[{"conference":{"location":"Honolulu, HA, United States","name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2017-07-26","start_date":"2017-07-21"},"page":"4950-4960","external_id":{"isi":["000418371405005"]},"year":"2017","date_published":"2017-07-01T00:00:00Z","month":"07","intvolume":" 2017","oa":1,"date_updated":"2023-09-26T15:41:11Z","doi":"10.1109/CVPR.2017.526","oa_version":"Submitted Version","ec_funded":1,"isi":1,"volume":2017,"day":"01","status":"public","date_created":"2018-12-11T11:49:11Z","ddc":["000"],"publist_id":"6524","department":[{"_id":"VlKo"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"IEEE","has_accepted_license":"1","author":[{"full_name":"Swoboda, Paul","last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuske, Jan","last_name":"Kuske","first_name":"Jan"},{"last_name":"Savchynskyy","first_name":"Bogdan","full_name":"Savchynskyy, Bogdan"}],"title":"A dual ascent framework for Lagrangean decomposition of combinatorial problems","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"2017_CVPR_Swoboda.pdf","date_created":"2019-01-18T12:45:55Z","date_updated":"2020-07-14T12:48:15Z","file_id":"5847","content_type":"application/pdf","creator":"dernst","file_size":898652,"checksum":"72fd291046bd8e5717961bd68f6b6f03","relation":"main_file","access_level":"open_access"}],"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"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."}],"scopus_import":"1","file_date_updated":"2020-07-14T12:48:15Z","type":"conference","citation":{"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","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.","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","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.","short":"P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 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.","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."},"publication_identifier":{"isbn":["978-153860457-1"]},"quality_controlled":"1","_id":"917"},{"status":"public","day":"23","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)"},"ddc":["580"],"date_created":"2021-02-24T17:06:13Z","volume":6,"pmid":1,"oa_version":"Published Version","publication":"eLife","doi":"10.7554/elife.30135","oa":1,"date_updated":"2021-03-02T09:33:54Z","article_number":"e30135","date_published":"2017-10-23T00:00:00Z","intvolume":" 6","month":"10","year":"2017","external_id":{"pmid":["29058667"]},"quality_controlled":"1","_id":"9190","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."}],"type":"journal_article","file_date_updated":"2021-03-02T09:29:56Z","citation":{"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.","ieee":"C. Gaillochet et al., “Control of plant cell fate transitions by transcriptional and hormonal signals,” eLife, vol. 6. eLife Sciences Publications, 2017.","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).","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.","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"},"extern":"1","publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","author":[{"first_name":"Christophe","last_name":"Gaillochet","full_name":"Gaillochet, Christophe"},{"full_name":"Stiehl, Thomas","first_name":"Thomas","last_name":"Stiehl"},{"first_name":"Christian","last_name":"Wenzl","full_name":"Wenzl, Christian"},{"first_name":"Juan-José","last_name":"Ripoll","full_name":"Ripoll, Juan-José"},{"full_name":"Bailey-Steinitz, Lindsay J","first_name":"Lindsay J","last_name":"Bailey-Steinitz"},{"orcid":"0000-0002-5607-272X","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","full_name":"Li, Lanxin"},{"full_name":"Pfeiffer, Anne","last_name":"Pfeiffer","first_name":"Anne"},{"first_name":"Andrej","last_name":"Miotk","full_name":"Miotk, Andrej"},{"full_name":"Hakenjos, Jana P","first_name":"Jana P","last_name":"Hakenjos"},{"last_name":"Forner","first_name":"Joachim","full_name":"Forner, Joachim"},{"full_name":"Yanofsky, Martin F","last_name":"Yanofsky","first_name":"Martin F"},{"last_name":"Marciniak-Czochra","first_name":"Anna","full_name":"Marciniak-Czochra, Anna"},{"full_name":"Lohmann, Jan U","first_name":"Jan U","last_name":"Lohmann"}],"title":"Control of plant cell fate transitions by transcriptional and hormonal signals","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"success":1,"file_name":"2017_eLife_Gaillochet.pdf","date_created":"2021-03-02T09:29:56Z","date_updated":"2021-03-02T09:29:56Z","content_type":"application/pdf","file_id":"9214","creator":"dernst","file_size":11669407,"access_level":"open_access","relation":"main_file","checksum":"51c8968a845df5077643c3e3e139d34f"}],"publisher":"eLife Sciences Publications","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"main_file_link":[{"url":"https://arxiv.org/abs/1703.06470","open_access":"1"}],"doi":"10.1063/1.5000973","publication":"Review of Scientific Instruments","oa_version":"Preprint","pmid":1,"volume":88,"status":"public","day":"08","date_created":"2018-12-11T11:44:35Z","external_id":{"pmid":["28964202"],"arxiv":["1703.06470"]},"year":"2017","article_number":"094701","month":"09","intvolume":" 88","date_published":"2017-09-08T00:00:00Z","issue":"9","oa":1,"date_updated":"2021-01-12T08:21:59Z","publication_status":"published","type":"journal_article","abstract":[{"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.","lang":"eng"}],"arxiv":1,"citation":{"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.","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","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.","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).","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.","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.","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"},"extern":"1","quality_controlled":"1","_id":"93","publist_id":"7961","language":[{"iso":"eng"}],"publisher":"American Institute of Physics","title":"Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Menke","first_name":"Tim","full_name":"Menke, Tim"},{"full_name":"Burns, Peter","first_name":"Peter","last_name":"Burns"},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P"},{"first_name":"N S","last_name":"Kampel","full_name":"Kampel, N S"},{"last_name":"Peterson","first_name":"Robert","full_name":"Peterson, Robert"},{"first_name":"Katarina","last_name":"Cicak","full_name":"Cicak, Katarina"},{"last_name":"Simmonds","first_name":"Raymond","full_name":"Simmonds, Raymond"},{"first_name":"Cindy","last_name":"Regal","full_name":"Regal, Cindy"},{"full_name":"Lehnert, Konrad","first_name":"Konrad","last_name":"Lehnert"}]},{"month":"02","intvolume":" 542","date_published":"2017-02-16T00:00:00Z","publisher":"Nature Publishing Group","date_updated":"2021-01-12T08:22:01Z","issue":"7641","title":"Identity and dynamics of mammary stem cells during branching morphogenesis","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Scheele, Colinda","last_name":"Scheele","first_name":"Colinda"},{"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":"Mauro","last_name":"Muraro","full_name":"Muraro, Mauro"},{"last_name":"Zomer","first_name":"Anoek","full_name":"Zomer, Anoek"},{"last_name":"Langedijk","first_name":"Nathalia","full_name":"Langedijk, Nathalia"},{"full_name":"Van Oudenaarden, Alexander","first_name":"Alexander","last_name":"Van Oudenaarden"},{"last_name":"Simons","first_name":"Benjamin","full_name":"Simons, Benjamin"},{"last_name":"Van Rheenen","first_name":"Jacco","full_name":"Van Rheenen, Jacco"}],"page":"313 - 317","publist_id":"6505","language":[{"iso":"eng"}],"year":"2017","citation":{"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","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.","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.","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.","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.","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","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."},"publication_identifier":{"issn":["00280836"]},"extern":"1","volume":542,"type":"journal_article","abstract":[{"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.","lang":"eng"}],"_id":"934","date_created":"2018-12-11T11:49:17Z","status":"public","quality_controlled":"1","day":"16","doi":"10.1038/nature21046","publication_status":"published","publication":"Nature","oa_version":"None"},{"year":"2017","language":[{"iso":"eng"}],"publist_id":"6507","issue":"5","author":[{"first_name":"Jakub","last_name":"Sedzinski","full_name":"Sedzinski, Jakub"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"full_name":"Tu, Fan","first_name":"Fan","last_name":"Tu"},{"first_name":"Maté","last_name":"Biro","full_name":"Biro, Maté"},{"full_name":"Wallingford, John","first_name":"John","last_name":"Wallingford"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"RhoA regulates actin network dynamics during apical surface emergence in multiciliated epithelial cells ","date_updated":"2021-01-12T08:22:02Z","publisher":"Company of Biologists","month":"01","intvolume":" 130","date_published":"2017-01-01T00:00:00Z","oa_version":"None","publication_status":"published","doi":"10.1242/jcs.202234","publication":"Journal of Cell Science","day":"01","status":"public","quality_controlled":"1","date_created":"2018-12-11T11:49:17Z","_id":"936","type":"journal_article","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"}],"extern":"1","citation":{"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).","short":"J. Sedzinski, E.B. Hannezo, F. Tu, M. Biro, J. Wallingford, Journal of Cell Science 130 (2017).","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.","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","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."},"volume":130},{"date_updated":"2021-01-12T08:22:02Z","title":"Transmission of cytokinesis forces via E cadherin dilution and actomyosin flows","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Pinheiro, Diana","first_name":"Diana","last_name":"Pinheiro"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sophie","last_name":"Herszterg","full_name":"Herszterg, Sophie"},{"first_name":"Floris","last_name":"Bosveld","full_name":"Bosveld, Floris"},{"first_name":"Isabelle","last_name":"Gaugué","full_name":"Gaugué, Isabelle"},{"full_name":"Balakireva, Maria","first_name":"Maria","last_name":"Balakireva"},{"full_name":"Wang, Zhimin","first_name":"Zhimin","last_name":"Wang"},{"first_name":"Inês","last_name":"Cristo","full_name":"Cristo, Inês"},{"full_name":"Rigaud, Stéphane","first_name":"Stéphane","last_name":"Rigaud"},{"full_name":"Markova, Olga","last_name":"Markova","first_name":"Olga"},{"full_name":"Bellaïche, Yohanns","first_name":"Yohanns","last_name":"Bellaïche"}],"issue":"7652","date_published":"2017-05-04T00:00:00Z","month":"05","intvolume":" 545","publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"year":"2017","page":"103 - 107","publist_id":"6504","date_created":"2018-12-11T11:49:18Z","_id":"937","day":"04","quality_controlled":"1","status":"public","volume":545,"publication_identifier":{"issn":["00280836"]},"extern":"1","citation":{"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","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.","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.","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.","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.","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","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."},"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"}],"type":"journal_article","oa_version":"None","publication":"Nature","doi":"10.1038/nature22041","publication_status":"published"},{"publication_status":"published","type":"dissertation","file_date_updated":"2020-07-14T12:48:15Z","abstract":[{"lang":"eng","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."}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 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.","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.","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.","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","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."},"_id":"938","publist_id":"6483","department":[{"_id":"JiFr"}],"article_processing_charge":"No","pubrep_id":"842","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","file":[{"file_name":"2017_Adamowski-Thesis_Source.docx","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:20Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6215","creator":"dernst","file_size":46903863,"relation":"source_file","access_level":"closed","checksum":"193425764d9aaaed3ac57062a867b315"},{"creator":"dernst","file_size":8698888,"file_id":"6216","content_type":"application/pdf","access_level":"open_access","checksum":"df5ab01be81f821e1b958596a1ec8d21","relation":"main_file","file_name":"2017_Adamowski-Thesis.pdf","date_created":"2019-04-05T09:03:19Z","date_updated":"2020-07-14T12:48:15Z"}],"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","author":[{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","full_name":"Adamowski, Maciek"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.15479/AT:ISTA:th_842","degree_awarded":"PhD","oa_version":"Published Version","related_material":{"record":[{"id":"1591","relation":"part_of_dissertation","status":"public"}]},"supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"status":"public","day":"02","ddc":["581","583","580"],"date_created":"2018-12-11T11:49:18Z","page":"117","year":"2017","month":"06","alternative_title":["ISTA Thesis"],"date_published":"2017-06-02T00:00:00Z","oa":1,"date_updated":"2023-09-07T12:06:09Z"},{"quality_controlled":"1","_id":"939","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","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."}],"publication_identifier":{"issn":["00319007"]},"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.","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.","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.","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","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.","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"},"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Midya","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","full_name":"Midya, Bikashkali"},{"full_name":"Konotop, Vladimir","first_name":"Vladimir","last_name":"Konotop"}],"title":"Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Physical Society","language":[{"iso":"eng"}],"publist_id":"6481","department":[{"_id":"MiLe"}],"article_processing_charge":"No","day":"18","status":"public","date_created":"2018-12-11T11:49:18Z","volume":119,"isi":1,"ec_funded":1,"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.04085 "}],"doi":"10.1103/PhysRevLett.119.033905","publication":"Physical Review Letters","issue":"3","oa":1,"date_updated":"2023-09-26T15:39:46Z","article_number":"033905","intvolume":" 119","month":"07","date_published":"2017-07-18T00:00:00Z","year":"2017","external_id":{"isi":["000405718200012"]}},{"date_published":"2017-10-06T00:00:00Z","intvolume":" 119","month":"10","article_number":"147703","date_updated":"2021-01-12T08:22:04Z","oa":1,"issue":"14","external_id":{"arxiv":["1705.09548"]},"year":"2017","volume":119,"date_created":"2018-12-11T11:44:35Z","day":"06","status":"public","publication":"APS Physics, Physical Review Letters","doi":"10.1103/PhysRevLett.119.147703","main_file_link":[{"url":"https://arxiv.org/abs/1705.09548","open_access":"1"}],"oa_version":"Submitted Version","publisher":"American Physical Society","author":[{"last_name":"Rosenthal","first_name":"Eric","full_name":"Rosenthal, Eric"},{"full_name":"Chapman, Benjamin","last_name":"Chapman","first_name":"Benjamin"},{"orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"},{"first_name":"Joseph","last_name":"Kerckhoff","full_name":"Kerckhoff, Joseph"},{"first_name":"Konrad","last_name":"Lehnert","full_name":"Lehnert, Konrad"}],"title":"Breaking Lorentz reciprocity with frequency conversion and delay","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7960","language":[{"iso":"eng"}],"citation":{"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.","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","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.","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","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.","short":"E. Rosenthal, B. Chapman, A.P. Higginbotham, J. Kerckhoff, K. Lehnert, APS Physics, Physical Review Letters 119 (2017).","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."},"extern":"1","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"}],"arxiv":1,"type":"journal_article","_id":"94","quality_controlled":"1","publication_status":"published"},{"date_updated":"2021-01-12T08:22:05Z","title":"JFIX: Semantics-based repair of Java programs via symbolic PathFinder","author":[{"first_name":"Xuan","last_name":"Le","full_name":"Le, Xuan"},{"id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep","last_name":"Chu","full_name":"Chu, Duc Hiep"},{"first_name":"David","last_name":"Lo","full_name":"Lo, David"},{"full_name":"Le Goues, Claire","last_name":"Le Goues","first_name":"Claire"},{"full_name":"Visser, Willem","first_name":"Willem","last_name":"Visser"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2017-07-10T00:00:00Z","month":"07","publisher":"ACM","language":[{"iso":"eng"}],"year":"2017","page":"376 - 379 ","publist_id":"6478","department":[{"_id":"ToHe"}],"conference":{"end_date":"2017-07-14","start_date":"2017-07-10","name":"ISSTA: International Symposium on Software Testing and Analysis","location":"Santa Barbara, CA, United States"},"_id":"941","date_created":"2018-12-11T11:49:19Z","status":"public","quality_controlled":"1","day":"10","citation":{"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.","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","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.","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.","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.","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"},"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"}],"scopus_import":1,"type":"conference","oa_version":"None","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"publication":"Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis","doi":"10.1145/3092703.3098225","publication_status":"published"},{"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publist_id":"6477","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Xuan","last_name":"Le","full_name":"Le, Xuan"},{"full_name":"Chu, Duc Hiep","first_name":"Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87","last_name":"Chu"},{"first_name":"David","last_name":"Lo","full_name":"Lo, David"},{"full_name":"Le Goues, Claire","first_name":"Claire","last_name":"Le Goues"},{"full_name":"Visser, Willem","first_name":"Willem","last_name":"Visser"}],"title":"S3: Syntax- and semantic-guided repair synthesis via programming by examples","publisher":"ACM","publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"quality_controlled":"1","_id":"942","type":"conference","abstract":[{"lang":"eng","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. "}],"scopus_import":"1","publication_identifier":{"isbn":["978-145035105-8"]},"citation":{"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.","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","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.","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.","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.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, 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"},"year":"2017","conference":{"location":"Paderborn, Germany","name":"FSE: Foundations of Software Engineering","start_date":"2017-09-04","end_date":"2017-09-08"},"external_id":{"isi":["000414279300055"]},"page":"593 - 604","date_updated":"2023-09-26T15:38:36Z","month":"09","date_published":"2017-09-01T00:00:00Z","isi":1,"oa_version":"None","doi":"10.1145/3106237.3106309","day":"01","status":"public","date_created":"2018-12-11T11:49:19Z","volume":"F130154"},{"date_created":"2018-12-11T11:49:20Z","day":"30","status":"public","pmid":1,"volume":356,"isi":1,"ec_funded":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/","open_access":"1"}],"doi":"10.1126/science.aam5887","publication":"Science","date_updated":"2023-09-26T15:38:05Z","issue":"6345","oa":1,"month":"06","intvolume":" 356","date_published":"2017-06-30T00:00:00Z","year":"2017","external_id":{"isi":["000404351500036"],"pmid":["28663499"]},"page":"1379 - 1383","_id":"943","quality_controlled":"1","citation":{"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","short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.","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.","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.","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.","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"},"publication_identifier":{"issn":["00368075"]},"type":"journal_article","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","project":[{"grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"},{"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","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"201439"}],"publication_status":"published","author":[{"first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P"},{"last_name":"Tabata","first_name":"Yoji","full_name":"Tabata, Yoji"},{"full_name":"Brandenberg, Nathalie","last_name":"Brandenberg","first_name":"Nathalie"},{"first_name":"Matthias","last_name":"Lutolf","full_name":"Lutolf, Matthias"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"full_name":"Bollenbach, Tobias","first_name":"Tobias","last_name":"Bollenbach"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","last_name":"Kicheva"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"6474","department":[{"_id":"AnKi"},{"_id":"GaTk"}]},{"date_created":"2018-12-11T11:49:20Z","status":"public","day":"03","volume":94,"ec_funded":1,"oa_version":"None","isi":1,"publication":"Neuron","doi":"10.1016/j.neuron.2017.04.012","date_updated":"2023-09-26T15:37:02Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"issue":"3","date_published":"2017-05-03T00:00:00Z","month":"05","intvolume":" 94","year":"2017","page":"517 - 533.e3","external_id":{"isi":["000400466700011"]},"_id":"944","quality_controlled":"1","citation":{"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.","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","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.","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.","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.","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"},"publication_identifier":{"issn":["08966273"]},"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","type":"journal_article","project":[{"call_identifier":"FP7","grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"}],"publication_status":"published","author":[{"full_name":"Beattie, Robert J","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","last_name":"Beattie"},{"full_name":"Postiglione, Maria P","last_name":"Postiglione","first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Burnett","orcid":"0000-0002-8937-410X","first_name":"Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","full_name":"Burnett, Laura"},{"last_name":"Laukoter","orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne","full_name":"Laukoter, Susanne"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen"},{"full_name":"Pauler, Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xiao","first_name":"Guanxi","full_name":"Xiao, Guanxi"},{"full_name":"Klezovitch, Olga","last_name":"Klezovitch","first_name":"Olga"},{"last_name":"Vasioukhin","first_name":"Valeri","full_name":"Vasioukhin, Valeri"},{"first_name":"Troy","last_name":"Ghashghaei","full_name":"Ghashghaei, Troy"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","publisher":"Cell Press","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"SiHi"},{"_id":"MaJö"}],"publist_id":"6473"},{"intvolume":" 6","month":"11","date_published":"2017-11-15T00:00:00Z","article_number":"e30674","date_updated":"2021-12-14T07:54:36Z","oa":1,"external_id":{"pmid":["29140247"]},"year":"2017","pmid":1,"volume":6,"date_created":"2021-06-02T14:28:58Z","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)"},"ddc":["570"],"status":"public","day":"15","doi":"10.7554/elife.30674","publication":"eLife","oa_version":"Published Version","has_accepted_license":"1","publisher":"eLife Sciences Publications","file":[{"creator":"cziletti","file_size":1603102,"content_type":"application/pdf","file_id":"9446","access_level":"open_access","checksum":"4cfcdd67511ae4aed3d993550e46e146","relation":"main_file","file_name":"2017_eLife_Lyons.pdf","success":1,"date_updated":"2021-06-02T14:33:36Z","date_created":"2021-06-02T14:33:36Z"}],"author":[{"full_name":"Lyons, David B","first_name":"David B","last_name":"Lyons"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","article_processing_charge":"No","department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"eissn":["2050-084X"]},"citation":{"apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674.","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674."},"extern":"1","file_date_updated":"2021-06-02T14:33:36Z","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"_id":"9445","quality_controlled":"1","publication_status":"published"},{"file_date_updated":"2020-07-14T12:48:15Z","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera."}],"publication_identifier":{"issn":["07374038"]},"citation":{"chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2017. https://doi.org/10.1093/molbev/msx190.","short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017.","ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:10.1093/molbev/msx190.","apa":"Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190"},"quality_controlled":"1","_id":"945","publication_status":"published","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF"}],"publisher":"Oxford University Press","has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-12T10:10:23Z","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","relation":"main_file","access_level":"open_access","checksum":"009fd68043211d645ceb9d1de28274f2","creator":"system","file_size":462863,"file_id":"4810","content_type":"application/pdf"}],"author":[{"full_name":"Huylmans, Ann K","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","last_name":"Huylmans"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BeVi"}],"publist_id":"6472","article_processing_charge":"Yes (in subscription journal)","pubrep_id":"848","language":[{"iso":"eng"}],"volume":34,"day":"06","status":"public","ddc":["570","576"],"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":"2018-12-11T11:49:20Z","doi":"10.1093/molbev/msx190","publication":"Molecular Biology and Evolution","isi":1,"oa_version":"Published Version","month":"07","intvolume":" 34","date_published":"2017-07-06T00:00:00Z","issue":"10","oa":1,"date_updated":"2023-09-26T15:36:34Z","external_id":{"isi":["000411814800016"]},"page":"2637 - 2649","year":"2017"},{"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","grant_number":"M02128","name":"Molecular basis of root growth inhibition by auxin","_id":"2572ED28-B435-11E9-9278-68D0E5697425"},{"grant_number":"I 1774-B16","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425"},{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"publication_status":"published","citation":{"apa":"von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., & Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.26792","mla":"von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences Publications, 2017, doi:10.7554/eLife.26792.","ista":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792.","short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","ieee":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017.","ama":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 2017;6. doi:10.7554/eLife.26792","chicago":"Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.26792."},"file_date_updated":"2020-07-14T12:48:15Z","type":"journal_article","scopus_import":"1","abstract":[{"text":"Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.","lang":"eng"}],"_id":"946","quality_controlled":"1","article_processing_charge":"Yes","publist_id":"6471","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"language":[{"iso":"eng"}],"pubrep_id":"847","has_accepted_license":"1","publisher":"eLife Sciences Publications","file":[{"date_created":"2018-12-12T10:17:57Z","date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","relation":"main_file","access_level":"open_access","checksum":"9af3398cb0d81f99d79016a616df22e9","file_id":"5315","content_type":"application/pdf","creator":"system","file_size":19581847}],"title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","author":[{"full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9767-8699","last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas"},{"orcid":"0000-0003-2676-3367","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Barone, Vanessa"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.7554/eLife.26792","publication":"eLife","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5566"}]},"isi":1,"ec_funded":1,"oa_version":"Published Version","volume":6,"date_created":"2018-12-11T11:49:21Z","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)"},"ddc":["570"],"status":"public","day":"19","external_id":{"isi":["000404728300001"]},"year":"2017","month":"06","intvolume":" 6","date_published":"2017-06-19T00:00:00Z","acknowledgement":"Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013 no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop at IST Austria for their contribution to the microscope setup and to Yvonne Kemper for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility","article_number":"e26792","date_updated":"2025-05-07T11:12:33Z","oa":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}]},{"date_updated":"2023-09-22T10:03:50Z","oa":1,"issue":"1","date_published":"2017-07-10T00:00:00Z","intvolume":" 96","month":"07","article_number":"010401","year":"2017","external_id":{"isi":["000405194200002"]},"date_created":"2018-12-11T11:49:21Z","status":"public","day":"10","volume":96,"oa_version":"Submitted Version","ec_funded":1,"isi":1,"publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","doi":"10.1103/PhysRevE.96.010401","main_file_link":[{"url":"https://arxiv.org/abs/1703.00219","open_access":"1"}],"title":"Quantifying the entropic cost of cellular growth control","author":[{"full_name":"De Martino, Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fabrizio","last_name":"Capuani","full_name":"Capuani, Fabrizio"},{"full_name":"De Martino, Andrea","last_name":"De Martino","first_name":"Andrea"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Institute of Physics","language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"6470","department":[{"_id":"GaTk"}],"_id":"947","quality_controlled":"1","citation":{"apa":"De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.010401","mla":"De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.010401.","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","ista":"De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 010401.","ama":"De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.010401","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.010401."},"publication_identifier":{"issn":["24700045"]},"abstract":[{"text":"Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence.","lang":"eng"}],"scopus_import":"1","type":"journal_article","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"publication_status":"published"},{"intvolume":" 10482","month":"01","alternative_title":["LNCS"],"date_published":"2017-01-01T00:00:00Z","date_updated":"2024-03-25T23:30:19Z","oa":1,"page":"59 - 66","external_id":{"isi":["000723567800004"]},"conference":{"location":"Pune, India","name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2017-10-03","end_date":"2017-10-06"},"year":"2017","volume":10482,"date_created":"2018-12-11T11:49:22Z","ddc":["005"],"day":"01","status":"public","doi":"10.1007/978-3-319-68167-2_4","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"isi":1,"ec_funded":1,"oa_version":"Submitted Version","has_accepted_license":"1","publisher":"Springer","file":[{"date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:10:45Z","file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","access_level":"open_access","relation":"main_file","checksum":"a0d9f5f94dc594c4e71e78525c9942f1","content_type":"application/pdf","file_id":"4835","file_size":948514,"creator":"system"}],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir"},{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"JTDec: A tool for tree decompositions in soot","article_processing_charge":"No","publist_id":"6468","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"pubrep_id":"845","publication_identifier":{"issn":["03029743"]},"citation":{"ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66.","ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66.","ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:10.1007/978-3-319-68167-2_4","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66. Springer, 2017. https://doi.org/10.1007/978-3-319-68167-2_4.","apa":"Chatterjee, K., Goharshady, A. K., & Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. https://doi.org/10.1007/978-3-319-68167-2_4","mla":"Chatterjee, Krishnendu, et al. JTDec: A Tool for Tree Decompositions in Soot. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:10.1007/978-3-319-68167-2_4."},"type":"conference","file_date_updated":"2020-07-14T12:48:16Z","scopus_import":"1","abstract":[{"text":"The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs.","lang":"eng"}],"editor":[{"first_name":"Deepak","last_name":"D'Souza","full_name":"D'Souza, Deepak"}],"_id":"949","quality_controlled":"1","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"}],"publication_status":"published"},{"publication_status":"published","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"file_date_updated":"2020-07-14T12:48:16Z","type":"conference","abstract":[{"text":"Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. \r\n","lang":"eng"}],"scopus_import":1,"arxiv":1,"citation":{"short":"G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.","ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21.","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21","mla":"Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21."},"publication_identifier":{"issn":["1868-8969"]},"quality_controlled":"1","_id":"950","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publist_id":"6466","pubrep_id":"844","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"5318","creator":"system","file_size":335170,"relation":"main_file","checksum":"6d5cccf755207b91ccbef95d8275b013","access_level":"open_access","file_name":"IST-2017-844-v1+1_concur-cr.pdf","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:18:00Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Infinite-duration bidding games","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"full_name":"Chonev, Ventsislav K","last_name":"Chonev","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.4230/LIPIcs.CONCUR.2017.21","oa_version":"Published Version","related_material":{"record":[{"id":"6752","relation":"later_version","status":"public"}]},"volume":85,"status":"public","day":"01","ddc":["000"],"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":"2018-12-11T11:49:22Z","conference":{"name":"CONCUR: Concurrency Theory","end_date":"2017-09-07","start_date":"2017-09-05","location":"Berlin, Germany"},"external_id":{"arxiv":["1705.01433"]},"year":"2017","article_number":"17","intvolume":" 85","month":"09","alternative_title":["LIPIcs"],"date_published":"2017-09-01T00:00:00Z","oa":1,"date_updated":"2023-08-29T07:02:13Z"},{"language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"article_processing_charge":"No","file":[{"date_created":"2021-06-07T12:31:36Z","date_updated":"2021-06-07T12:31:36Z","success":1,"file_name":"2017_GenomeBiology_Zilberman.pdf","checksum":"5a455ad914e7d225b1baa4ab07fd925e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"9507","file_size":278183,"creator":"asandaue"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"An evolutionary case for functional gene body methylation in plants and animals","author":[{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"publisher":"Springer Nature","has_accepted_license":"1","publication_status":"published","quality_controlled":"1","_id":"9506","file_date_updated":"2021-06-07T12:31:36Z","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation."}],"extern":"1","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"citation":{"mla":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature, 2017, doi:10.1186/s13059-017-1230-2.","apa":"Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2","chicago":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.","short":"D. Zilberman, Genome Biology 18 (2017).","ieee":"D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.","ista":"Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87.","ama":"Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2"},"year":"2017","external_id":{"pmid":["28486944"]},"issue":"1","oa":1,"date_updated":"2021-12-14T07:55:02Z","article_number":"87","month":"05","intvolume":" 18","date_published":"2017-05-09T00:00:00Z","oa_version":"Published Version","doi":"10.1186/s13059-017-1230-2","publication":"Genome Biology","status":"public","day":"09","ddc":["570"],"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":"2021-06-07T12:27:39Z","pmid":1,"volume":18}]