubret"},{"last_name":"Ramananarivo","first_name":"S.","full_name":"Ramananarivo, S."},{"last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Advances in colloidal synthesis allow for the design of particles with controlled patches. This article reviews routes towards colloidal locomotion, where energy is consumed and converted into motion, and its implementation with active patchy particles. A special emphasis is given to phoretic swimmers, where the self-propulsion originates from an interfacial phenomenon, raising experimental challenges and opening up opportunities for particles with controlled anisotropic surface chemistry and novel behaviors."}]},{"conference":{"location":"Honolulu, HA, United States","end_date":"2017-07-26","start_date":"2017-07-21","name":"CVPR: Computer Vision and Pattern Recognition"},"language":[{"iso":"eng"}],"month":"07","intvolume":" 2017","publication_status":"published","external_id":{"isi":["000418371405005"]},"oa_version":"Submitted Version","_id":"917","file_date_updated":"2020-07-14T12:48:15Z","status":"public","article_processing_charge":"No","author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul","first_name":"Paul"},{"full_name":"Kuske, Jan","first_name":"Jan","last_name":"Kuske"},{"last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan","first_name":"Bogdan"}],"quality_controlled":"1","has_accepted_license":"1","date_published":"2017-07-01T00:00:00Z","volume":2017,"publist_id":"6524","publication_identifier":{"isbn":["978-153860457-1"]},"date_created":"2018-12-11T11:49:11Z","type":"conference","oa":1,"ec_funded":1,"scopus_import":"1","date_updated":"2023-09-26T15:41:11Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2017","ddc":["000"],"abstract":[{"lang":"eng","text":"We propose a general dual ascent framework for Lagrangean decomposition of combinatorial problems. Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers."}],"page":"4950-4960","file":[{"creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"72fd291046bd8e5717961bd68f6b6f03","relation":"main_file","date_updated":"2020-07-14T12:48:15Z","file_size":898652,"file_id":"5847","file_name":"2017_CVPR_Swoboda.pdf","date_created":"2019-01-18T12:45:55Z"}],"doi":"10.1109/CVPR.2017.526","isi":1,"day":"01","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"department":[{"_id":"VlKo"}],"publisher":"IEEE","citation":{"ista":"Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4950–4960.","ieee":"P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean decomposition of combinatorial problems,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960.","ama":"Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:10.1109/CVPR.2017.526","chicago":"Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.526.","short":"P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.","mla":"Swoboda, Paul, et al. A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:10.1109/CVPR.2017.526.","apa":"Swoboda, P., Kuske, J., & Savchynskyy, B. (2017). A dual ascent framework for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.526"},"title":"A dual ascent framework for Lagrangean decomposition of combinatorial problems"},{"article_processing_charge":"No","author":[{"last_name":"Gaillochet","first_name":"Christophe","full_name":"Gaillochet, Christophe"},{"last_name":"Stiehl","first_name":"Thomas","full_name":"Stiehl, Thomas"},{"first_name":"Christian","full_name":"Wenzl, Christian","last_name":"Wenzl"},{"last_name":"Ripoll","full_name":"Ripoll, Juan-José","first_name":"Juan-José"},{"last_name":"Bailey-Steinitz","first_name":"Lindsay J","full_name":"Bailey-Steinitz, Lindsay J"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin"},{"last_name":"Pfeiffer","first_name":"Anne","full_name":"Pfeiffer, Anne"},{"last_name":"Miotk","full_name":"Miotk, Andrej","first_name":"Andrej"},{"first_name":"Jana P","full_name":"Hakenjos, Jana P","last_name":"Hakenjos"},{"first_name":"Joachim","full_name":"Forner, Joachim","last_name":"Forner"},{"last_name":"Yanofsky","first_name":"Martin F","full_name":"Yanofsky, Martin F"},{"full_name":"Marciniak-Czochra, Anna","first_name":"Anna","last_name":"Marciniak-Czochra"},{"last_name":"Lohmann","first_name":"Jan U","full_name":"Lohmann, Jan U"}],"quality_controlled":"1","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 6","external_id":{"pmid":["29058667"]},"_id":"9190","oa_version":"Published Version","file_date_updated":"2021-03-02T09:29:56Z","status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-03-02T09:33:54Z","year":"2017","has_accepted_license":"1","date_published":"2017-10-23T00:00:00Z","volume":6,"publication_identifier":{"issn":["2050-084X"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-24T17:06:13Z","type":"journal_article","abstract":[{"lang":"eng","text":"Plant meristems carry pools of continuously active stem cells, whose activity is controlled by developmental and environmental signals. After stem cell division, daughter cells that exit the stem cell domain acquire transit amplifying cell identity before they are incorporated into organs and differentiate. In this study, we used an integrated approach to elucidate the role of HECATE (HEC) genes in regulating developmental trajectories of shoot stem cells in Arabidopsis thaliana. Our work reveals that HEC function stabilizes cell fate in distinct zones of the shoot meristem thereby controlling the spatio-temporal dynamics of stem cell differentiation. Importantly, this activity is concomitant with the local modulation of cellular responses to cytokinin and auxin, two key phytohormones regulating cell behaviour. Mechanistically, we show that HEC factors transcriptionally control and physically interact with MONOPTEROS (MP), a key regulator of auxin signalling, and modulate the autocatalytic stabilization of auxin signalling output."}],"pmid":1,"file":[{"success":1,"date_created":"2021-03-02T09:29:56Z","file_name":"2017_eLife_Gaillochet.pdf","date_updated":"2021-03-02T09:29:56Z","file_size":11669407,"file_id":"9214","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"51c8968a845df5077643c3e3e139d34f","relation":"main_file"}],"article_number":"e30135","ddc":["580"],"day":"23","publisher":"eLife Sciences Publications","publication":"eLife","citation":{"ama":"Gaillochet C, Stiehl T, Wenzl C, et al. Control of plant cell fate transitions by transcriptional and hormonal signals. eLife. 2017;6. doi:10.7554/elife.30135","ieee":"C. Gaillochet et al., “Control of plant cell fate transitions by transcriptional and hormonal signals,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"Gaillochet C, Stiehl T, Wenzl C, Ripoll J-J, Bailey-Steinitz LJ, Li L, Pfeiffer A, Miotk A, Hakenjos JP, Forner J, Yanofsky MF, Marciniak-Czochra A, Lohmann JU. 2017. Control of plant cell fate transitions by transcriptional and hormonal signals. eLife. 6, e30135.","short":"C. Gaillochet, T. Stiehl, C. Wenzl, J.-J. Ripoll, L.J. Bailey-Steinitz, L. Li, A. Pfeiffer, A. Miotk, J.P. Hakenjos, J. Forner, M.F. Yanofsky, A. Marciniak-Czochra, J.U. Lohmann, ELife 6 (2017).","mla":"Gaillochet, Christophe, et al. “Control of Plant Cell Fate Transitions by Transcriptional and Hormonal Signals.” ELife, vol. 6, e30135, eLife Sciences Publications, 2017, doi:10.7554/elife.30135.","apa":"Gaillochet, C., Stiehl, T., Wenzl, C., Ripoll, J.-J., Bailey-Steinitz, L. J., Li, L., … Lohmann, J. U. (2017). Control of plant cell fate transitions by transcriptional and hormonal signals. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30135","chicago":"Gaillochet, Christophe, Thomas Stiehl, Christian Wenzl, Juan-José Ripoll, Lindsay J Bailey-Steinitz, Lanxin Li, Anne Pfeiffer, et al. “Control of Plant Cell Fate Transitions by Transcriptional and Hormonal Signals.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30135."},"title":"Control of plant cell fate transitions by transcriptional and hormonal signals","doi":"10.7554/elife.30135","extern":"1"},{"oa_version":"Preprint","_id":"93","status":"public","language":[{"iso":"eng"}],"month":"09","external_id":{"arxiv":["1703.06470"],"pmid":["28964202"]},"publication_status":"published","intvolume":" 88","quality_controlled":"1","author":[{"first_name":"Tim","full_name":"Menke, Tim","last_name":"Menke"},{"last_name":"Burns","first_name":"Peter","full_name":"Burns, Peter"},{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"},{"first_name":"N S","full_name":"Kampel, N S","last_name":"Kampel"},{"first_name":"Robert","full_name":"Peterson, Robert","last_name":"Peterson"},{"last_name":"Cicak","full_name":"Cicak, Katarina","first_name":"Katarina"},{"first_name":"Raymond","full_name":"Simmonds, Raymond","last_name":"Simmonds"},{"first_name":"Cindy","full_name":"Regal, Cindy","last_name":"Regal"},{"first_name":"Konrad","full_name":"Lehnert, Konrad","last_name":"Lehnert"}],"date_published":"2017-09-08T00:00:00Z","date_created":"2018-12-11T11:44:35Z","type":"journal_article","volume":88,"publist_id":"7961","oa":1,"year":"2017","arxiv":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:21:59Z","issue":"9","article_number":"094701","abstract":[{"lang":"eng","text":"An electro-optomechanical device capable of microwave-to-optics conversion has recently been demonstrated, with the vision of enabling optical networks of superconducting qubits. Here we present an improved converter design that uses a three-dimensional microwave cavity for coupling between the microwave transmission line and an integrated LC resonator on the converter chip. The new design simplifies the optical assembly and decouples it from the microwave part of the setup. Experimental demonstrations show that the modular device assembly allows us to flexibly tune the microwave coupling to the converter chip while maintaining small loss. We also find that electromechanical experiments are not impacted by the additional microwave cavity. Our design is compatible with a high-finesse optical cavity and will improve optical performance."}],"pmid":1,"doi":"10.1063/1.5000973","extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.06470","open_access":"1"}],"publisher":"American Institute of Physics","publication":"Review of Scientific Instruments","day":"08","title":"Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device","citation":{"apa":"Menke, T., Burns, P., Higginbotham, A. P., Kampel, N. S., Peterson, R., Cicak, K., … Lehnert, K. (2017). Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device. Review of Scientific Instruments. American Institute of Physics. https://doi.org/10.1063/1.5000973","short":"T. Menke, P. Burns, A.P. Higginbotham, N.S. Kampel, R. Peterson, K. Cicak, R. Simmonds, C. Regal, K. Lehnert, Review of Scientific Instruments 88 (2017).","mla":"Menke, Tim, et al. “Reconfigurable Re-Entrant Cavity for Wireless Coupling to an Electro-Optomechanical Device.” Review of Scientific Instruments, vol. 88, no. 9, 094701, American Institute of Physics, 2017, doi:10.1063/1.5000973.","chicago":"Menke, Tim, Peter Burns, Andrew P Higginbotham, N S Kampel, Robert Peterson, Katarina Cicak, Raymond Simmonds, Cindy Regal, and Konrad Lehnert. “Reconfigurable Re-Entrant Cavity for Wireless Coupling to an Electro-Optomechanical Device.” Review of Scientific Instruments. American Institute of Physics, 2017. https://doi.org/10.1063/1.5000973.","ama":"Menke T, Burns P, Higginbotham AP, et al. Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device. Review of Scientific Instruments. 2017;88(9). doi:10.1063/1.5000973","ieee":"T. Menke et al., “Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device,” Review of Scientific Instruments, vol. 88, no. 9. American Institute of Physics, 2017.","ista":"Menke T, Burns P, Higginbotham AP, Kampel NS, Peterson R, Cicak K, Simmonds R, Regal C, Lehnert K. 2017. Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device. Review of Scientific Instruments. 88(9), 094701."}},{"publisher":"Nature Publishing Group","publication":"Nature","day":"16","year":"2017","title":"Identity and dynamics of mammary stem cells during branching morphogenesis","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Scheele, Colinda, et al. “Identity and Dynamics of Mammary Stem Cells during Branching Morphogenesis.” Nature, vol. 542, no. 7641, Nature Publishing Group, 2017, pp. 313–17, doi:10.1038/nature21046.","short":"C. Scheele, E.B. Hannezo, M. Muraro, A. Zomer, N. Langedijk, A. Van Oudenaarden, B. Simons, J. Van Rheenen, Nature 542 (2017) 313–317.","apa":"Scheele, C., Hannezo, E. B., Muraro, M., Zomer, A., Langedijk, N., Van Oudenaarden, A., … Van Rheenen, J. (2017). Identity and dynamics of mammary stem cells during branching morphogenesis. Nature. Nature Publishing Group. https://doi.org/10.1038/nature21046","chicago":"Scheele, Colinda, Edouard B Hannezo, Mauro Muraro, Anoek Zomer, Nathalia Langedijk, Alexander Van Oudenaarden, Benjamin Simons, and Jacco Van Rheenen. “Identity and Dynamics of Mammary Stem Cells during Branching Morphogenesis.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature21046.","ama":"Scheele C, Hannezo EB, Muraro M, et al. Identity and dynamics of mammary stem cells during branching morphogenesis. Nature. 2017;542(7641):313-317. doi:10.1038/nature21046","ieee":"C. Scheele et al., “Identity and dynamics of mammary stem cells during branching morphogenesis,” Nature, vol. 542, no. 7641. Nature Publishing Group, pp. 313–317, 2017.","ista":"Scheele C, Hannezo EB, Muraro M, Zomer A, Langedijk N, Van Oudenaarden A, Simons B, Van Rheenen J. 2017. Identity and dynamics of mammary stem cells during branching morphogenesis. Nature. 542(7641), 313–317."},"date_updated":"2021-01-12T08:22:01Z","date_published":"2017-02-16T00:00:00Z","doi":"10.1038/nature21046","extern":"1","date_created":"2018-12-11T11:49:17Z","type":"journal_article","volume":542,"publist_id":"6505","publication_identifier":{"issn":["00280836"]},"abstract":[{"lang":"eng","text":"During puberty, the mouse mammary gland develops into a highly branched epithelial network. Owing to the absence of exclusive stem cell markers, the location, multiplicity, dynamics and fate of mammary stem cells (MaSCs), which drive branching morphogenesis, are unknown. Here we show that morphogenesis is driven by proliferative terminal end buds that terminate or bifurcate with near equal probability, in a stochastic and time-invariant manner, leading to a heterogeneous epithelial network. We show that the majority of terminal end bud cells function as highly proliferative, lineage-committed MaSCs that are heterogeneous in their expression profile and short-term contribution to ductal extension. Yet, through cell rearrangements during terminal end bud bifurcation, each MaSC is able to contribute actively to long-term growth. Our study shows that the behaviour of MaSCs is not directly linked to a single expression profile. Instead, morphogenesis relies upon lineage-restricted heterogeneous MaSC populations that function as single equipotent pools in the long term."}],"quality_controlled":"1","page":"313 - 317","author":[{"first_name":"Colinda","full_name":"Scheele, Colinda","last_name":"Scheele"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"full_name":"Muraro, Mauro","first_name":"Mauro","last_name":"Muraro"},{"last_name":"Zomer","first_name":"Anoek","full_name":"Zomer, Anoek"},{"first_name":"Nathalia","full_name":"Langedijk, Nathalia","last_name":"Langedijk"},{"first_name":"Alexander","full_name":"Van Oudenaarden, Alexander","last_name":"Van Oudenaarden"},{"first_name":"Benjamin","full_name":"Simons, Benjamin","last_name":"Simons"},{"last_name":"Van Rheenen","full_name":"Van Rheenen, Jacco","first_name":"Jacco"}],"issue":"7641","oa_version":"None","_id":"934","status":"public","language":[{"iso":"eng"}],"intvolume":" 542","publication_status":"published","month":"02"},{"publication":"Journal of Cell Science","publisher":"Company of Biologists","day":"01","year":"2017","title":"RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells ","date_updated":"2021-01-12T08:22:02Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sedzinski, Jakub, et al. “RhoA Regulates Actin Network Dynamics during Apical Surface Emergence in Multiciliated Epithelial Cells .” Journal of Cell Science, vol. 130, no. 5, Company of Biologists, 2017, doi:10.1242/jcs.202234.","short":"J. Sedzinski, E.B. Hannezo, F. Tu, M. Biro, J. Wallingford, Journal of Cell Science 130 (2017).","apa":"Sedzinski, J., Hannezo, E. B., Tu, F., Biro, M., & Wallingford, J. (2017). RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells . Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.202234","chicago":"Sedzinski, Jakub, Edouard B Hannezo, Fan Tu, Maté Biro, and John Wallingford. “RhoA Regulates Actin Network Dynamics during Apical Surface Emergence in Multiciliated Epithelial Cells .” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.202234.","ama":"Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells . Journal of Cell Science. 2017;130(5). doi:10.1242/jcs.202234","ieee":"J. Sedzinski, E. B. Hannezo, F. Tu, M. Biro, and J. Wallingford, “RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells ,” Journal of Cell Science, vol. 130, no. 5. Company of Biologists, 2017.","ista":"Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. 2017. RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells . Journal of Cell Science. 130(5)."},"date_published":"2017-01-01T00:00:00Z","extern":"1","doi":"10.1242/jcs.202234","type":"journal_article","date_created":"2018-12-11T11:49:17Z","volume":130,"publist_id":"6507","abstract":[{"text":"Homeostatic replacement of epithelial cells from basal precursors is a multistep process involving progenitor cell specification, radial intercalation and, finally, apical surface emergence. Recent data demonstrate that actin-based pushing under the control of the formin protein Fmn1 drives apical emergence in nascent multiciliated epithelial cells (MCCs), but little else is known about this actin network or the control of Fmn1. Here, we explore the role of the small GTPase RhoA in MCC apical emergence. Disruption of RhoA function reduced the rate of apical surface expansion and decreased the final size of the apical domain. Analysis of cell shapes suggests that RhoA alters the balance of forces exerted on the MCC apical surface. Finally, quantitative time-lapse imaging and fluorescence recovery after photobleaching studies argue that RhoA works in concert with Fmn1 to control assembly of the specialized apical actin network in MCCs. These data provide new molecular insights into epithelial apical surface assembly and could also shed light on mechanisms of apical lumen formation","lang":"eng"}],"quality_controlled":"1","author":[{"first_name":"Jakub","full_name":"Sedzinski, Jakub","last_name":"Sedzinski"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"last_name":"Tu","first_name":"Fan","full_name":"Tu, Fan"},{"last_name":"Biro","full_name":"Biro, Maté","first_name":"Maté"},{"first_name":"John","full_name":"Wallingford, John","last_name":"Wallingford"}],"issue":"5","status":"public","oa_version":"None","_id":"936","publication_status":"published","month":"01","intvolume":" 130","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"publication_status":"published","month":"05","intvolume":" 545","oa_version":"None","_id":"937","status":"public","issue":"7652","page":"103 - 107","author":[{"last_name":"Pinheiro","full_name":"Pinheiro, Diana","first_name":"Diana"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Herszterg","full_name":"Herszterg, Sophie","first_name":"Sophie"},{"last_name":"Bosveld","first_name":"Floris","full_name":"Bosveld, Floris"},{"full_name":"Gaugué, Isabelle","first_name":"Isabelle","last_name":"Gaugué"},{"last_name":"Balakireva","first_name":"Maria","full_name":"Balakireva, Maria"},{"full_name":"Wang, Zhimin","first_name":"Zhimin","last_name":"Wang"},{"full_name":"Cristo, Inês","first_name":"Inês","last_name":"Cristo"},{"full_name":"Rigaud, Stéphane","first_name":"Stéphane","last_name":"Rigaud"},{"last_name":"Markova","first_name":"Olga","full_name":"Markova, Olga"},{"last_name":"Bellaïche","first_name":"Yohanns","full_name":"Bellaïche, Yohanns"}],"quality_controlled":"1","abstract":[{"text":"During epithelial cytokinesis, the remodelling of adhesive cell-cell contacts between the dividing cell and its neighbours has profound implications for the integrity, arrangement and morphogenesis of proliferative tissues. In both vertebrates and invertebrates, this remodelling requires the activity of non-muscle myosin II (MyoII) in the interphasic cells neighbouring the dividing cell. However, the mechanisms that coordinate cytokinesis and MyoII activity in the neighbours are unknown. Here we show that in the Drosophila notum epithelium, each cell division is associated with a mechanosensing and transmission event that controls MyoII dynamics in neighbouring cells. We find that the ring pulling forces promote local junction elongation, which results in local E-cadherin dilution at the ingressing adherens junction. In turn, the reduction in E-cadherin concentration and the contractility of the neighbouring cells promote self-organized actomyosin flows, ultimately leading to accumulation of MyoII at the base of the ingressing junction. Although force transduction has been extensively studied in the context of adherens junction reinforcement to stabilize adhesive cell-cell contacts, we propose an alternative mechanosensing mechanism that coordinates actomyosin dynamics between epithelial cells and sustains the remodelling of the adherens junction in response to mechanical forces.","lang":"eng"}],"volume":545,"publist_id":"6504","publication_identifier":{"issn":["00280836"]},"date_created":"2018-12-11T11:49:18Z","type":"journal_article","doi":"10.1038/nature22041","extern":"1","date_published":"2017-05-04T00:00:00Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:22:02Z","citation":{"ama":"Pinheiro D, Hannezo EB, Herszterg S, et al. Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows. Nature. 2017;545(7652):103-107. doi:10.1038/nature22041","ieee":"D. Pinheiro et al., “Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows,” Nature, vol. 545, no. 7652. Nature Publishing Group, pp. 103–107, 2017.","ista":"Pinheiro D, Hannezo EB, Herszterg S, Bosveld F, Gaugué I, Balakireva M, Wang Z, Cristo I, Rigaud S, Markova O, Bellaïche Y. 2017. Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows. Nature. 545(7652), 103–107.","mla":"Pinheiro, Diana, et al. “Transmission of Cytokinesis Forces via E Cadherin Dilution and Actomyosin Flows.” Nature, vol. 545, no. 7652, Nature Publishing Group, 2017, pp. 103–07, doi:10.1038/nature22041.","short":"D. Pinheiro, E.B. Hannezo, S. Herszterg, F. Bosveld, I. Gaugué, M. Balakireva, Z. Wang, I. Cristo, S. Rigaud, O. Markova, Y. Bellaïche, Nature 545 (2017) 103–107.","apa":"Pinheiro, D., Hannezo, E. B., Herszterg, S., Bosveld, F., Gaugué, I., Balakireva, M., … Bellaïche, Y. (2017). Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows. Nature. Nature Publishing Group. https://doi.org/10.1038/nature22041","chicago":"Pinheiro, Diana, Edouard B Hannezo, Sophie Herszterg, Floris Bosveld, Isabelle Gaugué, Maria Balakireva, Zhimin Wang, et al. “Transmission of Cytokinesis Forces via E Cadherin Dilution and Actomyosin Flows.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature22041."},"title":"Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows","year":"2017","day":"04","publication":"Nature","publisher":"Nature Publishing Group"},{"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"oa":1,"year":"2017","date_updated":"2023-09-07T12:06:09Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2017-06-02T00:00:00Z","has_accepted_license":"1","date_created":"2018-12-11T11:49:18Z","type":"dissertation","publist_id":"6483","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","author":[{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek"}],"_id":"938","oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:15Z","status":"public","language":[{"iso":"eng"}],"publication_status":"published","month":"06","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","day":"02","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1591"}]},"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","citation":{"chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842.","mla":"Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842.","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","apa":"Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842"},"doi":"10.15479/AT:ISTA:th_842","abstract":[{"text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin.","lang":"eng"}],"file":[{"date_created":"2019-04-05T09:03:20Z","file_name":"2017_Adamowski-Thesis_Source.docx","file_size":46903863,"file_id":"6215","date_updated":"2020-07-14T12:48:15Z","checksum":"193425764d9aaaed3ac57062a867b315","relation":"source_file","access_level":"closed","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_name":"2017_Adamowski-Thesis.pdf","date_created":"2019-04-05T09:03:19Z","creator":"dernst","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"df5ab01be81f821e1b958596a1ec8d21","date_updated":"2020-07-14T12:48:15Z","file_id":"6216","file_size":8698888}],"page":"117","degree_awarded":"PhD","pubrep_id":"842","ddc":["581","583","580"]},{"year":"2017","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-26T15:39:46Z","ec_funded":1,"oa":1,"date_created":"2018-12-11T11:49:18Z","type":"journal_article","publist_id":"6481","volume":119,"publication_identifier":{"issn":["00319007"]},"date_published":"2017-07-18T00:00:00Z","quality_controlled":"1","author":[{"first_name":"Bikashkali","full_name":"Midya, Bikashkali","last_name":"Midya","id":"456187FC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Konotop, Vladimir","first_name":"Vladimir","last_name":"Konotop"}],"article_processing_charge":"No","_id":"939","oa_version":"Submitted Version","status":"public","language":[{"iso":"eng"}],"external_id":{"isi":["000405718200012"]},"month":"07","intvolume":" 119","publication_status":"published","title":"Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons","citation":{"chicago":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.033905.","apa":"Midya, B., & Konotop, V. (2017). Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.033905","mla":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.033905.","short":"B. Midya, V. Konotop, Physical Review Letters 119 (2017).","ista":"Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.","ieee":"B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” Physical Review Letters, vol. 119, no. 3. American Physical Society, 2017.","ama":"Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 2017;119(3). doi:10.1103/PhysRevLett.119.033905"},"department":[{"_id":"MiLe"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.04085 "}],"publication":"Physical Review Letters","publisher":"American Physical Society","day":"18","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"doi":"10.1103/PhysRevLett.119.033905","isi":1,"abstract":[{"text":"We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding.","lang":"eng"}],"article_number":"033905","issue":"3"},{"date_published":"2017-10-06T00:00:00Z","type":"journal_article","date_created":"2018-12-11T11:44:35Z","volume":119,"publist_id":"7960","oa":1,"year":"2017","arxiv":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:22:04Z","status":"public","oa_version":"Submitted Version","_id":"94","month":"10","intvolume":" 119","external_id":{"arxiv":["1705.09548"]},"publication_status":"published","language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"full_name":"Rosenthal, Eric","first_name":"Eric","last_name":"Rosenthal"},{"first_name":"Benjamin","full_name":"Chapman, Benjamin","last_name":"Chapman"},{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"},{"first_name":"Joseph","full_name":"Kerckhoff, Joseph","last_name":"Kerckhoff"},{"last_name":"Lehnert","first_name":"Konrad","full_name":"Lehnert, Konrad"}],"extern":"1","doi":"10.1103/PhysRevLett.119.147703","publisher":"American Physical Society","publication":"APS Physics, Physical Review Letters","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.09548"}],"day":"06","title":"Breaking Lorentz reciprocity with frequency conversion and delay","citation":{"ista":"Rosenthal E, Chapman B, Higginbotham AP, Kerckhoff J, Lehnert K. 2017. Breaking Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical Review Letters. 119(14), 147703.","ieee":"E. Rosenthal, B. Chapman, A. P. Higginbotham, J. Kerckhoff, and K. Lehnert, “Breaking Lorentz reciprocity with frequency conversion and delay,” APS Physics, Physical Review Letters, vol. 119, no. 14. American Physical Society, 2017.","ama":"Rosenthal E, Chapman B, Higginbotham AP, Kerckhoff J, Lehnert K. Breaking Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical Review Letters. 2017;119(14). doi:10.1103/PhysRevLett.119.147703","chicago":"Rosenthal, Eric, Benjamin Chapman, Andrew P Higginbotham, Joseph Kerckhoff, and Konrad Lehnert. “Breaking Lorentz Reciprocity with Frequency Conversion and Delay.” APS Physics, Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.147703.","apa":"Rosenthal, E., Chapman, B., Higginbotham, A. P., Kerckhoff, J., & Lehnert, K. (2017). Breaking Lorentz reciprocity with frequency conversion and delay. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.147703","short":"E. Rosenthal, B. Chapman, A.P. Higginbotham, J. Kerckhoff, K. Lehnert, APS Physics, Physical Review Letters 119 (2017).","mla":"Rosenthal, Eric, et al. “Breaking Lorentz Reciprocity with Frequency Conversion and Delay.” APS Physics, Physical Review Letters, vol. 119, no. 14, 147703, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.147703."},"issue":"14","article_number":"147703","abstract":[{"text":"We introduce a method for breaking Lorentz reciprocity based upon the noncommutation of frequency conversion and delay. The method requires no magnetic materials or resonant physics, allowing for the design of scalable and broadband nonreciprocal circuits. With this approach, two types of gyrators - universal building blocks for linear, nonreciprocal circuits - are constructed. Using one of these gyrators, we create a circulator with >15 dB of isolation across the 5-9 GHz band. Our designs may be readily extended to any platform with suitable frequency conversion elements, including semiconducting devices for telecommunication or an on-chip superconducting implementation for quantum information processing.","lang":"eng"}]},{"type":"conference","date_created":"2018-12-11T11:49:19Z","publist_id":"6478","date_published":"2017-07-10T00:00:00Z","doi":"10.1145/3092703.3098225","title":"JFIX: Semantics-based repair of Java programs via symbolic PathFinder","year":"2017","citation":{"chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, 376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.","apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis (pp. 376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–379.","mla":"Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ISSTA: International Symposium on Software Testing and Analysis, 376–379.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ACM; 2017:376-379. doi:10.1145/3092703.3098225","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa Barbara, CA, United States, 2017, pp. 376–379."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:22:05Z","scopus_import":1,"publisher":"ACM","publication":"Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis","department":[{"_id":"ToHe"}],"day":"10","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"status":"public","oa_version":"None","_id":"941","publication_status":"published","month":"07","language":[{"iso":"eng"}],"conference":{"name":"ISSTA: International Symposium on Software Testing and Analysis","location":"Santa Barbara, CA, United States","end_date":"2017-07-14","start_date":"2017-07-10"},"quality_controlled":"1","author":[{"first_name":"Xuan","full_name":"Le, Xuan","last_name":"Le"},{"last_name":"Chu","id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep","full_name":"Chu, Duc Hiep"},{"last_name":"Lo","first_name":"David","full_name":"Lo, David"},{"last_name":"Le Goues","first_name":"Claire","full_name":"Le Goues, Claire"},{"last_name":"Visser","first_name":"Willem","full_name":"Visser, Willem"}],"page":"376 - 379 ","abstract":[{"text":"Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ ","lang":"eng"}]},{"conference":{"start_date":"2017-09-04","end_date":"2017-09-08","location":"Paderborn, Germany","name":"FSE: Foundations of Software Engineering"},"oa_version":"None","_id":"942","status":"public","language":[{"iso":"eng"}],"external_id":{"isi":["000414279300055"]},"month":"09","publication_status":"published","article_processing_charge":"No","quality_controlled":"1","author":[{"full_name":"Le, Xuan","first_name":"Xuan","last_name":"Le"},{"full_name":"Chu, Duc Hiep","first_name":"Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87","last_name":"Chu"},{"last_name":"Lo","full_name":"Lo, David","first_name":"David"},{"first_name":"Claire","full_name":"Le Goues, Claire","last_name":"Le Goues"},{"first_name":"Willem","full_name":"Visser, Willem","last_name":"Visser"}],"date_published":"2017-09-01T00:00:00Z","date_created":"2018-12-11T11:49:19Z","type":"conference","volume":"F130154","publist_id":"6477","publication_identifier":{"isbn":["978-145035105-8"]},"year":"2017","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-26T15:38:36Z","abstract":[{"text":"A notable class of techniques for automatic program repair is known as semantics-based. Such techniques, e.g., Angelix, infer semantic specifications via symbolic execution, and then use program synthesis to construct new code that satisfies those inferred specifications. However, the obtained specifications are naturally incomplete, leaving the synthesis engine with a difficult task of synthesizing a general solution from a sparse space of many possible solutions that are consistent with the provided specifications but that do not necessarily generalize. We present S3, a new repair synthesis engine that leverages programming-by-examples methodology to synthesize high-quality bug repairs. The novelty in S3 that allows it to tackle the sparse search space to create more general repairs is three-fold: (1) A systematic way to customize and constrain the syntactic search space via a domain-specific language, (2) An efficient enumeration-based search strategy over the constrained search space, and (3) A number of ranking features based on measures of the syntactic and semantic distances between candidate solutions and the original buggy program. We compare S3’s repair effectiveness with state-of-the-art synthesis engines Angelix, Enumerative, and CVC4. S3 can successfully and correctly fix at least three times more bugs than the best baseline on datasets of 52 bugs in small programs, and 100 bugs in real-world large programs. ","lang":"eng"}],"page":"593 - 604","doi":"10.1145/3106237.3106309","isi":1,"department":[{"_id":"ToHe"}],"publisher":"ACM","project":[{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"day":"01","title":"S3: Syntax- and semantic-guided repair synthesis via programming by examples","citation":{"ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. S3: Syntax- and semantic-guided repair synthesis via programming by examples. FSE: Foundations of Software Engineering vol. F130154, 593–604.","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “S3: Syntax- and semantic-guided repair synthesis via programming by examples,” presented at the FSE: Foundations of Software Engineering, Paderborn, Germany, 2017, vol. F130154, pp. 593–604.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. S3: Syntax- and semantic-guided repair synthesis via programming by examples. In: Vol F130154. ACM; 2017:593-604. doi:10.1145/3106237.3106309","chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples,” F130154:593–604. ACM, 2017. https://doi.org/10.1145/3106237.3106309.","apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). S3: Syntax- and semantic-guided repair synthesis via programming by examples (Vol. F130154, pp. 593–604). Presented at the FSE: Foundations of Software Engineering, Paderborn, Germany: ACM. https://doi.org/10.1145/3106237.3106309","mla":"Le, Xuan, et al. S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples. Vol. F130154, ACM, 2017, pp. 593–604, doi:10.1145/3106237.3106309.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604."}},{"oa":1,"ec_funded":1,"scopus_import":"1","date_updated":"2023-09-26T15:38:05Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2017","date_published":"2017-06-30T00:00:00Z","publist_id":"6474","volume":356,"publication_identifier":{"issn":["00368075"]},"date_created":"2018-12-11T11:49:20Z","type":"journal_article","article_processing_charge":"No","author":[{"last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762"},{"full_name":"Tabata, Yoji","first_name":"Yoji","last_name":"Tabata"},{"full_name":"Brandenberg, Nathalie","first_name":"Nathalie","last_name":"Brandenberg"},{"last_name":"Lutolf","full_name":"Lutolf, Matthias","first_name":"Matthias"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper"},{"last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna"}],"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":" 356","month":"06","external_id":{"isi":["000404351500036"],"pmid":["28663499"]},"publication_status":"published","_id":"943","oa_version":"Submitted Version","status":"public","project":[{"call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"},{"call_identifier":"H2020","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425","grant_number":"201439","call_identifier":"FP7"}],"day":"30","department":[{"_id":"AnKi"},{"_id":"GaTk"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/"}],"publisher":"American Association for the Advancement of Science","publication":"Science","citation":{"apa":"Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam5887","mla":"Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.","short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.","chicago":"Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887.","ama":"Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887","ieee":"M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017.","ista":"Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383."},"title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","doi":"10.1126/science.aam5887","isi":1,"abstract":[{"lang":"eng","text":"Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation."}],"page":"1379 - 1383","pmid":1,"issue":"6345"},{"article_processing_charge":"No","quality_controlled":"1","author":[{"last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J"},{"full_name":"Postiglione, Maria P","first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","last_name":"Postiglione"},{"first_name":"Laura","full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X","last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87"},{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010","first_name":"Susanne"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","first_name":"Florian"},{"full_name":"Xiao, Guanxi","first_name":"Guanxi","last_name":"Xiao"},{"full_name":"Klezovitch, Olga","first_name":"Olga","last_name":"Klezovitch"},{"full_name":"Vasioukhin, Valeri","first_name":"Valeri","last_name":"Vasioukhin"},{"last_name":"Ghashghaei","first_name":"Troy","full_name":"Ghashghaei, Troy"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"status":"public","_id":"944","oa_version":"None","external_id":{"isi":["000400466700011"]},"intvolume":" 94","publication_status":"published","month":"05","language":[{"iso":"eng"}],"ec_funded":1,"year":"2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-26T15:37:02Z","scopus_import":"1","date_published":"2017-05-03T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"type":"journal_article","date_created":"2018-12-11T11:49:20Z","publication_identifier":{"issn":["08966273"]},"volume":94,"publist_id":"6473","abstract":[{"lang":"eng","text":"The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms."}],"page":"517 - 533.e3","issue":"3","publication":"Neuron","publisher":"Cell Press","department":[{"_id":"SiHi"},{"_id":"MaJö"}],"project":[{"call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}],"day":"03","title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","citation":{"ista":"Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3.","ama":"Beattie RJ, Postiglione MP, Burnett L, et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 2017;94(3):517-533.e3. doi:10.1016/j.neuron.2017.04.012","ieee":"R. J. Beattie et al., “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” Neuron, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017.","chicago":"Beattie, Robert J, Maria P Postiglione, Laura Burnett, Susanne Laukoter, Carmen Streicher, Florian Pauler, Guanxi Xiao, et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron. Cell Press, 2017. https://doi.org/10.1016/j.neuron.2017.04.012.","mla":"Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:10.1016/j.neuron.2017.04.012.","short":"R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3.","apa":"Beattie, R. J., Postiglione, M. P., Burnett, L., Laukoter, S., Streicher, C., Pauler, F., … Hippenmeyer, S. (2017). Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2017.04.012"},"isi":1,"doi":"10.1016/j.neuron.2017.04.012"}]