[{"file_date_updated":"2020-07-14T12:47:01Z","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis"}],"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:51:14Z","citation":{"chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, 10.15479/AT:ISTA:37.","mla":"Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:37.","short":"D. Field, T. Ellis, (2016).","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37","apa":"Field, D., & Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:37"},"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"5553","license":"https://creativecommons.org/publicdomain/zero/1.0/","contributor":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","contributor_type":"project_manager"}],"date_created":"2018-12-12T12:31:30Z","date_published":"2016-02-19T00:00:00Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"doi":"10.15479/AT:ISTA:37","file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","file_id":"5620","checksum":"4ae751b1fa4897fa216241f975a57313","file_size":132808,"date_updated":"2020-07-14T12:47:01Z","creator":"system","file_name":"IST-2016-37-v1+1_paternity_archive.zip","date_created":"2018-12-12T13:03:02Z"}],"day":"19","year":"2016","datarep_id":"37","has_accepted_license":"1","month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org.","lang":"eng"}]},{"file_date_updated":"2020-07-14T12:47:01Z","department":[{"_id":"NiBa"}],"title":"Data on pollinator observations and offpsring phenotypes","article_processing_charge":"No","author":[{"last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","short":"T. Ellis, (2016).","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:35."},"date_updated":"2024-02-21T13:51:27Z","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"5551","contributor":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"date_created":"2018-12-12T12:31:29Z","related_material":{"record":[{"relation":"research_paper","id":"1398","status":"public"}]},"doi":"10.15479/AT:ISTA:35","date_published":"2016-02-19T00:00:00Z","day":"19","file":[{"file_name":"IST-2016-35-v1+1_array_data.zip","date_created":"2018-12-12T13:05:12Z","file_size":32775,"date_updated":"2020-07-14T12:47:01Z","creator":"system","file_id":"5640","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","content_type":"application/zip","relation":"main_file","access_level":"open_access"}],"datarep_id":"35","year":"2016","has_accepted_license":"1","month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}]},{"status":"public","type":"research_data","_id":"5552","file_date_updated":"2020-07-14T12:47:01Z","department":[{"_id":"NiBa"}],"title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","article_processing_charge":"No","author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"T. Ellis, (2016).","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:36","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36","mla":"Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:36.","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, 10.15479/AT:ISTA:36.","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:36."},"date_updated":"2024-02-21T13:51:40Z","month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation.","lang":"eng"}],"contributor":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-12T12:31:30Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"doi":"10.15479/AT:ISTA:36","date_published":"2016-02-19T00:00:00Z","day":"19","file":[{"date_created":"2018-12-12T13:03:07Z","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","creator":"system","date_updated":"2020-07-14T12:47:01Z","file_size":44905,"file_id":"5625","checksum":"cbc61b523d4d475a04a737d50dc470ef","access_level":"open_access","relation":"main_file","content_type":"application/zip"}],"year":"2016","datarep_id":"36","has_accepted_license":"1"},{"date_updated":"2024-02-21T13:50:34Z","citation":{"chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43.","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.","mla":"Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","short":"M. Tugrul, (2016).","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","file_date_updated":"2020-07-14T12:47:01Z","_id":"5554","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"status":"public","datarep_id":"43","year":"2016","has_accepted_license":"1","file":[{"content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","file_id":"5626","date_updated":"2020-07-14T12:47:01Z","file_size":1123495,"creator":"system","date_created":"2018-12-12T13:03:08Z","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip"}],"day":"12","date_created":"2018-12-12T12:31:30Z","contributor":[{"contributor_type":"researcher","first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück"},{"last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","first_name":"Fabienne","contributor_type":"researcher"}],"doi":"10.15479/AT:ISTA:43","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1131"}]},"date_published":"2016-05-12T00:00:00Z","abstract":[{"text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"05"},{"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"640","_id":"5558","publist_id":"6238","author":[{"orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten","last_name":"Bojsen-Hansen","first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:02Z","department":[{"_id":"ChWo"}],"title":"Tracking, Correcting and Absorbing Water Surface Waves","citation":{"apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48","ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:10.15479/AT:ISTA:48","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","short":"M. Bojsen-Hansen, (2016).","mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 10.15479/AT:ISTA:48.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48."},"date_updated":"2024-02-21T13:50:48Z","ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa":1,"month":"09","abstract":[{"text":"PhD thesis LaTeX source code","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"other","status":"public","id":"1122"}]},"doi":"10.15479/AT:ISTA:48","date_published":"2016-09-23T00:00:00Z","date_created":"2018-12-12T12:31:31Z","has_accepted_license":"1","year":"2016","datarep_id":"48","file":[{"file_id":"5589","checksum":"5b1b256ad796fbddb4b7729f5e45e444","access_level":"open_access","relation":"main_file","content_type":"application/x-bzip2","date_created":"2018-12-12T13:02:18Z","file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","creator":"system","date_updated":"2020-07-14T12:47:02Z","file_size":55237885}],"day":"23"},{"type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"status":"public","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"_id":"5556","author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Lukacisin","full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177"},{"first_name":"Matthieu","full_name":"Landon, Matthieu","last_name":"Landon"},{"first_name":"Rishi","last_name":"Jajoo","full_name":"Jajoo, Rishi"}],"article_processing_charge":"No","title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:47:02Z","date_updated":"2024-02-21T13:51:53Z","citation":{"chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:45.","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:45.","mla":"Lukacisin, Martin, et al. MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:45.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:45","ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:10.15479/AT:ISTA:45","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016."},"ddc":["571"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa":1,"month":"08","abstract":[{"text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"deleted","id":"8431"},{"id":"1029","status":"public","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:45","date_published":"2016-08-25T00:00:00Z","date_created":"2018-12-12T12:31:31Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","has_accepted_license":"1","year":"2016","datarep_id":"45","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5616","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","creator":"system","file_size":296722548,"date_updated":"2020-07-14T12:47:02Z","file_name":"IST-2016-45-v1+1_PaperCode.zip","date_created":"2018-12-12T13:02:58Z"}],"day":"25"},{"_id":"1183","article_type":"original","type":"journal_article","pubrep_id":"771","status":"public","date_updated":"2024-03-27T23:30:12Z","ddc":["576","616"],"department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:44:37Z","abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function."}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 167","month":"12","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5030","checksum":"7fe01ab12a6610d3db421e0136db2f77","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","date_created":"2018-12-12T10:13:44Z","file_size":73907957,"date_updated":"2020-07-14T12:44:37Z","creator":"system"}],"related_material":{"record":[{"id":"395","status":"public","relation":"dissertation_contains"}]},"volume":167,"issue":"6","project":[{"grant_number":"F03523","name":"Transmembrane Transporters in Health and Disease","_id":"25473368-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"short":"D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.","ieee":"D.-C. Tarlungeanu et al., “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” Cell, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016.","apa":"Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.013","ama":"Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 2016;167(6):1481-1494. doi:10.1016/j.cell.2016.11.013","mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:10.1016/j.cell.2016.11.013.","ista":"Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.","chicago":"Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.013."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","full_name":"Tarlungeanu, Dora-Clara","last_name":"Tarlungeanu"},{"orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena","last_name":"Deliu","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"last_name":"Dotter","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"last_name":"Kara","full_name":"Kara, Majdi","first_name":"Majdi"},{"last_name":"Janiesch","full_name":"Janiesch, Philipp","first_name":"Philipp"},{"first_name":"Mariafrancesca","last_name":"Scalise","full_name":"Scalise, Mariafrancesca"},{"full_name":"Galluccio, Michele","last_name":"Galluccio","first_name":"Michele"},{"last_name":"Tesulov","full_name":"Tesulov, Mateja","first_name":"Mateja"},{"first_name":"Emanuela","id":"3F4D1282-F248-11E8-B48F-1D18A9856A87","full_name":"Morelli, Emanuela","last_name":"Morelli"},{"first_name":"Fatma","last_name":"Sönmez","full_name":"Sönmez, Fatma"},{"last_name":"Bilgüvar","full_name":"Bilgüvar, Kaya","first_name":"Kaya"},{"first_name":"Ryuichi","full_name":"Ohgaki, Ryuichi","last_name":"Ohgaki"},{"last_name":"Kanai","full_name":"Kanai, Yoshikatsu","first_name":"Yoshikatsu"},{"first_name":"Anide","full_name":"Johansen, Anide","last_name":"Johansen"},{"first_name":"Seham","full_name":"Esharif, Seham","last_name":"Esharif"},{"full_name":"Ben Omran, Tawfeg","last_name":"Ben Omran","first_name":"Tawfeg"},{"first_name":"Meral","last_name":"Topcu","full_name":"Topcu, Meral"},{"first_name":"Avner","full_name":"Schlessinger, Avner","last_name":"Schlessinger"},{"first_name":"Cesare","last_name":"Indiveri","full_name":"Indiveri, Cesare"},{"first_name":"Kent","full_name":"Duncan, Kent","last_name":"Duncan"},{"first_name":"Ahmet","last_name":"Caglayan","full_name":"Caglayan, Ahmet"},{"first_name":"Murat","last_name":"Günel","full_name":"Günel, Murat"},{"full_name":"Gleeson, Joseph","last_name":"Gleeson","first_name":"Joseph"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"publist_id":"6170","title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","acknowledgement":"This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility","oa":1,"publisher":"Cell Press","quality_controlled":"1","year":"2016","has_accepted_license":"1","publication":"Cell","day":"01","page":"1481 - 1494","date_created":"2018-12-11T11:50:35Z","date_published":"2016-12-01T00:00:00Z","doi":"10.1016/j.cell.2016.11.013"},{"month":"10","intvolume":" 18","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion."}],"acknowledged_ssus":[{"_id":"SSU"}],"volume":18,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"323"}]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file":[{"checksum":"e1411cb7c99a2d9089c178a6abef25e7","file_id":"7844","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-14T16:33:46Z","file_name":"2018_NatureCell_Leithner.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:43Z","file_size":4433280}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"1321","file_date_updated":"2020-07-14T12:44:43Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"ddc":["570"],"date_updated":"2024-03-27T23:30:16Z","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the German Research Foundation (DFG) Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria for excellent technical support.","date_published":"2016-10-24T00:00:00Z","doi":"10.1038/ncb3426","date_created":"2018-12-11T11:51:21Z","page":"1253 - 1259","day":"24","publication":"Nature Cell Biology","has_accepted_license":"1","year":"2016","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes","publist_id":"5949","author":[{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"},{"first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","last_name":"Eichner","full_name":"Eichner, Alexander"},{"full_name":"Müller, Jan","last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan"},{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","last_name":"Reversat","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928"},{"first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Markus"},{"last_name":"Schwarz","full_name":"Schwarz, Jan","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"first_name":"David","last_name":"De Gorter","full_name":"De Gorter, David"},{"first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078"},{"last_name":"Bayerl","full_name":"Bayerl, Jonathan","first_name":"Jonathan"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"last_name":"Wieser","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"first_name":"Frank","last_name":"Lai","full_name":"Lai, Frank"},{"first_name":"Markus","last_name":"Moser","full_name":"Moser, Markus"},{"full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki","first_name":"Dontscho"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"},{"last_name":"Small","full_name":"Small, Victor","first_name":"Victor"},{"first_name":"Theresia","last_name":"Stradal","full_name":"Stradal, Theresia"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature Cell Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/ncb3426.","ista":"Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J, De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 18, 1253–1259.","mla":"Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature Cell Biology, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:10.1038/ncb3426.","ama":"Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 2016;18:1253-1259. doi:10.1038/ncb3426","apa":"Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz, J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3426","short":"A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz, J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild, F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt, Nature Cell Biology 18 (2016) 1253–1259.","ieee":"A. F. Leithner et al., “Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes,” Nature Cell Biology, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016."}},{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation."}],"intvolume":" 16","month":"07","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2018-12-12T10:11:04Z","file_size":3921947,"date_created":"2018-12-12T10:11:04Z","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4857"}],"publication_status":"published","ec_funded":1,"issue":"3","volume":16,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"},{"relation":"dissertation_contains","id":"50","status":"public"}]},"_id":"1100","pubrep_id":"754","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570","576"],"date_updated":"2024-03-27T23:30:25Z","file_date_updated":"2018-12-12T10:11:04Z","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.","oa":1,"publisher":"Cell Press","quality_controlled":"1","publication":"Cell Reports","day":"19","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:50:08Z","date_published":"2016-07-19T00:00:00Z","doi":"10.1016/j.celrep.2016.06.036","page":"866 - 877","project":[{"call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","grant_number":"T 560-B17"},{"grant_number":"I 812-B12","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"K. Sako et al., “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” Cell Reports, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877.","ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 2016;16(3):866-877. doi:10.1016/j.celrep.2016.06.036","apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.06.036","mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:10.1016/j.celrep.2016.06.036.","ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877.","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports. Cell Press, 2016. https://doi.org/10.1016/j.celrep.2016.06.036."},"title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","publist_id":"6275","author":[{"last_name":"Sako","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","first_name":"Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Saurabh","full_name":"Pradhan, Saurabh","last_name":"Pradhan"},{"orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mueller, Patrick","last_name":"Mueller","first_name":"Patrick"},{"first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht"},{"orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","last_name":"Capek","first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sanjeev","last_name":"Galande","full_name":"Galande, Sanjeev"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}]},{"department":[{"_id":"KrCh"}],"date_updated":"2024-03-27T23:30:32Z","status":"public","conference":{"start_date":"2016-01-20","location":"St. Petersburg, FL, USA","end_date":"2016-01-22","name":"POPL: Principles of Programming Languages"},"type":"conference","_id":"1437","ec_funded":1,"related_material":{"record":[{"status":"public","id":"5441","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5442"},{"status":"public","id":"821","relation":"dissertation_contains"},{"id":"6009","status":"public","relation":"later_version"},{"status":"public","id":"8934","relation":"dissertation_contains"}]},"volume":"20-22","language":[{"iso":"eng"}],"publication_status":"published","month":"01","main_file_link":[{"url":"http://arxiv.org/abs/1510.07565","open_access":"1"}],"scopus_import":1,"alternative_title":["POPL"],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks."}],"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","external_id":{"arxiv":["1510.07565"]},"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"}],"publist_id":"5761","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. https://doi.org/10.1145/2837614.2837624.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837624","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:10.1145/2837614.2837624","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","mla":"Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. Vol. 20–22, ACM, 2016, pp. 733–47, doi:10.1145/2837614.2837624."},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:52:01Z","doi":"10.1145/2837614.2837624","date_published":"2016-01-11T00:00:00Z","page":"733 - 747","day":"11","year":"2016","oa":1,"publisher":"ACM","quality_controlled":"1"},{"day":"01","year":"2016","date_created":"2018-12-11T11:51:43Z","doi":"10.1007/978-3-319-41528-4_1","date_published":"2016-07-01T00:00:00Z","page":"3 - 22","oa":1,"quality_controlled":"1","publisher":"Springer","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2016). Termination analysis of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41528-4_1","ama":"Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:10.1007/978-3-319-41528-4_1","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9779, pp. 3–22.","mla":"Chatterjee, Krishnendu, et al. Termination Analysis of Probabilistic Programs through Positivstellensatz’s. Vol. 9779, Springer, 2016, pp. 3–22, doi:10.1007/978-3-319-41528-4_1.","ista":"Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS, vol. 9779, 3–22.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer, 2016. https://doi.org/10.1007/978-3-319-41528-4_1."},"title":"Termination analysis of probabilistic programs through Positivstellensatz's","publist_id":"5824","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","full_name":"Fu, Hongfei"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":9779,"related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs."}],"intvolume":" 9779","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1604.07169"}],"alternative_title":["LNCS"],"scopus_import":1,"date_updated":"2024-03-27T23:30:32Z","department":[{"_id":"KrCh"}],"_id":"1386","status":"public","conference":{"location":"Toronto, Canada","end_date":"2016-07-23","start_date":"2016-07-17","name":"CAV: Computer Aided Verification"},"type":"conference"},{"date_created":"2022-02-25T11:42:25Z","doi":"10.3389/fenvs.2015.00042","date_published":"2015-06-10T00:00:00Z","year":"2015","has_accepted_license":"1","publication":"Frontiers in Environmental Science","day":"10","oa":1,"quality_controlled":"1","publisher":"Frontiers","acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","article_processing_charge":"No","author":[{"last_name":"Parise","full_name":"Parise, Francesca","first_name":"Francesca"},{"last_name":"Lygeros","full_name":"Lygeros, John","first_name":"John"},{"orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob"}],"title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","citation":{"ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” Frontiers in Environmental Science, vol. 3. Frontiers, 2015.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","apa":"Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042","ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_number":"42","ec_funded":1,"volume":3,"publication_status":"published","publication_identifier":{"issn":["2296-665X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"26c222487564e1be02a11d688d6f769d","file_id":"10795","file_size":1371201,"date_updated":"2022-02-25T11:55:26Z","creator":"dernst","file_name":"2015_FrontiersEnvironmScience_Parise.pdf","date_created":"2022-02-25T11:55:26Z"}],"scopus_import":"1","intvolume":" 3","month":"06","abstract":[{"lang":"eng","text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation."}],"oa_version":"Published Version","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"file_date_updated":"2022-02-25T11:55:26Z","date_updated":"2022-02-25T11:59:23Z","ddc":["000","570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["General Environmental Science"],"status":"public","_id":"10794"},{"publication":"Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","year":"2015","date_created":"2022-02-25T12:18:43Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1137/1.9781611973730.69","page":"1018-1029","acknowledgement":"The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","quality_controlled":"1","publisher":"SIAM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2015:1018–29. SIAM, 2015. https://doi.org/10.1137/1.9781611973730.69.","ama":"Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2015. SIAM; 2015:1018-1029. doi:10.1137/1.9781611973730.69","apa":"Chatterjee, K., & Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. https://doi.org/10.1137/1.9781611973730.69","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:10.1137/1.9781611973730.69."},"title":"The value 1 problem under finite-memory strategies for concurrent mean-payoff games","external_id":{"arxiv":["1409.6690"]},"article_processing_charge":"No","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-161197374-7"]},"ec_funded":1,"volume":2015,"issue":"1","oa_version":"Preprint","abstract":[{"text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy).","lang":"eng"}],"intvolume":" 2015","month":"01","scopus_import":"1","date_updated":"2022-02-25T12:33:32Z","department":[{"_id":"KrCh"}],"_id":"10796","status":"public","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2015-01-04","end_date":"2015-01-06","location":"San Diego, CA, United States"},"type":"conference"},{"title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","author":[{"last_name":"Yu","full_name":"Yu, Luo","first_name":"Luo"},{"first_name":"Stefan","last_name":"Scholl","full_name":"Scholl, Stefan"},{"first_name":"Anett","full_name":"Doering, Anett","last_name":"Doering"},{"first_name":"Zhang","last_name":"Yi","full_name":"Yi, Zhang"},{"last_name":"Irani","full_name":"Irani, Niloufer","first_name":"Niloufer"},{"last_name":"Di Rubbo","full_name":"Di Rubbo, Simone","first_name":"Simone"},{"first_name":"Lutz","full_name":"Neumetzler, Lutz","last_name":"Neumetzler"},{"full_name":"Krishnamoorthy, Praveen","last_name":"Krishnamoorthy","first_name":"Praveen"},{"first_name":"Isabelle","full_name":"Van Houtte, Isabelle","last_name":"Van Houtte"},{"last_name":"Mylle","full_name":"Mylle, Evelien","first_name":"Evelien"},{"first_name":"Volker","last_name":"Bischoff","full_name":"Bischoff, Volker"},{"first_name":"Samantha","last_name":"Vernhettes","full_name":"Vernhettes, Samantha"},{"first_name":"Johan","last_name":"Winne","full_name":"Winne, Johan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"York","last_name":"Stierhof","full_name":"Stierhof, York"},{"last_name":"Schumacher","full_name":"Schumacher, Karin","first_name":"Karin"},{"full_name":"Persson, Staffan","last_name":"Persson","first_name":"Staffan"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"}],"publist_id":"5827","article_processing_charge":"No","external_id":{"pmid":["27250258"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing Group, 2015. https://doi.org/10.1038/nplants.2015.94.","ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094.","mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:10.1038/nplants.2015.94.","ieee":"L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing Group, 2015.","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015).","ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7). doi:10.1038/nplants.2015.94","apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94"},"article_number":"15094","date_published":"2015-07-06T00:00:00Z","doi":"10.1038/nplants.2015.94","date_created":"2018-12-11T11:51:42Z","day":"06","publication":"Nature Plants","year":"2015","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:50:18Z","status":"public","type":"journal_article","article_type":"original","_id":"1383","volume":1,"issue":"7","language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 1","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/","open_access":"1"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants.","lang":"eng"}]},{"author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","full_name":"Pentina, Anastasia","last_name":"Pentina"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"publist_id":"5781","title":"Lifelong learning with non-i.i.d. tasks","citation":{"mla":"Pentina, Anastasia, and Christoph Lampert. Lifelong Learning with Non-i.i.d. Tasks. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48.","ieee":"A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 2015, pp. 1540–1548.","short":"A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015, pp. 1540–1548.","apa":"Pentina, A., & Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks (Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ama":"Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015. Neural Information Processing Systems; 2015:1540-1548.","chicago":"Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d. Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015.","ista":"Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 2015, 1540–1548."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"page":"1540 - 1548","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:51:57Z","year":"2015","day":"01","quality_controlled":"1","publisher":"Neural Information Processing Systems","oa":1,"department":[{"_id":"ChLa"}],"date_updated":"2021-01-12T06:50:39Z","type":"conference","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2015-12-07","location":"Montreal, Canada","end_date":"2015-12-12"},"status":"public","_id":"1425","volume":2015,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"alternative_title":["Advances in Neural Information Processing Systems"],"main_file_link":[{"open_access":"1","url":"http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks"}],"month":"01","intvolume":" 2015","abstract":[{"lang":"eng","text":"In this work we aim at extending the theoretical foundations of lifelong learning. Previous work analyzing this scenario is based on the assumption that learning tasks are sampled i.i.d. from a task environment or limited to strongly constrained data distributions. Instead, we study two scenarios when lifelong learning is possible, even though the observed tasks do not form an i.i.d. sample: first, when they are sampled from the same environment, but possibly with dependencies, and second, when the task environment is allowed to change over time in a consistent way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct generalization of the analogous previous result for the i.i.d. case. For the second scenario we propose to learn an inductive bias in form of a transfer procedure. We present a generalization bound and show on a toy example how it can be used to identify a beneficial transfer algorithm."}],"oa_version":"None"},{"language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","date_created":"2018-12-11T11:51:56Z","date_published":"2015-12-01T00:00:00Z","volume":28,"page":"3070 - 3078","acknowledgement":"This work was partially supported by the Austrian Science FUnd, project no. KLI 00012.","oa_version":"Submitted Version","abstract":[{"text":"We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data.","lang":"eng"}],"intvolume":" 28","month":"12","main_file_link":[{"url":"https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective","open_access":"1"}],"oa":1,"alternative_title":["Advances in Neural Information Processing Systems"],"publisher":"Neural Information Processing Systems","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems; 2015:3070-3078.","apa":"Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","short":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems, 2015, pp. 3070–3078.","ieee":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.","mla":"Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective. Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78.","ista":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.","chicago":"Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems, 2015."},"date_updated":"2021-01-12T06:50:38Z","title":"Statistical topological data analysis-A kernel perspective","department":[{"_id":"HeEd"}],"author":[{"last_name":"Kwitt","full_name":"Kwitt, Roland","first_name":"Roland"},{"first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","last_name":"Huber"},{"first_name":"Marc","full_name":"Niethammer, Marc","last_name":"Niethammer"},{"first_name":"Weili","full_name":"Lin, Weili","last_name":"Lin"},{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","last_name":"Bauer"}],"publist_id":"5782","_id":"1424","status":"public","conference":{"end_date":"2015-12-12","location":"Montreal, Canada","start_date":"2015-12-07","name":"NIPS: Neural Information Processing Systems"},"type":"conference"},{"type":"conference","conference":{"name":"GECCO: Genetic and evolutionary computation conference","start_date":"2015-07-11","location":"Madrid, Spain","end_date":"2015-07-15"},"project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"}],"status":"public","_id":"1430","author":[{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao"},{"first_name":"Dirk","full_name":"Sudholt, Dirk","last_name":"Sudholt"},{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova"}],"publist_id":"5768","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"title":"First steps towards a runtime comparison of natural and artificial evolution","date_updated":"2021-01-12T06:50:41Z","citation":{"mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.","apa":"Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758","ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462.","chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758.","ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","scopus_import":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.06260"}],"oa":1,"month":"07","abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"oa_version":"Preprint","page":"1455 - 1462","doi":"10.1145/2739480.2754758","date_published":"2015-07-11T00:00:00Z","date_created":"2018-12-11T11:51:58Z","ec_funded":1,"publication_status":"published","year":"2015","day":"11","language":[{"iso":"eng"}],"publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation"},{"publication_status":"published","year":"2015","language":[{"iso":"eng"}],"day":"04","page":"46-60","ec_funded":1,"date_created":"2018-12-11T11:52:14Z","doi":"10.1109/CSF.2015.11","date_published":"2015-09-04T00:00:00Z","abstract":[{"lang":"eng","text":"Cryptographic access control offers selective access to encrypted data via a combination of key management and functionality-rich cryptographic schemes, such as attribute-based encryption. Using this approach, publicly available meta-data may inadvertently leak information on the access policy that is enforced by cryptography, which renders cryptographic access control unusable in settings where this information is highly sensitive. We begin to address this problem by presenting rigorous definitions for policy privacy in cryptographic access control. For concreteness we set our results in the model of Role-Based Access Control (RBAC), where we identify and formalize several different flavors of privacy, however, our framework should serve as inspiration for other models of access control. Based on our insights we propose a new system which significantly improves on the privacy properties of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving attribute-based encryption, which we introduce and show how to instantiate. We present our results in the context of a cryptographic RBAC system by Ferrara et al. (CSF'13), which uses cryptography to control read access to files, while write access is still delegated to trusted monitors. We give an extension of the construction that permits cryptographic control over write access. Our construction assumes that key management uses out-of-band channels between the policy enforcer and the users but eliminates completely the need for monitoring read/write access to the data."}],"oa_version":"Submitted Version","oa":1,"main_file_link":[{"open_access":"1","url":"http://epubs.surrey.ac.uk/808055/"}],"publisher":"IEEE","quality_controlled":"1","month":"09","citation":{"short":"A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60.","ieee":"A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic access control,” presented at the CSF: Computer Security Foundations, Verona, Italy, 2015, pp. 46–60.","ama":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic access control. In: IEEE; 2015:46-60. doi:10.1109/CSF.2015.11","apa":"Ferrara, A., Fuchsbauer, G., Liu, B., & Warinschi, B. (2015). Policy privacy in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security Foundations, Verona, Italy: IEEE. https://doi.org/10.1109/CSF.2015.11","mla":"Ferrara, Anna, et al. Policy Privacy in Cryptographic Access Control. IEEE, 2015, pp. 46–60, doi:10.1109/CSF.2015.11.","ista":"Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic access control. CSF: Computer Security Foundations, 46–60.","chicago":"Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. https://doi.org/10.1109/CSF.2015.11."},"date_updated":"2021-01-12T06:50:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"5722","author":[{"first_name":"Anna","last_name":"Ferrara","full_name":"Ferrara, Anna"},{"last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"full_name":"Liu, Bin","last_name":"Liu","first_name":"Bin"},{"first_name":"Bogdan","last_name":"Warinschi","full_name":"Warinschi, Bogdan"}],"title":"Policy privacy in cryptographic access control","department":[{"_id":"KrPi"}],"_id":"1474","conference":{"name":"CSF: Computer Security Foundations","location":"Verona, Italy","end_date":"2015-07-17","start_date":"2015-07-13"},"type":"conference","status":"public","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}]},{"year":"2015","publication_status":"published","publication_identifier":{"eisbn":["978-1-4673-6964-0 "]},"language":[{"iso":"eng"}],"day":"14","page":"4741 - 4748","date_created":"2018-12-11T11:52:17Z","date_published":"2015-10-14T00:00:00Z","doi":"10.1109/CVPR.2015.7299106","abstract":[{"lang":"eng","text":"Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes."}],"oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1412.6821","open_access":"1"}],"oa":1,"scopus_import":1,"publisher":"IEEE","month":"10","date_updated":"2021-01-12T06:51:03Z","citation":{"mla":"Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106.","ieee":"J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel for topological machine learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.","short":"J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.","ama":"Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106","apa":"Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106","chicago":"Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106.","ista":"Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel for topological machine learning. CVPR: Computer Vision and Pattern Recognition, 4741–4748."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer"},{"last_name":"Kwitt","full_name":"Kwitt, Roland","first_name":"Roland"}],"publist_id":"5709","department":[{"_id":"HeEd"}],"title":"A stable multi-scale kernel for topological machine learning","_id":"1483","conference":{"location":"Boston, MA, USA","end_date":"2015-06-12","start_date":"2015-06-07","name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","status":"public"},{"series_title":"Leibniz International Proceedings in Informatics","_id":"1498","conference":{"end_date":"2015-05-06","location":"Asilomar, CA, United States","start_date":"2015-05-03","name":"SNAPL: Summit oN Advances in Programming Languages"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"499","status":"public","date_updated":"2020-08-11T10:09:14Z","ddc":["005"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:44:58Z","abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 32","month":"01","publication_status":"published","publication_identifier":{"isbn":["978-3-939897-80-4 "]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"cf5e94baa89a2dc4c5de01abc676eda8","file_id":"5050","date_updated":"2020-07-14T12:44:58Z","file_size":489362,"creator":"system","date_created":"2018-12-12T10:14:02Z","file_name":"IST-2016-499-v1+1_9.pdf"}],"ec_funded":1,"volume":32,"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for Language Support for Fault-Tolerant Distributed Systems.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90.","ista":"Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for fault-tolerant distributed systems. 32, 90–102.","mla":"Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 90–102, 2015.","ama":"Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90","apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language support for fault-tolerant distributed systems. Presented at the SNAPL: Summit oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Dragoi","full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Zufferey","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien"}],"publist_id":"5681","title":"The need for language support for fault-tolerant distributed systems","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","year":"2015","has_accepted_license":"1","day":"01","page":"90 - 102","date_created":"2018-12-11T11:52:22Z","date_published":"2015-01-01T00:00:00Z","doi":"10.4230/LIPIcs.SNAPL.2015.90"},{"department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:44:58Z","date_updated":"2021-01-12T06:51:09Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"1497","issue":"21","volume":43,"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"385b83854fd0eb2e4f386867da2823e2","file_id":"5768","date_updated":"2020-07-14T12:44:58Z","file_size":6863297,"creator":"dernst","date_created":"2018-12-20T14:18:57Z","file_name":"2015_NucleicAcidsRes_Andergassen.pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"07","intvolume":" 43","abstract":[{"lang":"eng","text":"Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide."}],"oa_version":"Published Version","author":[{"full_name":"Andergassen, Daniel","last_name":"Andergassen","first_name":"Daniel"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Dotter, Christoph","last_name":"Dotter"},{"first_name":"Tomasz","full_name":"Kulinski, Tomasz","last_name":"Kulinski"},{"first_name":"Philipp","last_name":"Guenzl","full_name":"Guenzl, Philipp"},{"first_name":"Philipp","last_name":"Bammer","full_name":"Bammer, Philipp"},{"first_name":"Denise","last_name":"Barlow","full_name":"Barlow, Denise"},{"first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"first_name":"Quanah","full_name":"Hudson, Quanah","last_name":"Hudson"}],"publist_id":"5682","title":"Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data","citation":{"mla":"Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727.","short":"D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).","ieee":"D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” Nucleic Acids Research, vol. 43, no. 21. Oxford University Press, 2015.","apa":"Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv727","ama":"Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 2015;43(21). doi:10.1093/nar/gkv727","chicago":"Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727.","ista":"Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e146","date_published":"2015-07-21T00:00:00Z","doi":"10.1093/nar/gkv727","date_created":"2018-12-11T11:52:22Z","has_accepted_license":"1","year":"2015","day":"21","publication":"Nucleic Acids Research","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"acknowledgement":"Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna."},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Madrid, Spain","end_date":"2015-09-04","start_date":"2015-09-01","name":"CONCUR: Concurrency Theory"},"type":"conference","pubrep_id":"498","status":"public","_id":"1499","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:44:58Z","date_updated":"2021-01-12T06:51:10Z","ddc":["000","003"],"scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 42","month":"01","abstract":[{"text":"We consider weighted automata with both positive and negative integer weights on edges and\r\nstudy the problem of synchronization using adaptive strategies that may only observe whether\r\nthe current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":42,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:08:12Z","file_name":"IST-2016-498-v1+1_32.pdf","creator":"system","date_updated":"2020-07-14T12:44:58Z","file_size":623563,"checksum":"49eb5021caafaabe5356c65b9c5f8c9c","file_id":"4672","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"publist_id":"5680","author":[{"last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kim","last_name":"Larsen","full_name":"Larsen, Kim"},{"first_name":"Simon","full_name":"Laursen, Simon","last_name":"Laursen"},{"full_name":"Srba, Jiří","last_name":"Srba","first_name":"Jiří"}],"title":"Polynomial time decidability of weighted synchronization under partial observability","citation":{"chicago":"Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time Decidability of Weighted Synchronization under Partial Observability,” 42:142–54. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142.","ista":"Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability of weighted synchronization under partial observability. CONCUR: Concurrency Theory, LIPIcs, vol. 42, 142–154.","mla":"Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142.","ama":"Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142","apa":"Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial time decidability of weighted synchronization under partial observability (Vol. 42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142","ieee":"J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability of weighted synchronization under partial observability,” presented at the CONCUR: Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.","short":"J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–154."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Czech Science Foundation under grant agreement P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734.","page":"142 - 154","date_created":"2018-12-11T11:52:22Z","doi":"10.4230/LIPIcs.CONCUR.2015.142","date_published":"2015-01-01T00:00:00Z","year":"2015","has_accepted_license":"1","day":"01"},{"month":"08","scopus_import":1,"quality_controlled":"1","publisher":"Queen's University","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.03402"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. "}],"volume":"2015-August","date_published":"2015-08-01T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:52:21Z","page":"128-135","day":"01","publication":"Proceedings of the 27th Canadian Conference on Computational Geometry","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","status":"public","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","name":"Topological Complex Systems"}],"type":"conference","conference":{"location":"Ontario, Canada","end_date":"2015-08-12","start_date":"2015-08-10","name":"CCCG: Canadian Conference on Computational Geometry"},"_id":"1495","department":[{"_id":"HeEd"}],"title":"Relaxed disk packing","author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel"},{"first_name":"Vitaliy","full_name":"Kurlin, Vitaliy","last_name":"Kurlin"}],"publist_id":"5684","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:09Z","citation":{"mla":"Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the 27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s University, 2015, pp. 128–35.","apa":"Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk packing. In Proceedings of the 27th Canadian Conference on Computational Geometry (Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.","ama":"Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings of the 27th Canadian Conference on Computational Geometry. Vol 2015-August. Queen’s University; 2015:128-135.","ieee":"H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in Proceedings of the 27th Canadian Conference on Computational Geometry, Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.","short":"H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.","chicago":"Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational Geometry, 2015–August:128–35. Queen’s University, 2015.","ista":"Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry vol. 2015–August, 128–135."}},{"day":"11","has_accepted_license":"1","year":"2015","doi":"10.4230/LIPIcs.SOCG.2015.842","date_published":"2015-06-11T00:00:00Z","date_created":"2018-12-11T11:52:26Z","page":"842 - 856","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.842.","ista":"Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.","mla":"Franek, Peter, and Marek Krcál. On Computability and Triviality of Well Groups. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–56, doi:10.4230/LIPIcs.SOCG.2015.842.","short":"P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856.","ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 842–856.","apa":"Franek, P., & Krcál, M. (2015). On computability and triviality of well groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.842","ama":"Franek P, Krcál M. On computability and triviality of well groups. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:10.4230/LIPIcs.SOCG.2015.842"},"title":"On computability and triviality of well groups","publist_id":"5667","author":[{"last_name":"Franek","full_name":"Franek, Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"last_name":"Krcál","full_name":"Krcál, Marek","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"49eb5021caafaabe5356c65b9c5f8c9c","file_id":"5001","creator":"system","file_size":623563,"date_updated":"2020-07-14T12:44:59Z","file_name":"IST-2016-503-v1+1_32.pdf","date_created":"2018-12-12T10:13:19Z"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","id":"1408","status":"public"}]},"volume":34,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. ","lang":"eng"}],"month":"06","intvolume":" 34","alternative_title":["LIPIcs"],"scopus_import":1,"ddc":["510"],"date_updated":"2023-02-21T17:02:57Z","file_date_updated":"2020-07-14T12:44:59Z","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"_id":"1510","status":"public","pubrep_id":"503","type":"conference","conference":{"start_date":"2015-06-22","location":"Eindhoven, Netherlands","end_date":"2015-06-25","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"status":"public","type":"journal_article","_id":"1505","title":"Universality for the largest eigenvalue of sample covariance matrices with general population","department":[{"_id":"LaEr"}],"author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang"},{"last_name":"Pan","full_name":"Pan, Guangming","first_name":"Guangming"},{"first_name":"Wang","last_name":"Zhou","full_name":"Zhou, Wang"}],"publist_id":"5672","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 43(1), 382–421.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/14-AOS1281.","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/14-AOS1281","ama":"Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 2015;43(1):382-421. doi:10.1214/14-AOS1281","ieee":"Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample covariance matrices with general population,” Annals of Statistics, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.","short":"Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.","mla":"Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:10.1214/14-AOS1281."},"date_updated":"2021-01-12T06:51:14Z","intvolume":" 43","month":"02","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1304.5690","open_access":"1"}],"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","acknowledgement":"B.Z. was supported in part by NSFC Grant 11071213, ZJNSF Grant R6090034 and SRFDP Grant 20100101110001. P.G. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11, and by a Grant R-155-000-131-112 at the National University of Singapore\r\n","oa_version":"Preprint","abstract":[{"text":"This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed.","lang":"eng"}],"date_created":"2018-12-11T11:52:25Z","volume":43,"date_published":"2015-02-01T00:00:00Z","doi":"10.1214/14-AOS1281","issue":"1","page":"382 - 421","language":[{"iso":"eng"}],"publication":"Annals of Statistics","day":"01","publication_status":"published","year":"2015"},{"type":"journal_article","status":"public","_id":"1508","publist_id":"5669","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"last_name":"Yau","full_name":"Yau, Horng","first_name":"Horng"}],"department":[{"_id":"LaEr"}],"title":"Gap universality of generalized Wigner and β ensembles","date_updated":"2021-01-12T06:51:15Z","citation":{"chicago":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society. European Mathematical Society, 2015. https://doi.org/10.4171/JEMS/548.","ista":"Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036.","mla":"Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society, vol. 17, no. 8, European Mathematical Society, 2015, pp. 1927–2036, doi:10.4171/JEMS/548.","apa":"Erdös, L., & Yau, H. (2015). Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/548","ama":"Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 2015;17(8):1927-2036. doi:10.4171/JEMS/548","ieee":"L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,” Journal of the European Mathematical Society, vol. 17, no. 8. European Mathematical Society, pp. 1927–2036, 2015.","short":"L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1211.3786"}],"oa":1,"scopus_import":1,"quality_controlled":"1","publisher":"European Mathematical Society","intvolume":" 17","month":"08","abstract":[{"text":"We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential.","lang":"eng"}],"oa_version":"Preprint","page":"1927 - 2036","date_created":"2018-12-11T11:52:26Z","issue":"8","date_published":"2015-08-01T00:00:00Z","volume":17,"doi":"10.4171/JEMS/548","publication_status":"published","year":"2015","publication":"Journal of the European Mathematical Society","language":[{"iso":"eng"}],"day":"01"},{"type":"journal_article","status":"public","_id":"1506","publist_id":"5671","author":[{"full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang"},{"first_name":"Guangming","last_name":"Pan","full_name":"Pan, Guangming"},{"full_name":"Zhou, Wang","last_name":"Zhou","first_name":"Wang"}],"department":[{"_id":"LaEr"}],"title":"The logarithmic law of random determinant","date_updated":"2021-01-12T06:51:14Z","citation":{"ista":"Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2015. https://doi.org/10.3150/14-BEJ615.","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). The logarithmic law of random determinant. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/14-BEJ615","ama":"Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. Bernoulli. 2015;21(3):1600-1628. doi:10.3150/14-BEJ615","ieee":"Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” Bernoulli, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015.","short":"Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.","mla":"Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” Bernoulli, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:10.3150/14-BEJ615."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Bernoulli Society for Mathematical Statistics and Probability","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.5823"}],"month":"08","intvolume":" 21","abstract":[{"text":"Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).","lang":"eng"}],"oa_version":"Preprint","page":"1600 - 1628","volume":21,"doi":"10.3150/14-BEJ615","date_published":"2015-08-01T00:00:00Z","issue":"3","date_created":"2018-12-11T11:52:25Z","publication_status":"published","year":"2015","day":"01","publication":"Bernoulli","language":[{"iso":"eng"}]},{"quality_controlled":"1","publisher":"Oxford University Press","oa":1,"day":"01","publication":"Genome Biology and Evolution","has_accepted_license":"1","year":"2015","date_published":"2015-12-01T00:00:00Z","doi":"10.1093/gbe/evv215","date_created":"2018-12-11T11:52:27Z","page":"3259 - 3268","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.","ista":"Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12), 3259–3268.","mla":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.","ama":"Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268. doi:10.1093/gbe/evv215","apa":"Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215","ieee":"A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” Genome Biology and Evolution, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268."},"title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression","author":[{"first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","full_name":"Pal, Arka"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"publist_id":"5664","article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. ","lang":"eng"}],"month":"12","intvolume":" 7","scopus_import":1,"file":[{"creator":"system","file_size":858027,"date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","date_created":"2018-12-12T10:17:29Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","file_id":"5284"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"12","volume":7,"ec_funded":1,"_id":"1513","status":"public","pubrep_id":"496","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2021-01-12T06:51:18Z","file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"BeVi"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:10.1214/ECP.v20-4315.","ama":"Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 2015;20. doi:10.1214/ECP.v20-4315","apa":"Erbar, M., Maas, J., & Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v20-4315","short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015).","ieee":"M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” Electronic Communications in Probability, vol. 20. Institute of Mathematical Statistics, 2015.","chicago":"Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/ECP.v20-4315.","ista":"Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89."},"title":"From large deviations to Wasserstein gradient flows in multiple dimensions","author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Michiel","last_name":"Renger","full_name":"Renger, Michiel"}],"publist_id":"5660","article_number":"89","day":"29","publication":"Electronic Communications in Probability","has_accepted_license":"1","year":"2015","doi":"10.1214/ECP.v20-4315","date_published":"2015-11-29T00:00:00Z","date_created":"2018-12-11T11:52:29Z","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"ddc":["519"],"date_updated":"2021-01-12T06:51:19Z","file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"JaMa"}],"_id":"1517","status":"public","pubrep_id":"494","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"checksum":"135741c17d3e1547ca696b6fbdcd559c","file_id":"4828","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf","date_created":"2018-12-12T10:10:39Z","creator":"system","file_size":230525,"date_updated":"2020-07-14T12:45:00Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":20,"oa_version":"Published Version","abstract":[{"text":"We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n","lang":"eng"}],"month":"11","intvolume":" 20","scopus_import":1},{"oa":1,"quality_controlled":"1","publisher":"Wiley","page":"1101 - 1112","date_created":"2018-12-11T11:52:29Z","date_published":"2015-03-19T00:00:00Z","doi":"10.1111/evo.12641","year":"2015","has_accepted_license":"1","publication":"Evolution","day":"19","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"publist_id":"5656","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Servedio","full_name":"Servedio, Maria","first_name":"Maria"}],"title":"The interpretation of selection coefficients","citation":{"chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641","apa":"Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 69","month":"03","abstract":[{"lang":"eng","text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so."}],"oa_version":"Submitted Version","ec_funded":1,"issue":"5","volume":69,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:00Z","file_size":188872,"creator":"system","date_created":"2018-12-12T10:10:34Z","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"fd8d23f476bc194419929b72ca265c02","file_id":"4822"},{"file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","date_created":"2018-12-12T10:10:35Z","file_size":577415,"date_updated":"2020-07-14T12:45:00Z","creator":"system","file_id":"4823","checksum":"b774911e70044641d556e258efcb52ef","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"type":"journal_article","pubrep_id":"560","status":"public","_id":"1519","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:00Z","date_updated":"2021-01-12T06:51:20Z","ddc":["570"]},{"day":"01","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-3496-9"]},"year":"2015","publication_status":"published","date_published":"2015-08-01T00:00:00Z","doi":"10.1145/2786784.2786803","date_created":"2018-12-11T11:52:30Z","page":"93 - 100","oa_version":"None","abstract":[{"text":"Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs.","lang":"eng"}],"month":"08","publisher":"ACM","scopus_import":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:21Z","citation":{"ista":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. 2015. Computational design of walking automata. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 93–100.","chicago":"Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100. ACM, 2015. https://doi.org/10.1145/2786784.2786803.","ieee":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, and H. Pfister, “Computational design of walking automata,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States, 2015, pp. 93–100.","short":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister, in:, ACM, 2015, pp. 93–100.","apa":"Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., & Pfister, H. (2015). Computational design of walking automata (pp. 93–100). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2786784.2786803","ama":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational design of walking automata. In: ACM; 2015:93-100. doi:10.1145/2786784.2786803","mla":"Bharaj, Gaurav, et al. Computational Design of Walking Automata. ACM, 2015, pp. 93–100, doi:10.1145/2786784.2786803."},"title":"Computational design of walking automata","department":[{"_id":"BeBi"}],"publist_id":"5655","author":[{"first_name":"Gaurav","full_name":"Bharaj, Gaurav","last_name":"Bharaj"},{"first_name":"Stelian","last_name":"Coros","full_name":"Coros, Stelian"},{"first_name":"Bernhard","last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard"},{"first_name":"James","last_name":"Tompkin","full_name":"Tompkin, James"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hanspeter","full_name":"Pfister, Hanspeter","last_name":"Pfister"}],"_id":"1520","status":"public","type":"conference","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2015-08-07","location":"Los Angeles, CA, United States","end_date":"2015-08-09"}},{"publisher":"CSIRO","quality_controlled":"1","publication":"Functional Plant Biology","day":"01","year":"2015","date_created":"2018-12-11T11:52:34Z","doi":"10.1071/FP14171","date_published":"2015-03-01T00:00:00Z","page":"239 - 251","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.","chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology. CSIRO, 2015. https://doi.org/10.1071/FP14171.","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” Functional Plant Biology, vol. 42, no. 3. CSIRO, pp. 239–251, 2015.","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 2015;42(3):239-251. doi:10.1071/FP14171","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., & Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. CSIRO. https://doi.org/10.1071/FP14171","mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:10.1071/FP14171."},"title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","article_processing_charge":"No","external_id":{"pmid":["32480670"]},"author":[{"last_name":"Yang","full_name":"Yang, Huaiyu","first_name":"Huaiyu"},{"last_name":"Von Der Fecht Bartenbach","full_name":"Von Der Fecht Bartenbach, Jenny","first_name":"Jenny"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lohmann, Jan","last_name":"Lohmann","first_name":"Jan"},{"first_name":"Benjamin","full_name":"Neuhäuser, Benjamin","last_name":"Neuhäuser"},{"full_name":"Ludewig, Uwe","last_name":"Ludewig","first_name":"Uwe"}],"publist_id":"5639","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels."}],"intvolume":" 42","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1445-4408"]},"issue":"3","volume":42,"_id":"1532","status":"public","article_type":"original","type":"journal_article","date_updated":"2022-05-24T09:02:24Z","department":[{"_id":"JiFr"}]},{"month":"01","intvolume":" 40","scopus_import":"1","alternative_title":["Mathematics and Visualization"],"oa_version":"None","abstract":[{"lang":"eng","text":"The Heat Kernel Signature (HKS) is a scalar quantity which is derived from the heat kernel of a given shape. Due to its robustness, isometry invariance, and multiscale nature, it has been successfully applied in many geometric applications. From a more general point of view, the HKS can be considered as a descriptor of the metric of a Riemannian manifold. Given a symmetric positive definite tensor field we may interpret it as the metric of some Riemannian manifold and thereby apply the HKS to visualize and analyze the given tensor data. In this paper, we propose a generalization of this approach that enables the treatment of indefinite tensor fields, like the stress tensor, by interpreting them as a generator of a positive definite tensor field. To investigate the usefulness of this approach we consider the stress tensor from the two-point-load model example and from a mechanical work piece."}],"volume":40,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-319-15089-5"]},"publication_status":"published","status":"public","type":"book_chapter","_id":"1531","department":[{"_id":"HeEd"}],"date_updated":"2022-06-10T09:50:14Z","quality_controlled":"1","publisher":"Springer","edition":"1","doi":"10.1007/978-3-319-15090-1_13","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:52:33Z","page":"257 - 267","day":"01","publication":"Visualization and Processing of Higher Order Descriptors for Multi-Valued Data","year":"2015","title":"Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature","editor":[{"first_name":"Ingrid","full_name":"Hotz, Ingrid","last_name":"Hotz"},{"last_name":"Schultz","full_name":"Schultz, Thomas","first_name":"Thomas"}],"publist_id":"5640","author":[{"first_name":"Valentin","last_name":"Zobel","full_name":"Zobel, Valentin"},{"full_name":"Reininghaus, Jan","last_name":"Reininghaus","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hotz","full_name":"Hotz, Ingrid","first_name":"Ingrid"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz, 1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:10.1007/978-3-319-15090-1_13.","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature,” in Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., vol. 40, I. Hotz and T. Schultz, Eds. Springer, 2015, pp. 257–267.","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer, 2015, pp. 257–267.","ama":"Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Vol 40. 1st ed. Springer; 2015:257-267. doi:10.1007/978-3-319-15090-1_13","apa":"Zobel, V., Reininghaus, J., & Hotz, I. (2015). Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In I. Hotz & T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data (1st ed., Vol. 40, pp. 257–267). Springer. https://doi.org/10.1007/978-3-319-15090-1_13","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. https://doi.org/10.1007/978-3-319-15090-1_13.","ista":"Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization, vol. 40, 257–267."}},{"publication_status":"published","year":"2015","day":"25","language":[{"iso":"eng"}],"publication":"Physical Biology","issue":"6","doi":"10.1088/1478-3975/12/6/066003","volume":12,"date_published":"2015-09-25T00:00:00Z","date_created":"2018-12-11T11:52:33Z","abstract":[{"text":"In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle.","lang":"eng"}],"oa_version":"None","publisher":"IOP Publishing Ltd.","quality_controlled":"1","scopus_import":1,"month":"09","intvolume":" 12","citation":{"apa":"Bierbaum, V., & Klumpp, S. (2015). Impact of the cell division cycle on gene circuits. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/12/6/066003","ama":"Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. Physical Biology. 2015;12(6). doi:10.1088/1478-3975/12/6/066003","short":"V. Bierbaum, S. Klumpp, Physical Biology 12 (2015).","ieee":"V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,” Physical Biology, vol. 12, no. 6. IOP Publishing Ltd., 2015.","mla":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” Physical Biology, vol. 12, no. 6, 066003, IOP Publishing Ltd., 2015, doi:10.1088/1478-3975/12/6/066003.","ista":"Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits. Physical Biology. 12(6), 066003.","chicago":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” Physical Biology. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1478-3975/12/6/066003."},"date_updated":"2021-01-12T06:51:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5641","author":[{"full_name":"Bierbaum, Veronika","last_name":"Bierbaum","first_name":"Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan","last_name":"Klumpp","full_name":"Klumpp, Stefan"}],"department":[{"_id":"MiSi"}],"title":"Impact of the cell division cycle on gene circuits","_id":"1530","article_number":"066003","type":"journal_article","status":"public"},{"title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space","publist_id":"5632","author":[{"last_name":"Ruess","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937.","ama":"Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 2015;143(24). doi:10.1063/1.4937937","apa":"Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/1.4937937","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","ieee":"J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015.","chicago":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937.","ista":"Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103."},"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_number":"244103","doi":"10.1063/1.4937937","date_published":"2015-12-22T00:00:00Z","date_created":"2018-12-11T11:52:36Z","day":"22","publication":"Journal of Chemical Physics","has_accepted_license":"1","year":"2015","publisher":"American Institute of Physics","quality_controlled":"1","oa":1,"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:01Z","ddc":["000"],"date_updated":"2021-01-12T06:51:28Z","status":"public","pubrep_id":"593","type":"journal_article","_id":"1539","issue":"24","volume":143,"ec_funded":1,"file":[{"creator":"system","date_updated":"2020-07-14T12:45:01Z","file_size":605355,"date_created":"2018-12-12T10:07:43Z","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"838657118ae286463a2b7737319f35ce","file_id":"4641"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"12","intvolume":" 143","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. "}]},{"volume":6,"ec_funded":1,"file":[{"checksum":"3c06735fc7cd7e482ca830cbd26001bf","file_id":"5259","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","date_created":"2018-12-12T10:17:07Z","file_size":1852268,"date_updated":"2020-07-14T12:45:01Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"11","intvolume":" 6","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:01Z","department":[{"_id":"JiFr"}],"ddc":["570"],"date_updated":"2021-01-12T06:51:26Z","status":"public","pubrep_id":"485","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1534","doi":"10.1038/ncomms9822","date_published":"2015-11-18T00:00:00Z","date_created":"2018-12-11T11:52:34Z","day":"18","publication":"Nature Communications","has_accepted_license":"1","year":"2015","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","author":[{"last_name":"Wang","full_name":"Wang, Hongzhe","first_name":"Hongzhe"},{"first_name":"Kezhen","last_name":"Yang","full_name":"Yang, Kezhen"},{"first_name":"Junjie","last_name":"Zou","full_name":"Zou, Junjie"},{"last_name":"Zhu","full_name":"Zhu, Lingling","first_name":"Lingling"},{"last_name":"Xie","full_name":"Xie, Zidian","first_name":"Zidian"},{"first_name":"Miyoterao","last_name":"Morita","full_name":"Morita, Miyoterao"},{"first_name":"Masao","full_name":"Tasaka, Masao","last_name":"Tasaka"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"full_name":"Grotewold, Erich","last_name":"Grotewold","first_name":"Erich"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Sack","full_name":"Sack, Fred","first_name":"Fred"},{"first_name":"Jie","last_name":"Le","full_name":"Le, Jie"}],"publist_id":"5637","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822.","chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822.","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 2015;6. doi:10.1038/ncomms9822","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","ieee":"H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications, vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822."},"project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"article_number":"8822"},{"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time.","lang":"eng"}],"month":"06","intvolume":" 112","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":112,"issue":"26","ec_funded":1,"_id":"1538","status":"public","type":"journal_article","date_updated":"2021-01-12T06:51:27Z","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"acknowledgement":"J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"day":"30","publication":"PNAS","year":"2015","date_published":"2015-06-30T00:00:00Z","doi":"10.1073/pnas.1423947112","date_created":"2018-12-11T11:52:36Z","page":"8148 - 8153","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.","chicago":"Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423947112.","apa":"Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112","ama":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112","short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","ieee":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015.","mla":"Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112."},"title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","publist_id":"5633","author":[{"full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","last_name":"Ruess","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Francesca","full_name":"Parise, Francesca","last_name":"Parise"},{"first_name":"Andreas","full_name":"Milias Argeitis, Andreas","last_name":"Milias Argeitis"},{"last_name":"Khammash","full_name":"Khammash, Mustafa","first_name":"Mustafa"},{"first_name":"John","full_name":"Lygeros, John","last_name":"Lygeros"}],"external_id":{"pmid":["26085136"]}},{"language":[{"iso":"eng"}],"publication_status":"published","issue":"2","volume":8,"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress.","lang":"eng"}],"intvolume":" 8","month":"10","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/","open_access":"1"}],"scopus_import":1,"date_updated":"2021-01-12T06:51:26Z","department":[{"_id":"PeJo"}],"_id":"1535","status":"public","article_type":"original","type":"journal_article","publication":"Current Molecular Pharmacology","day":"01","year":"2015","date_created":"2018-12-11T11:52:35Z","doi":"10.2174/1874467208666150507105443","date_published":"2015-10-01T00:00:00Z","page":"149 - 161","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","oa":1,"quality_controlled":"1","publisher":"Bentham Science Publishers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Vandael, D. H., Marcantoni, A., & Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. Bentham Science Publishers. https://doi.org/10.2174/1874467208666150507105443","ama":"Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 2015;8(2):149-161. doi:10.2174/1874467208666150507105443","ieee":"D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” Current Molecular Pharmacology, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015.","short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161.","mla":"Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:10.2174/1874467208666150507105443.","ista":"Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161.","chicago":"Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology. Bentham Science Publishers, 2015. https://doi.org/10.2174/1874467208666150507105443."},"title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","external_id":{"pmid":["25966692"]},"article_processing_charge":"No","author":[{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"first_name":"Andrea","full_name":"Marcantoni, Andrea","last_name":"Marcantoni"},{"first_name":"Emilio","last_name":"Carbone","full_name":"Carbone, Emilio"}],"publist_id":"5636"},{"oa_version":"None","acknowledgement":"This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification.","abstract":[{"text":"Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil.","lang":"eng"}],"month":"02","intvolume":" 25","quality_controlled":"1","scopus_import":1,"publisher":"Cell Press","day":"12","publication":"Current Biology","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","date_published":"2015-02-12T00:00:00Z","doi":"10.1016/j.cub.2015.01.015","volume":25,"issue":"5","date_created":"2018-12-11T11:52:35Z","page":"647 - 655","_id":"1536","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:10.1016/j.cub.2015.01.015.","short":"J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.","ieee":"J. Sasse et al., “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” Current Biology, vol. 25, no. 5. Cell Press, pp. 647–655, 2015.","apa":"Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.01.015","ama":"Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 2015;25(5):647-655. doi:10.1016/j.cub.2015.01.015","chicago":"Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology. Cell Press, 2015. https://doi.org/10.1016/j.cub.2015.01.015.","ista":"Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655."},"date_updated":"2021-01-12T06:51:27Z","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","department":[{"_id":"JiFr"}],"author":[{"first_name":"Joëlle","last_name":"Sasse","full_name":"Sasse, Joëlle"},{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"first_name":"Christian","full_name":"Gübeli, Christian","last_name":"Gübeli"},{"first_name":"Guowei","full_name":"Liu, Guowei","last_name":"Liu"},{"full_name":"Cheng, Xi","last_name":"Cheng","first_name":"Xi"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Bouwmeester","full_name":"Bouwmeester, Harro","first_name":"Harro"},{"full_name":"Martinoia, Enrico","last_name":"Martinoia","first_name":"Enrico"},{"last_name":"Borghi","full_name":"Borghi, Lorenzo","first_name":"Lorenzo"}],"publist_id":"5635"},{"scopus_import":1,"quality_controlled":"1","publisher":"IEEE","intvolume":" 25","month":"08","abstract":[{"lang":"eng","text":"This paper addresses the problem of semantic segmentation, where the possible class labels are from a predefined set. We exploit top-down guidance, i.e., the coarse localization of the objects and their class labels provided by object detectors. For each detected bounding box, figure-ground segmentation is performed and the final result is achieved by merging the figure-ground segmentations. The main idea of the proposed approach, which is presented in our preliminary work, is to reformulate the figure-ground segmentation problem as sparse reconstruction pursuing the object mask in a nonparametric manner. The latent segmentation mask should be coherent subject to sparse error caused by intra-category diversity; thus, the object mask is inferred by making use of sparse representations over the training set. To handle local spatial deformations, local patch-level masks are also considered and inferred by sparse representations over the spatially nearby patches. The sparse reconstruction coefficients and the latent mask are alternately optimized by applying the Lasso algorithm and the accelerated proximal gradient method. The proposed formulation results in a convex optimization problem; thus, the global optimal solution is achieved. In this paper, we provide theoretical analysis of the convergence and optimality. We also give an extended numerical analysis of the proposed algorithm and a comprehensive comparison with the related semantic segmentation methods on the challenging PASCAL visual object class object segmentation datasets and the Weizmann horse dataset. The experimental results demonstrate that the proposed algorithm achieves a competitive performance when compared with the state of the arts."}],"oa_version":"None","page":"1295 - 1308","date_created":"2018-12-11T11:52:34Z","volume":25,"date_published":"2015-08-01T00:00:00Z","issue":"8","doi":"10.1109/TCSVT.2014.2379972","year":"2015","publication_status":"published","publication":"IEEE Transactions on Circuits and Systems for Video Technology","language":[{"iso":"eng"}],"day":"01","type":"journal_article","status":"public","_id":"1533","author":[{"first_name":"Wei","full_name":"Xia, Wei","last_name":"Xia"},{"id":"492DACF8-F248-11E8-B48F-1D18A9856A87","first_name":"Csaba","last_name":"Domokos","full_name":"Domokos, Csaba"},{"first_name":"Junjun","last_name":"Xiong","full_name":"Xiong, Junjun"},{"full_name":"Cheong, Loongfah","last_name":"Cheong","first_name":"Loongfah"},{"full_name":"Yan, Shuicheng","last_name":"Yan","first_name":"Shuicheng"}],"publist_id":"5638","department":[{"_id":"ChLa"}],"title":"Segmentation over detection via optimal sparse reconstructions","citation":{"short":"W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits and Systems for Video Technology 25 (2015) 1295–1308.","ieee":"W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection via optimal sparse reconstructions,” IEEE Transactions on Circuits and Systems for Video Technology, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.","apa":"Xia, W., Domokos, C., Xiong, J., Cheong, L., & Yan, S. (2015). Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. IEEE. https://doi.org/10.1109/TCSVT.2014.2379972","ama":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 2015;25(8):1295-1308. doi:10.1109/TCSVT.2014.2379972","mla":"Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions on Circuits and Systems for Video Technology, vol. 25, no. 8, IEEE, 2015, pp. 1295–308, doi:10.1109/TCSVT.2014.2379972.","ista":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 25(8), 1295–1308.","chicago":"Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan. “Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions on Circuits and Systems for Video Technology. IEEE, 2015. https://doi.org/10.1109/TCSVT.2014.2379972."},"date_updated":"2021-01-12T06:51:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:45:01Z","ddc":["570"],"date_updated":"2021-01-12T06:51:29Z","pubrep_id":"483","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","_id":"1542","ec_funded":1,"volume":383,"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":595307,"date_updated":"2020-07-14T12:45:01Z","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","date_created":"2018-12-12T10:16:53Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"33b60ecfea60764756a9ee9df5eb65ca","file_id":"5244"}],"publication_status":"published","intvolume":" 383","month":"10","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"title":"Toward a unifying framework for evolutionary processes","publist_id":"5629","author":[{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"first_name":"Golnaz","last_name":"Badkobeh","full_name":"Badkobeh, Golnaz"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Doğan","last_name":"Çörüş","full_name":"Çörüş, Doğan"},{"first_name":"Duccuong","last_name":"Dang","full_name":"Dang, Duccuong"},{"first_name":"Tobias","full_name":"Friedrich, Tobias","last_name":"Friedrich"},{"first_name":"Per","last_name":"Lehre","full_name":"Lehre, Per"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"first_name":"Andrew","last_name":"Sutton","full_name":"Sutton, Andrew"},{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","ieee":"T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011."},"project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"date_created":"2018-12-11T11:52:37Z","date_published":"2015-10-21T00:00:00Z","doi":"10.1016/j.jtbi.2015.07.011","page":"28 - 43","publication":" Journal of Theoretical Biology","day":"21","year":"2015","has_accepted_license":"1","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:45:01Z","date_updated":"2021-01-12T06:51:31Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"482","_id":"1546","issue":"1","volume":85,"publication_status":"published","file":[{"file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf","date_created":"2018-12-12T10:15:47Z","file_size":3080111,"date_updated":"2020-07-14T12:45:01Z","creator":"system","file_id":"5170","checksum":"725f4d5be2dbb44b283ce722645ef37d","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"01","intvolume":" 85","abstract":[{"lang":"eng","text":"Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (<30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This "perimeter release model" provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course."}],"oa_version":"Published Version","publist_id":"5625","author":[{"last_name":"Nakamura","full_name":"Nakamura, Yukihiro","first_name":"Yukihiro"},{"last_name":"Harada","full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Naomi","last_name":"Kamasawa","full_name":"Kamasawa, Naomi"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"},{"last_name":"Rothman","full_name":"Rothman, Jason","first_name":"Jason"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"first_name":"R Angus","full_name":"Silver, R Angus","last_name":"Silver"},{"last_name":"Digregorio","full_name":"Digregorio, David","first_name":"David"},{"full_name":"Takahashi, Tomoyuki","last_name":"Takahashi","first_name":"Tomoyuki"}],"title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","citation":{"chicago":"Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2014.11.019.","ista":"Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158.","mla":"Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:10.1016/j.neuron.2014.11.019.","apa":"Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.11.019","ama":"Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 2015;85(1):145-158. doi:10.1016/j.neuron.2014.11.019","ieee":"Y. Nakamura et al., “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” Neuron, vol. 85, no. 1. Elsevier, pp. 145–158, 2015.","short":"Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"145 - 158","date_published":"2015-01-07T00:00:00Z","doi":"10.1016/j.neuron.2014.11.019","date_created":"2018-12-11T11:52:39Z","has_accepted_license":"1","year":"2015","day":"07","publication":"Neuron","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS."},{"date_created":"2018-12-11T11:52:37Z","date_published":"2015-11-28T00:00:00Z","doi":"10.1007/978-3-319-26287-1_1","page":"3 - 18","day":"28","year":"2015","publisher":"Springer","quality_controlled":"1","acknowledgement":"This work was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","title":"XSpeed: Accelerating reachability analysis on multi-core processors","author":[{"first_name":"Rajarshi","full_name":"Ray, Rajarshi","last_name":"Ray"},{"full_name":"Gurung, Amit","last_name":"Gurung","first_name":"Amit"},{"first_name":"Binayak","full_name":"Das, Binayak","last_name":"Das"},{"last_name":"Bartocci","full_name":"Bartocci, Ezio","first_name":"Ezio"},{"orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"}],"publist_id":"5630","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed: Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer, pp. 3–18, 2015.","short":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015) 3–18.","apa":"Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., & Grosu, R. (2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_1","ama":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating reachability analysis on multi-core processors. 2015;9434:3-18. doi:10.1007/978-3-319-26287-1_1","mla":"Ray, Rajarshi, et al. XSpeed: Accelerating Reachability Analysis on Multi-Core Processors. Vol. 9434, Springer, 2015, pp. 3–18, doi:10.1007/978-3-319-26287-1_1.","ista":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating reachability analysis on multi-core processors. 9434, 3–18.","chicago":"Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov, and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_1."},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"ec_funded":1,"volume":9434,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 9434","month":"11","alternative_title":["LNCS"],"scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"We present XSpeed a parallel state-space exploration algorithm for continuous systems with linear dynamics and nondeterministic inputs. The motivation of having parallel algorithms is to exploit the computational power of multi-core processors to speed-up performance. The parallelization is achieved on two fronts. First, we propose a parallel implementation of the support function algorithm by sampling functions in parallel. Second, we propose a parallel state-space exploration by slicing the time horizon and computing the reachable states in the time slices in parallel. The second method can be however applied only to a class of linear systems with invertible dynamics and fixed input. A GP-GPU implementation is also presented following a lazy evaluation strategy on support functions. The parallel algorithms are implemented in the tool XSpeed. We evaluated the performance on two benchmarks including an 28 dimension Helicopter model. Comparison with the sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario), the state of the art tool for reachability analysis of linear hybrid systems. Experiments illustrate that our parallel algorithm with time slicing not only speeds-up performance but also improves precision."}],"department":[{"_id":"ToHe"}],"date_updated":"2020-08-11T10:09:17Z","status":"public","conference":{"start_date":"2015-11-17","end_date":"2015-11-19","location":"Haifa, Israel","name":"HVC: Haifa Verification Conference"},"type":"conference","series_title":"Lecture Notes in Computer Science","_id":"1541"},{"type":"journal_article","status":"public","_id":"1543","publist_id":"5628","author":[{"first_name":"Yadira","full_name":"Olvera Carrillo, Yadira","last_name":"Olvera Carrillo"},{"full_name":"Van Bel, Michiel","last_name":"Van Bel","first_name":"Michiel"},{"full_name":"Van Hautegem, Tom","last_name":"Van Hautegem","first_name":"Tom"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"last_name":"Huysmans","full_name":"Huysmans, Marlies","first_name":"Marlies"},{"first_name":"Mária","last_name":"Šimášková","full_name":"Šimášková, Mária"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"first_name":"Pierre","last_name":"Buscaill","full_name":"Buscaill, Pierre"},{"full_name":"Rivas, Susana","last_name":"Rivas","first_name":"Susana"},{"first_name":"Núria","last_name":"Coll","full_name":"Coll, Núria"},{"first_name":"Frederik","full_name":"Coppens, Frederik","last_name":"Coppens"},{"full_name":"Maere, Steven","last_name":"Maere","first_name":"Steven"},{"first_name":"Moritz","full_name":"Nowack, Moritz","last_name":"Nowack"}],"department":[{"_id":"JiFr"}],"title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","date_updated":"2021-01-12T06:51:30Z","citation":{"apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.15.00769","ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699. doi:10.1104/pp.15.00769","short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","ieee":"Y. Olvera Carrillo et al., “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015.","mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769.","ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699.","chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology. American Society of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publisher":"American Society of Plant Biologists","month":"12","intvolume":" 169","abstract":[{"text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta.","lang":"eng"}],"oa_version":"None","page":"2684 - 2699","volume":169,"doi":"10.1104/pp.15.00769","issue":"4","date_published":"2015-12-01T00:00:00Z","date_created":"2018-12-11T11:52:38Z","publication_status":"published","year":"2015","day":"01","language":[{"iso":"eng"}],"publication":"Plant Physiology"},{"title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","publist_id":"5627","author":[{"first_name":"Phuong","full_name":"Nguyen, Phuong","last_name":"Nguyen"},{"first_name":"Christine","full_name":"Field, Christine","last_name":"Field"},{"first_name":"Aaron","full_name":"Groen, Aaron","last_name":"Groen"},{"first_name":"Timothy","full_name":"Mitchison, Timothy","last_name":"Mitchison"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"external_id":{"pmid":["25997350"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241.","ieee":"P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in Building a Cell from its Components Parts, vol. 128, Academic Press, 2015, pp. 223–241.","ama":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007","apa":"Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241). Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007","mla":"Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” Building a Cell from Its Components Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007.","ista":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241.","chicago":"Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007."},"doi":"10.1016/bs.mcb.2015.01.007","date_published":"2015-04-08T00:00:00Z","date_created":"2018-12-11T11:52:38Z","page":"223 - 241","day":"08","publication":"Building a Cell from its Components Parts","year":"2015","publisher":"Academic Press","quality_controlled":"1","oa":1,"department":[{"_id":"MaLo"}],"date_updated":"2021-01-12T06:51:30Z","status":"public","type":"book_chapter","_id":"1544","volume":128,"language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 128","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/","open_access":"1"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility."}]},{"publication_status":"published","year":"2015","language":[{"iso":"eng"}],"publication":"Journal of Experimental Botany","day":"05","page":"5029 - 5042","date_created":"2018-12-11T11:52:36Z","volume":66,"date_published":"2015-05-05T00:00:00Z","issue":"16","doi":"10.1093/jxb/erv256","abstract":[{"text":"Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented.","lang":"eng"}],"acknowledgement":"The work was supported by grants from: the Employment of Best Young Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037) to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and the EU (FP7/2007–2013 People Programme), to HSR.","oa_version":"None","publisher":"Oxford University Press","quality_controlled":"1","scopus_import":1,"intvolume":" 66","month":"05","citation":{"chicago":"Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv256.","ista":"Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 66(16), 5029–5042.","mla":"Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:10.1093/jxb/erv256.","ieee":"H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5029–5042, 2015.","short":"H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental Botany 66 (2015) 5029–5042.","apa":"Robert, H., Crhák Khaitová, L., Mroue, S., & Benková, E. (2015). The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv256","ama":"Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 2015;66(16):5029-5042. doi:10.1093/jxb/erv256"},"date_updated":"2021-01-12T06:51:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5631","author":[{"first_name":"Hélène","full_name":"Robert, Hélène","last_name":"Robert"},{"first_name":"Lucie","last_name":"Crhák Khaitová","full_name":"Crhák Khaitová, Lucie"},{"first_name":"Souad","last_name":"Mroue","full_name":"Mroue, Souad"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis","department":[{"_id":"EvBe"}],"_id":"1540","type":"journal_article","status":"public"},{"date_updated":"2021-01-12T06:51:33Z","ddc":["570"],"department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:45:02Z","_id":"1551","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"481","publication_status":"published","file":[{"creator":"system","file_size":3468956,"date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-481-v1+1_journal.pbio.1002169.pdf","date_created":"2018-12-12T10:14:13Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"30dee7a2c11ed09f2f5634655c0146f8","file_id":"5063"}],"language":[{"iso":"eng"}],"volume":13,"issue":"6","ec_funded":1,"abstract":[{"text":"Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"06","intvolume":" 13","citation":{"chicago":"El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann, Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002169.","ista":"El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.","mla":"El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology, vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:10.1371/journal.pbio.1002169.","ieee":"L. El Masri et al., “Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes,” PLoS Biology, vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.","short":"L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther, S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R. Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30.","ama":"El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 2015;13(6):1-30. doi:10.1371/journal.pbio.1002169","apa":"El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther, P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002169"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"El Masri, Leila","last_name":"El Masri","first_name":"Leila","id":"349A6E66-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Branca","full_name":"Branca, Antoine","first_name":"Antoine"},{"first_name":"Anna","last_name":"Sheppard","full_name":"Sheppard, Anna"},{"full_name":"Papkou, Andrei","last_name":"Papkou","first_name":"Andrei"},{"first_name":"David","full_name":"Laehnemann, David","last_name":"Laehnemann"},{"first_name":"Patrick","full_name":"Guenther, Patrick","last_name":"Guenther"},{"last_name":"Prahl","full_name":"Prahl, Swantje","first_name":"Swantje"},{"full_name":"Saebelfeld, Manja","last_name":"Saebelfeld","first_name":"Manja"},{"first_name":"Jacqueline","full_name":"Hollensteiner, Jacqueline","last_name":"Hollensteiner"},{"full_name":"Liesegang, Heiko","last_name":"Liesegang","first_name":"Heiko"},{"full_name":"Brzuszkiewicz, Elzbieta","last_name":"Brzuszkiewicz","first_name":"Elzbieta"},{"first_name":"Rolf","full_name":"Daniel, Rolf","last_name":"Daniel"},{"first_name":"Nico","full_name":"Michiels, Nico","last_name":"Michiels"},{"last_name":"Schulte","full_name":"Schulte, Rebecca","first_name":"Rebecca"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"first_name":"Philip","full_name":"Rosenstiel, Philip","last_name":"Rosenstiel"},{"first_name":"Arndt","full_name":"Telschow, Arndt","last_name":"Telschow"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"},{"last_name":"Schulenburg","full_name":"Schulenburg, Hinrich","first_name":"Hinrich"}],"publist_id":"5620","title":"Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2015","day":"04","publication":"PLoS Biology","page":"1 - 30","doi":"10.1371/journal.pbio.1002169","date_published":"2015-06-04T00:00:00Z","date_created":"2018-12-11T11:52:40Z","acknowledgement":"We are very grateful for funding from the German Science Foundation (DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI 1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission) to LM.","publisher":"Public Library of Science","quality_controlled":"1","oa":1},{"scopus_import":1,"month":"09","intvolume":" 869","abstract":[{"text":"Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology.","lang":"eng"}],"oa_version":"Submitted Version","volume":869,"publication_identifier":{"isbn":["978-1-4939-2844-6"]},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:01Z","file_size":1919655,"creator":"system","date_created":"2018-12-12T10:11:02Z","file_name":"IST-2017-839-v1+1_mckenzie.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"bd1bfdf2423a0c3b6e7cabfa8b44bc0f","file_id":"4854"}],"language":[{"iso":"eng"}],"type":"book_chapter","status":"public","pubrep_id":"839","series_title":"Advances in Experimental Medicine and Biology","_id":"1549","file_date_updated":"2020-07-14T12:45:01Z","department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T06:51:32Z","ddc":["571","576"],"quality_controlled":"1","publisher":"Springer","oa":1,"page":"101 - 117","date_published":"2015-09-18T00:00:00Z","doi":"10.1007/978-1-4939-2845-3_6","date_created":"2018-12-11T11:52:39Z","has_accepted_license":"1","year":"2015","day":"18","publication":"Novel chemical tools to study ion channel biology","author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine"},{"first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"}],"publist_id":"5622","title":"Flipping the photoswitch: Ion channels under light control","citation":{"short":"C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117.","ieee":"C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in Novel chemical tools to study ion channel biology, vol. 869, Springer, 2015, pp. 101–117.","apa":"Mckenzie, C., Sanchez-Romero, I., & Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In Novel chemical tools to study ion channel biology (Vol. 869, pp. 101–117). Springer. https://doi.org/10.1007/978-1-4939-2845-3_6","ama":"Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: Novel Chemical Tools to Study Ion Channel Biology. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:10.1007/978-1-4939-2845-3_6","mla":"Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” Novel Chemical Tools to Study Ion Channel Biology, vol. 869, Springer, 2015, pp. 101–17, doi:10.1007/978-1-4939-2845-3_6.","ista":"Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117.","chicago":"Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In Novel Chemical Tools to Study Ion Channel Biology, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. https://doi.org/10.1007/978-1-4939-2845-3_6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":81,"issue":"23","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 81","month":"12","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/"}],"scopus_import":1,"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen."}],"department":[{"_id":"SyCr"}],"date_updated":"2021-01-12T06:51:31Z","status":"public","type":"journal_article","_id":"1548","date_created":"2018-12-11T11:52:39Z","date_published":"2015-12-01T00:00:00Z","doi":"10.1128/AEM.02051-15","page":"8135 - 8144","publication":"Applied and Environmental Microbiology","day":"01","year":"2015","oa":1,"publisher":"American Society for Microbiology","quality_controlled":"1","title":"Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination","external_id":{"pmid":["26386058"]},"publist_id":"5623","author":[{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Höfling","full_name":"Höfling, Christina","first_name":"Christina"},{"last_name":"Futo","full_name":"Futo, Momir","first_name":"Momir"},{"last_name":"Scharsack","full_name":"Scharsack, Jörn","first_name":"Jörn"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144.","chicago":"Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology. American Society for Microbiology, 2015. https://doi.org/10.1128/AEM.02051-15.","ieee":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” Applied and Environmental Microbiology, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015.","short":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144.","apa":"Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., & Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. American Society for Microbiology. https://doi.org/10.1128/AEM.02051-15","ama":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 2015;81(23):8135-8144. doi:10.1128/AEM.02051-15","mla":"Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:10.1128/AEM.02051-15."}},{"date_updated":"2021-01-12T06:51:33Z","citation":{"ista":"Maiuri P, Rupprecht J, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M, De Beco S, Gov N, Heisenberg C-PJ, Lage Crespo C, Lautenschlaeger F, Le Berre M, Lennon Duménil A, Raab M, Thiam H, Piel M, Sixt MK, Voituriez R. 2015. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 161(2), 374–386.","chicago":"Maiuri, Paolo, Jean Rupprecht, Stefan Wieser, Verena Ruprecht, Olivier Bénichou, Nicolas Carpi, Mathieu Coppey, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.056.","short":"P. Maiuri, J. Rupprecht, S. Wieser, V. Ruprecht, O. Bénichou, N. Carpi, M. Coppey, S. De Beco, N. Gov, C.-P.J. Heisenberg, C. Lage Crespo, F. Lautenschlaeger, M. Le Berre, A. Lennon Duménil, M. Raab, H. Thiam, M. Piel, M.K. Sixt, R. Voituriez, Cell 161 (2015) 374–386.","ieee":"P. Maiuri et al., “Actin flows mediate a universal coupling between cell speed and cell persistence,” Cell, vol. 161, no. 2. Cell Press, pp. 374–386, 2015.","apa":"Maiuri, P., Rupprecht, J., Wieser, S., Ruprecht, V., Bénichou, O., Carpi, N., … Voituriez, R. (2015). Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.056","ama":"Maiuri P, Rupprecht J, Wieser S, et al. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 2015;161(2):374-386. doi:10.1016/j.cell.2015.01.056","mla":"Maiuri, Paolo, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” Cell, vol. 161, no. 2, Cell Press, 2015, pp. 374–86, doi:10.1016/j.cell.2015.01.056."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Maiuri, Paolo","last_name":"Maiuri","first_name":"Paolo"},{"first_name":"Jean","full_name":"Rupprecht, Jean","last_name":"Rupprecht"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","last_name":"Wieser"},{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","last_name":"Ruprecht","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633"},{"first_name":"Olivier","last_name":"Bénichou","full_name":"Bénichou, Olivier"},{"first_name":"Nicolas","last_name":"Carpi","full_name":"Carpi, Nicolas"},{"first_name":"Mathieu","last_name":"Coppey","full_name":"Coppey, Mathieu"},{"full_name":"De Beco, Simon","last_name":"De Beco","first_name":"Simon"},{"full_name":"Gov, Nir","last_name":"Gov","first_name":"Nir"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Carolina","full_name":"Lage Crespo, Carolina","last_name":"Lage Crespo"},{"full_name":"Lautenschlaeger, Franziska","last_name":"Lautenschlaeger","first_name":"Franziska"},{"last_name":"Le Berre","full_name":"Le Berre, Maël","first_name":"Maël"},{"last_name":"Lennon Duménil","full_name":"Lennon Duménil, Ana","first_name":"Ana"},{"full_name":"Raab, Matthew","last_name":"Raab","first_name":"Matthew"},{"last_name":"Thiam","full_name":"Thiam, Hawa","first_name":"Hawa"},{"full_name":"Piel, Matthieu","last_name":"Piel","first_name":"Matthieu"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Voituriez","full_name":"Voituriez, Raphaël","first_name":"Raphaël"}],"publist_id":"5618","department":[{"_id":"MiSi"},{"_id":"CaHe"}],"title":"Actin flows mediate a universal coupling between cell speed and cell persistence","_id":"1553","type":"journal_article","status":"public","project":[{"call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","grant_number":"T 560-B17"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"},{"_id":"25ABD200-B435-11E9-9278-68D0E5697425","grant_number":"RGP0058/2011","name":"Cell migration in complex environments: from in vivo experiments to theoretical models"}],"year":"2015","publication_status":"published","day":"09","language":[{"iso":"eng"}],"publication":"Cell","page":"374 - 386","date_published":"2015-04-09T00:00:00Z","volume":161,"doi":"10.1016/j.cell.2015.01.056","issue":"2","date_created":"2018-12-11T11:52:41Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Cell movement has essential functions in development, immunity, and cancer. Various cell migration patterns have been reported, but no general rule has emerged so far. Here, we show on the basis of experimental data in vitro and in vivo that cell persistence, which quantifies the straightness of trajectories, is robustly coupled to cell migration speed. We suggest that this universal coupling constitutes a generic law of cell migration, which originates in the advection of polarity cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis relies on a theoretical model that we validate by measuring the persistence of cells upon modulation of actin flow speeds and upon optogenetic manipulation of the binding of an actin regulator to actin filaments. Beyond the quantitative prediction of the coupling, the model yields a generic phase diagram of cellular trajectories, which recapitulates the full range of observed migration patterns."}],"oa_version":"None","scopus_import":1,"publisher":"Cell Press","quality_controlled":"1","month":"04","intvolume":" 161"},{"status":"public","type":"journal_article","_id":"1550","department":[{"_id":"SiHi"}],"date_updated":"2021-01-12T06:51:32Z","intvolume":" 87","month":"09","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/","open_access":"1"}],"scopus_import":1,"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute."}],"issue":"5","volume":87,"language":[{"iso":"eng"}],"publication_status":"published","title":"Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries","external_id":{"pmid":["26299473"]},"publist_id":"5621","author":[{"first_name":"Christian","last_name":"Mayer","full_name":"Mayer, Christian"},{"full_name":"Jaglin, Xavier","last_name":"Jaglin","first_name":"Xavier"},{"last_name":"Cobbs","full_name":"Cobbs, Lucy","first_name":"Lucy"},{"last_name":"Bandler","full_name":"Bandler, Rachel","first_name":"Rachel"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"first_name":"Constance","last_name":"Cepko","full_name":"Cepko, Constance"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"full_name":"Fishell, Gord","last_name":"Fishell","first_name":"Gord"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"C. Mayer et al., “Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries,” Neuron, vol. 87, no. 5. Elsevier, pp. 989–998, 2015.","short":"C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998.","ama":"Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 2015;87(5):989-998. doi:10.1016/j.neuron.2015.07.011","apa":"Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., … Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.07.011","mla":"Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron, vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:10.1016/j.neuron.2015.07.011.","ista":"Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S, Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 87(5), 989–998.","chicago":"Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher, Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.07.011."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"Research in the G.F. laboratory is supported by NIH (NS 081297, MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF (1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n","date_created":"2018-12-11T11:52:40Z","date_published":"2015-09-02T00:00:00Z","doi":"10.1016/j.neuron.2015.07.011","page":"989 - 998","publication":"Neuron","day":"02","year":"2015"},{"status":"public","type":"journal_article","_id":"1547","department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:51:31Z","month":"05","intvolume":" 52","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0901.3015"}],"oa_version":"Preprint","abstract":[{"text":"Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice.","lang":"eng"}],"volume":52,"issue":"3","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2234-3016"]},"publication_status":"published","title":"Resolution of unmixed bipartite graphs","publist_id":"5624","author":[{"id":"2C29581E-F248-11E8-B48F-1D18A9856A87","first_name":"Fatemeh","last_name":"Mohammadi","full_name":"Mohammadi, Fatemeh"},{"first_name":"Somayeh","last_name":"Moradi","full_name":"Moradi, Somayeh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society. Korean Mathematical Society, 2015. https://doi.org/10.4134/BKMS.2015.52.3.977.","ista":"Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986.","mla":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:10.4134/BKMS.2015.52.3.977.","apa":"Mohammadi, F., & Moradi, S. (2015). Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. Korean Mathematical Society. https://doi.org/10.4134/BKMS.2015.52.3.977","ama":"Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 2015;52(3):977-986. doi:10.4134/BKMS.2015.52.3.977","ieee":"F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” Bulletin of the Korean Mathematical Society, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015.","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986."},"quality_controlled":"1","publisher":"Korean Mathematical Society","oa":1,"doi":"10.4134/BKMS.2015.52.3.977","date_published":"2015-05-31T00:00:00Z","date_created":"2018-12-11T11:52:39Z","page":"977 - 986","day":"31","publication":"Bulletin of the Korean Mathematical Society","year":"2015"},{"publisher":"Oxford University Press","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"01","publication":"Journal of Experimental Botany","page":"4631 - 4642","doi":"10.1093/jxb/erv230","date_published":"2015-08-01T00:00:00Z","date_created":"2018-12-11T11:52:42Z","citation":{"ista":"Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642.","chicago":"Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv230.","apa":"Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230","ama":"Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 2015;66(15):4631-4642. doi:10.1093/jxb/erv230","ieee":"Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” Journal of Experimental Botany, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015.","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642.","mla":"Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5615","author":[{"first_name":"Yuebin","full_name":"Jia, Yuebin","last_name":"Jia"},{"last_name":"Tian","full_name":"Tian, Huiyu","first_name":"Huiyu"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","last_name":"Li"},{"first_name":"Qianqian","last_name":"Yu","full_name":"Yu, Qianqian"},{"first_name":"Lei","last_name":"Wang","full_name":"Wang, Lei"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Ding","full_name":"Ding, Zhaojun","first_name":"Zhaojun"}],"title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development","abstract":[{"text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"08","intvolume":" 66","publication_status":"published","file":[{"checksum":"257919be0ce3d306185d3891ad7acf39","file_id":"5051","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","date_created":"2018-12-12T10:14:02Z","creator":"system","file_size":7753043,"date_updated":"2020-07-14T12:45:02Z"}],"language":[{"iso":"eng"}],"volume":66,"issue":"15","_id":"1556","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"480","date_updated":"2021-01-12T06:51:35Z","ddc":["570"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:02Z"},{"abstract":[{"lang":"eng","text":"We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations."}],"oa_version":"Published Version","main_file_link":[{"url":"http://discovery.ucl.ac.uk/1473750/1/99393.pdf","open_access":"1"}],"scopus_import":1,"intvolume":" 14","month":"01","publication_status":"published","publication_identifier":{"eissn":["1536-0040"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":14,"issue":"2","_id":"1555","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-01-12T06:51:34Z","ddc":["510"],"department":[{"_id":"HeEd"}],"acknowledgement":"Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559 in the framework of the EPIDELAY project.","oa":1,"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","year":"2015","publication":"SIAM Journal on Applied Dynamical Systems","day":"01","page":"980 - 1017","date_created":"2018-12-11T11:52:42Z","doi":"10.1137/140993934","date_published":"2015-01-01T00:00:00Z","project":[{"_id":"255F06BE-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"622033","name":"Persistent Homology - Images, Data and Maps"}],"citation":{"chicago":"Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140993934.","ista":"Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017.","mla":"Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2, Society for Industrial and Applied Mathematics , 2015, pp. 980–1017, doi:10.1137/140993934.","ieee":"D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015.","short":"D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017.","ama":"Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 2015;14(2):980-1017. doi:10.1137/140993934","apa":"Knipl, D., Pilarczyk, P., & Röst, G. (2015). Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140993934"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"5616","author":[{"last_name":"Knipl","full_name":"Knipl, Diána","first_name":"Diána"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel"},{"first_name":"Gergely","full_name":"Röst, Gergely","last_name":"Röst"}],"title":"Rich bifurcation structure in a two patch vaccination model"},{"_id":"1558","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Ivanchenko et al., “The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation,” Development, vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015.","short":"M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso, M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015) 712–721.","apa":"Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler, M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. Company of Biologists. https://doi.org/10.1242/dev.113225","ama":"Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 2015;142(4):712-721. doi:10.1242/dev.113225","mla":"Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:10.1242/dev.113225.","ista":"Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 142(4), 712–721.","chicago":"Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du, Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.113225."},"date_updated":"2021-01-12T06:51:35Z","department":[{"_id":"JiFr"}],"title":"The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation","publist_id":"5613","author":[{"full_name":"Ivanchenko, Maria","last_name":"Ivanchenko","first_name":"Maria"},{"first_name":"Jinsheng","last_name":"Zhu","full_name":"Zhu, Jinsheng"},{"first_name":"Bangjun","full_name":"Wang, Bangjun","last_name":"Wang"},{"first_name":"Eva","id":"298814E2-F248-11E8-B48F-1D18A9856A87","full_name":"Medvecka, Eva","last_name":"Medvecka"},{"last_name":"Du","full_name":"Du, Yunlong","first_name":"Yunlong"},{"first_name":"Elisa","full_name":"Azzarello, Elisa","last_name":"Azzarello"},{"first_name":"Stefano","full_name":"Mancuso, Stefano","last_name":"Mancuso"},{"full_name":"Megraw, Molly","last_name":"Megraw","first_name":"Molly"},{"last_name":"Filichkin","full_name":"Filichkin, Sergei","first_name":"Sergei"},{"last_name":"Dubrovsky","full_name":"Dubrovsky, Joseph","first_name":"Joseph"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"}],"oa_version":"None","abstract":[{"lang":"eng","text":"CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation."}],"intvolume":" 142","month":"02","publisher":"Company of Biologists","scopus_import":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Development","day":"15","year":"2015","publication_status":"published","date_created":"2018-12-11T11:52:42Z","volume":142,"doi":"10.1242/dev.113225","date_published":"2015-02-15T00:00:00Z","issue":"4","page":"712 - 721"},{"status":"public","type":"journal_article","_id":"1557","title":"Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats","department":[{"_id":"RySh"}],"publist_id":"5614","author":[{"first_name":"Fariba","full_name":"Javdani, Fariba","last_name":"Javdani"},{"first_name":"Krisztina","last_name":"Holló","full_name":"Holló, Krisztina"},{"first_name":"Krisztina","full_name":"Hegedűs, Krisztina","last_name":"Hegedűs"},{"first_name":"Gréta","last_name":"Kis","full_name":"Kis, Gréta"},{"last_name":"Hegyi","full_name":"Hegyi, Zoltán","first_name":"Zoltán"},{"full_name":"Dócs, Klaudia","last_name":"Dócs","first_name":"Klaudia"},{"full_name":"Kasugai, Yu","last_name":"Kasugai","first_name":"Yu"},{"last_name":"Fukazawa","full_name":"Fukazawa, Yugo","first_name":"Yugo"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"first_name":"Miklós","last_name":"Antal","full_name":"Antal, Miklós"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Javdani, Fariba, et al. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology, vol. 523, no. 13, Wiley-Blackwell, 2015, pp. 1967–83, doi:10.1002/cne.23774.","short":"F. Javdani, K. Holló, K. Hegedűs, G. Kis, Z. Hegyi, K. Dócs, Y. Kasugai, Y. Fukazawa, R. Shigemoto, M. Antal, Journal of Comparative Neurology 523 (2015) 1967–1983.","ieee":"F. Javdani et al., “Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats,” Journal of Comparative Neurology, vol. 523, no. 13. Wiley-Blackwell, pp. 1967–1983, 2015.","apa":"Javdani, F., Holló, K., Hegedűs, K., Kis, G., Hegyi, Z., Dócs, K., … Antal, M. (2015). Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23774","ama":"Javdani F, Holló K, Hegedűs K, et al. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 2015;523(13):1967-1983. doi:10.1002/cne.23774","chicago":"Javdani, Fariba, Krisztina Holló, Krisztina Hegedűs, Gréta Kis, Zoltán Hegyi, Klaudia Dócs, Yu Kasugai, Yugo Fukazawa, Ryuichi Shigemoto, and Miklós Antal. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology. Wiley-Blackwell, 2015. https://doi.org/10.1002/cne.23774.","ista":"Javdani F, Holló K, Hegedűs K, Kis G, Hegyi Z, Dócs K, Kasugai Y, Fukazawa Y, Shigemoto R, Antal M. 2015. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 523(13), 1967–1983."},"date_updated":"2021-01-12T06:51:35Z","month":"09","intvolume":" 523","quality_controlled":"1","publisher":"Wiley-Blackwell","scopus_import":1,"oa_version":"None","acknowledgement":"Funded by:\r\nHungarian Academy of Sciences. Grant Number: MTA-TKI 242\r\nHungarian Brain Research Program. Grant Number: KTIA_NAP_13-1-2013-0001\r\nSolution Oriented Research for Science and Technology from the Japan Science and Technology Agency Japanese Ministry of Education, Culture, Sports, Science and Technology","abstract":[{"lang":"eng","text":"γ-Aminobutyric acid (GABA)- and glycine-mediated hyperpolarizing inhibition is associated with a chloride influx that depends on the inwardly directed chloride electrochemical gradient. In neurons, the extrusion of chloride from the cytosol primarily depends on the expression of an isoform of potassium-chloride cotransporters (KCC2s). KCC2 is crucial in the regulation of the inhibitory tone of neural circuits, including pain processing neural assemblies. Thus we investigated the cellular distribution of KCC2 in neurons underlying pain processing in the superficial spinal dorsal horn of rats by using high-resolution immunocytochemical methods. We demonstrated that perikarya and dendrites widely expressed KCC2, but axon terminals proved to be negative for KCC2. In single ultrathin sections, silver deposits labeling KCC2 molecules showed different densities on the surface of dendritic profiles, some of which were negative for KCC2. In freeze fracture replicas and tissue sections double stained for the β3-subunit of GABAA receptors and KCC2, GABAA receptors were revealed on dendritic segments with high and also with low KCC2 densities. By measuring the distances between spots immunoreactive for gephyrin (a scaffolding protein of GABAA and glycine receptors) and KCC2 on the surface of neurokinin 1 (NK1) receptor-immunoreactive dendrites, we found that gephyrin-immunoreactive spots were located at various distances from KCC2 cotransporters; 5.7 % of them were recovered in the middle of 4-10-μm-long dendritic segments that were free of KCC2 immunostaining. The variable local densities of KCC2 may result in variable postsynaptic potentials evoked by the activation of GABAA and glycine receptors along the dendrites of spinal neurons."}],"volume":523,"date_published":"2015-09-01T00:00:00Z","issue":"13","doi":"10.1002/cne.23774","date_created":"2018-12-11T11:52:42Z","page":"1967 - 1983","day":"01","publication":"Journal of Comparative Neurology","language":[{"iso":"eng"}],"year":"2015","publication_status":"published"},{"_id":"1559","type":"journal_article","status":"public","date_updated":"2021-01-12T06:51:36Z","department":[{"_id":"KrCh"}],"abstract":[{"text":"There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/","open_access":"1"}],"scopus_import":1,"intvolume":" 112","month":"12","publication_status":"published","language":[{"iso":"eng"}],"volume":112,"issue":"51","citation":{"chicago":"Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511366112.","ista":"Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641.","mla":"Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS, vol. 112, no. 51, National Academy of Sciences, 2015, pp. 15636–41, doi:10.1073/pnas.1511366112.","ama":"Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 2015;112(51):15636-15641. doi:10.1073/pnas.1511366112","apa":"Ibsen-Jensen, R., Chatterjee, K., & Nowak, M. (2015). Computational complexity of ecological and evolutionary spatial dynamics. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511366112","short":"R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641.","ieee":"R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of ecological and evolutionary spatial dynamics,” PNAS, vol. 112, no. 51. National Academy of Sciences, pp. 15636–15641, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["26644569"]},"publist_id":"5612","author":[{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"title":"Computational complexity of ecological and evolutionary spatial dynamics","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","year":"2015","publication":"PNAS","day":"22","page":"15636 - 15641","date_created":"2018-12-11T11:52:43Z","doi":"10.1073/pnas.1511366112","date_published":"2015-12-22T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Heger K, Kober M, Rieß D, et al. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 2015;45(6):1614-1620. doi:10.1002/eji.201545457","apa":"Heger, K., Kober, M., Rieß, D., Drees, C., de Vries, I., Bertossi, A., … Schmidt Supprian, M. (2015). A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. Wiley. https://doi.org/10.1002/eji.201545457","short":"K. Heger, M. Kober, D. Rieß, C. Drees, I. de Vries, A. Bertossi, A. Roers, M.K. Sixt, M. Schmidt Supprian, European Journal of Immunology 45 (2015) 1614–1620.","ieee":"K. Heger et al., “A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors,” European Journal of Immunology, vol. 45, no. 6. Wiley, pp. 1614–1620, 2015.","mla":"Heger, Klaus, et al. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology, vol. 45, no. 6, Wiley, 2015, pp. 1614–20, doi:10.1002/eji.201545457.","ista":"Heger K, Kober M, Rieß D, Drees C, de Vries I, Bertossi A, Roers A, Sixt MK, Schmidt Supprian M. 2015. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 45(6), 1614–1620.","chicago":"Heger, Klaus, Maike Kober, David Rieß, Christoph Drees, Ingrid de Vries, Arianna Bertossi, Axel Roers, Michael K Sixt, and Marc Schmidt Supprian. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology. Wiley, 2015. https://doi.org/10.1002/eji.201545457."},"date_updated":"2021-01-12T06:51:36Z","title":"A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors","department":[{"_id":"MiSi"}],"author":[{"first_name":"Klaus","full_name":"Heger, Klaus","last_name":"Heger"},{"first_name":"Maike","full_name":"Kober, Maike","last_name":"Kober"},{"first_name":"David","last_name":"Rieß","full_name":"Rieß, David"},{"first_name":"Christoph","last_name":"Drees","full_name":"Drees, Christoph"},{"last_name":"De Vries","full_name":"De Vries, Ingrid","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bertossi","full_name":"Bertossi, Arianna","first_name":"Arianna"},{"last_name":"Roers","full_name":"Roers, Axel","first_name":"Axel"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Marc","last_name":"Schmidt Supprian","full_name":"Schmidt Supprian, Marc"}],"publist_id":"5610","_id":"1561","status":"public","type":"journal_article","day":"01","language":[{"iso":"eng"}],"publication":"European Journal of Immunology","publication_status":"published","year":"2015","volume":45,"doi":"10.1002/eji.201545457","issue":"6","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:52:44Z","page":"1614 - 1620","oa_version":"None","abstract":[{"text":"Replication-deficient recombinant adenoviruses are potent vectors for the efficient transient expression of exogenous genes in resting immune cells. However, most leukocytes are refractory to efficient adenoviral transduction as they lack expression of the coxsackie/adenovirus receptor (CAR). To circumvent this obstacle, we generated the R26/CAG-CARΔ1StopF (where R26 is ROSA26 and CAG is CMV early enhancer/chicken β actin promoter) knock-in mouse line. This strain allows monitoring of in situ Cre recombinase activity through expression of CARΔ1. Simultaneously, CARΔ1 expression permits selective and highly efficient adenoviral transduction of immune cell populations, such as mast cells or T cells, directly ex vivo in bulk cultures without prior cell purification or activation. Furthermore, we show that CARΔ1 expression dramatically improves adenoviral infection of in vitro differentiated conventional and plasmacytoid dendritic cells (DCs), basophils, mast cells, as well as Hoxb8-immortalized hematopoietic progenitor cells. This novel dual function mouse strain will hence be a valuable tool to rapidly dissect the function of specific genes in leukocyte physiology.","lang":"eng"}],"month":"06","intvolume":" 45","publisher":"Wiley","quality_controlled":"1","scopus_import":1},{"abstract":[{"lang":"eng","text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species."}],"oa_version":"Submitted Version","pmid":1,"scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/","open_access":"1"}],"month":"02","intvolume":" 12","publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":12,"_id":"1554","type":"journal_article","status":"public","date_updated":"2021-01-12T06:51:34Z","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"year":"2015","day":"26","publication":"Nature Methods","page":"207 - 210","doi":"10.1038/nmeth.3279","date_published":"2015-02-26T00:00:00Z","date_created":"2018-12-11T11:52:41Z","citation":{"chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279.","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279.","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279","ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Cheyang","last_name":"Liao","full_name":"Liao, Cheyang"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"last_name":"Brunoud","full_name":"Brunoud, Géraldine","first_name":"Géraldine"},{"last_name":"Yoshida","full_name":"Yoshida, Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"first_name":"Teva","full_name":"Vernoux, Teva","last_name":"Vernoux"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"}],"publist_id":"5617","external_id":{"pmid":["25643149"]},"title":"Reporters for sensitive and quantitative measurement of auxin response"},{"title":"The lymph node filter revealed","department":[{"_id":"MiSi"}],"publist_id":"5611","author":[{"first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav","last_name":"Hons"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hons, Miroslav, and Michael K Sixt. “The Lymph Node Filter Revealed.” Nature Immunology. Nature Publishing Group, 2015. https://doi.org/10.1038/ni.3126.","ista":"Hons M, Sixt MK. 2015. The lymph node filter revealed. Nature Immunology. 16(4), 338–340.","mla":"Hons, Miroslav, and Michael K. Sixt. “The Lymph Node Filter Revealed.” Nature Immunology, vol. 16, no. 4, Nature Publishing Group, 2015, pp. 338–40, doi:10.1038/ni.3126.","apa":"Hons, M., & Sixt, M. K. (2015). The lymph node filter revealed. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3126","ama":"Hons M, Sixt MK. The lymph node filter revealed. Nature Immunology. 2015;16(4):338-340. doi:10.1038/ni.3126","ieee":"M. Hons and M. K. Sixt, “The lymph node filter revealed,” Nature Immunology, vol. 16, no. 4. Nature Publishing Group, pp. 338–340, 2015.","short":"M. Hons, M.K. Sixt, Nature Immunology 16 (2015) 338–340."},"date_updated":"2021-01-12T06:51:36Z","status":"public","type":"journal_article","_id":"1560","date_published":"2015-03-19T00:00:00Z","doi":"10.1038/ni.3126","issue":"4","volume":16,"date_created":"2018-12-11T11:52:43Z","page":"338 - 340","day":"19","language":[{"iso":"eng"}],"publication":"Nature Immunology","year":"2015","publication_status":"published","month":"03","intvolume":" 16","publisher":"Nature Publishing Group","scopus_import":1,"quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP is a crucial component of this selector function."}]},{"page":"4835 - 4853","doi":"10.1113/JP271078","date_published":"2015-11-15T00:00:00Z","date_created":"2018-12-11T11:52:45Z","year":"2015","day":"15","publication":"Journal of Physiology","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"acknowledgement":"This work was supported by the Compagnia di San Paolo Foundation ‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank Dr Claudio Franchino for cell preparation and for providing excellent technical support.","author":[{"first_name":"Daniela","full_name":"Gavello, Daniela","last_name":"Gavello"},{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"full_name":"Gosso, Sara","last_name":"Gosso","first_name":"Sara"},{"full_name":"Carbone, Emilio","last_name":"Carbone","first_name":"Emilio"},{"first_name":"Valentina","last_name":"Carabelli","full_name":"Carabelli, Valentina"}],"publist_id":"5606","external_id":{"pmid":["26282459"]},"title":"Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells","citation":{"mla":"Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell, 2015, pp. 4835–53, doi:10.1113/JP271078.","ama":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 2015;593(22):4835-4853. doi:10.1113/JP271078","apa":"Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015). Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078","ieee":"D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015.","short":"D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853.","chicago":"Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078.","ista":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 593(22), 4835–4853."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":593,"issue":"22","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/","open_access":"1"}],"month":"11","intvolume":" 593","abstract":[{"text":"Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T06:51:38Z","type":"journal_article","status":"public","_id":"1565"},{"publisher":"Oxford University Press","quality_controlled":"1","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG- 20101109-PSDP to JF); the European Social Fund and the state budget of the Czech Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR) [project 13-40637S to JF].","page":"5055 - 5065","date_created":"2018-12-11T11:52:44Z","doi":"10.1093/jxb/erv177","date_published":"2015-08-01T00:00:00Z","year":"2015","publication":"Journal of Experimental Botany","day":"01","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"author":[{"last_name":"Grones","full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu","last_name":"Chen"},{"first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Riet","full_name":"De Rycke, Riet","last_name":"De Rycke"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"5609","title":"Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles","citation":{"ieee":"P. Grones et al., “Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.","short":"P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E. Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065.","ama":"Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 2015;66(16):5055-5065. doi:10.1093/jxb/erv177","apa":"Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T., … Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv177","mla":"Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:10.1093/jxb/erv177.","ista":"Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065.","chicago":"Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv177."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 66","month":"08","abstract":[{"lang":"eng","text":"The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor."}],"oa_version":"None","ec_funded":1,"volume":66,"issue":"16","publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"1562","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"date_updated":"2023-02-23T10:04:26Z"},{"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"145","author":[{"last_name":"Gilson","full_name":"Gilson, Matthieu","first_name":"Matthieu"},{"last_name":"Savin","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"},{"full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann"}],"publist_id":"5607","title":"Editorial: Emergent neural computation from the interaction of different forms of plasticity","citation":{"chicago":"Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.","ista":"Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.","mla":"Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.","ieee":"M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.","short":"M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015).","apa":"Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145","ama":"Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 2015;9(11). doi:10.3389/fncom.2015.00145"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Frontiers Research Foundation","quality_controlled":"1","date_created":"2018-12-11T11:52:45Z","date_published":"2015-11-30T00:00:00Z","doi":"10.3389/fncom.2015.00145","year":"2015","has_accepted_license":"1","publication":"Frontiers in Computational Neuroscience","day":"30","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"479","status":"public","_id":"1564","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:02Z","date_updated":"2021-01-12T06:51:37Z","ddc":["570"],"scopus_import":1,"intvolume":" 9","month":"11","oa_version":"Published Version","ec_funded":1,"issue":"11","volume":9,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":187038,"date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-479-v1+1_fncom-09-00145.pdf","date_created":"2018-12-12T10:12:09Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"cea73b6d3ef1579f32da10b82f4de4fd","file_id":"4927"}]},{"publist_id":"5603","author":[{"first_name":"Olga","last_name":"Dunaeva","full_name":"Dunaeva, Olga"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lukyanov, Anton","last_name":"Lukyanov","first_name":"Anton"},{"first_name":"Michael","last_name":"Machin","full_name":"Machin, Michael"},{"first_name":"Daria","last_name":"Malkova","full_name":"Malkova, Daria"}],"department":[{"_id":"HeEd"}],"title":"The classification of endoscopy images with persistent homology","citation":{"ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. 2015. The classification of endoscopy images with persistent homology. Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC: Symbolic and Numeric Algorithms for Scientific Computing, 7034731.","chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, and Daria Malkova. “The Classification of Endoscopy Images with Persistent Homology.” In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, 7034731. IEEE, 2015. https://doi.org/10.1109/SYNASC.2014.81.","ieee":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, and D. Malkova, “The classification of endoscopy images with persistent homology,” in Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, Timisoara, Romania, 2015, p. 7034731.","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, in:, Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731.","apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., & Malkova, D. (2015). The classification of endoscopy images with persistent homology. In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (p. 7034731). Timisoara, Romania: IEEE. https://doi.org/10.1109/SYNASC.2014.81","ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. The classification of endoscopy images with persistent homology. In: Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. IEEE; 2015:7034731. doi:10.1109/SYNASC.2014.81","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731, doi:10.1109/SYNASC.2014.81."},"date_updated":"2023-02-21T16:57:29Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","conference":{"name":"SYNASC: Symbolic and Numeric Algorithms for Scientific Computing","start_date":"2014-09-22","location":"Timisoara, Romania","end_date":"2014-09-25"},"type":"conference","status":"public","_id":"1568","page":"7034731","date_created":"2018-12-11T11:52:46Z","date_published":"2015-02-05T00:00:00Z","doi":"10.1109/SYNASC.2014.81","related_material":{"record":[{"relation":"later_version","id":"1289","status":"public"}]},"year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing","day":"05","quality_controlled":"1","publisher":"IEEE","scopus_import":1,"month":"02","abstract":[{"text":"Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI) magnifying endoscopy (ME) images of the stomach, we combine methods from image processing, computational topology, and machine learning to classify patterns into normal, tubular, vessel. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.","lang":"eng"}],"acknowledgement":"This research is supported by the project No. 477 of P.G. Demidov Yaroslavl State University within State Assignment for Research.","oa_version":"None"},{"date_created":"2018-12-11T11:52:46Z","volume":9411,"date_published":"2015-01-01T00:00:00Z","publication":"23rd International Symposium","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015","intvolume":" 9411","month":"01","publisher":"Springer Nature","quality_controlled":"1","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"None","abstract":[{"text":"My personal journey to the fascinating world of geometric forms started more than 30 years ago with the invention of alpha shapes in the plane. It took about 10 years before we generalized the concept to higher dimensions, we produced working software with a graphics interface for the three-dimensional case. At the same time, we added homology to the computations. Needless to say that this foreshadowed the inception of persistent homology, because it suggested the study of filtrations to capture the scale of a shape or data set. Importantly, this method has fast algorithms. The arguably most useful result on persistent homology is the stability of its diagrams under perturbations.","lang":"eng"}],"title":"Shape, homology, persistence, and stability","department":[{"_id":"HeEd"}],"article_processing_charge":"No","publist_id":"5604","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” 23rd International Symposium, vol. 9411, Springer Nature, 2015.","apa":"Edelsbrunner, H. (2015). Shape, homology, persistence, and stability. In 23rd International Symposium (Vol. 9411). Los Angeles, CA, United States: Springer Nature.","ama":"Edelsbrunner H. Shape, homology, persistence, and stability. In: 23rd International Symposium. Vol 9411. Springer Nature; 2015.","short":"H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015.","ieee":"H. Edelsbrunner, “Shape, homology, persistence, and stability,” in 23rd International Symposium, Los Angeles, CA, United States, 2015, vol. 9411.","chicago":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” In 23rd International Symposium, Vol. 9411. Springer Nature, 2015.","ista":"Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411."},"date_updated":"2022-01-28T08:25:00Z","status":"public","conference":{"name":"GD: Graph Drawing and Network Visualization","start_date":"2015-09-24","location":"Los Angeles, CA, United States","end_date":"2015-09-26"},"type":"conference","_id":"1567"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Graff G, Pilarczyk P. 2015. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 45(1), 273–286.","chicago":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies, 2015. https://doi.org/10.12775/TMNA.2015.014.","ama":"Graff G, Pilarczyk P. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 2015;45(1):273-286. doi:10.12775/TMNA.2015.014","apa":"Graff, G., & Pilarczyk, P. (2015). An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies. https://doi.org/10.12775/TMNA.2015.014","short":"G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015) 273–286.","ieee":"G. Graff and P. Pilarczyk, “An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds,” Topological Methods in Nonlinear Analysis, vol. 45, no. 1. Juliusz Schauder Center for Nonlinear Studies, pp. 273–286, 2015.","mla":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis, vol. 45, no. 1, Juliusz Schauder Center for Nonlinear Studies, 2015, pp. 273–86, doi:10.12775/TMNA.2015.014."},"date_updated":"2021-01-12T06:51:37Z","department":[{"_id":"HeEd"}],"title":"An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds","publist_id":"5608","author":[{"last_name":"Graff","full_name":"Graff, Grzegorz","first_name":"Grzegorz"},{"first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk"}],"_id":"1563","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication":"Topological Methods in Nonlinear Analysis","day":"01","year":"2015","publication_status":"published","date_created":"2018-12-11T11:52:44Z","date_published":"2015-03-01T00:00:00Z","issue":"1","volume":45,"doi":"10.12775/TMNA.2015.014","page":"273 - 286","oa_version":"None","abstract":[{"lang":"eng","text":"For a given self-map $f$ of $M$, a closed smooth connected and simply-connected manifold of dimension $m\\geq 4$, we provide an algorithm for estimating the values of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic points in the smooth homotopy class of $f$. Our results are based on the combinatorial scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm programmed in C++ is publicly available at {\\tt http://www.pawelpilarczyk.com/combtop/}."}],"intvolume":" 45","month":"03","publisher":"Juliusz Schauder Center for Nonlinear Studies","scopus_import":1,"quality_controlled":"1"},{"article_number":"8821","citation":{"ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821.","chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.","short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","ieee":"Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821","ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821","mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5597","author":[{"last_name":"Chen","full_name":"Chen, Qian","first_name":"Qian"},{"full_name":"Liu, Yang","last_name":"Liu","first_name":"Yang"},{"first_name":"Steven","last_name":"Maere","full_name":"Maere, Steven"},{"first_name":"Eunkyoung","full_name":"Lee, Eunkyoung","last_name":"Lee"},{"first_name":"Gert","last_name":"Van Isterdael","full_name":"Van Isterdael, Gert"},{"first_name":"Zidian","last_name":"Xie","full_name":"Xie, Zidian"},{"last_name":"Xuan","full_name":"Xuan, Wei","first_name":"Wei"},{"last_name":"Lucas","full_name":"Lucas, Jessica","first_name":"Jessica"},{"first_name":"Valya","full_name":"Vassileva, Valya","last_name":"Vassileva"},{"first_name":"Saeko","last_name":"Kitakura","full_name":"Kitakura, Saeko"},{"last_name":"Marhavy","orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter","first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T"},{"first_name":"Niko","full_name":"Geldner, Niko","last_name":"Geldner"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Le","full_name":"Le, Jie","first_name":"Jie"},{"last_name":"Fukaki","full_name":"Fukaki, Hidehiro","first_name":"Hidehiro"},{"first_name":"Erich","last_name":"Grotewold","full_name":"Grotewold, Erich"},{"first_name":"Chuanyou","full_name":"Li, Chuanyou","last_name":"Li"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Sack, Fred","last_name":"Sack","first_name":"Fred"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"}],"title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"18","publication":"Nature Communications","doi":"10.1038/ncomms9821","date_published":"2015-11-18T00:00:00Z","date_created":"2018-12-11T11:52:48Z","_id":"1574","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"477","date_updated":"2021-01-12T06:51:42Z","ddc":["580"],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:02Z","abstract":[{"text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"11","intvolume":" 6","publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:02Z","file_size":1701815,"creator":"system","date_created":"2018-12-12T10:14:32Z","file_name":"IST-2016-477-v1+1_ncomms9821.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5085","checksum":"8ff5c108899b548806e1cb7a302fe76d"}],"language":[{"iso":"eng"}],"volume":6},{"_id":"1575","pubrep_id":"476","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:51:42Z","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:02Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space."}],"intvolume":" 6","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_id":"4915","checksum":"bae12e86be2adb28253f890b8bba8315","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:11:58Z","file_name":"IST-2016-476-v1+1_ncomms8526.pdf","creator":"system","date_updated":"2020-07-14T12:45:02Z","file_size":4530215}],"publication_status":"published","volume":6,"article_number":"7526","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526.","chicago":"Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526.","ieee":"M. Chabaud et al., “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","short":"M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015).","apa":"Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms8526","ama":"Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 2015;6. doi:10.1038/ncomms8526","mla":"Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications, vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526."},"title":"Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells","publist_id":"5596","author":[{"full_name":"Chabaud, Mélanie","last_name":"Chabaud","first_name":"Mélanie"},{"last_name":"Heuzé","full_name":"Heuzé, Mélina","first_name":"Mélina"},{"last_name":"Bretou","full_name":"Bretou, Marine","first_name":"Marine"},{"first_name":"Pablo","last_name":"Vargas","full_name":"Vargas, Pablo"},{"first_name":"Paolo","last_name":"Maiuri","full_name":"Maiuri, Paolo"},{"first_name":"Paola","full_name":"Solanes, Paola","last_name":"Solanes"},{"first_name":"Mathieu","last_name":"Maurin","full_name":"Maurin, Mathieu"},{"first_name":"Emmanuel","last_name":"Terriac","full_name":"Terriac, Emmanuel"},{"first_name":"Maël","last_name":"Le Berre","full_name":"Le Berre, Maël"},{"full_name":"Lankar, Danielle","last_name":"Lankar","first_name":"Danielle"},{"full_name":"Piolot, Tristan","last_name":"Piolot","first_name":"Tristan"},{"first_name":"Robert","last_name":"Adelstein","full_name":"Adelstein, Robert"},{"last_name":"Zhang","full_name":"Zhang, Yingfan","first_name":"Yingfan"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Jordan","last_name":"Jacobelli","full_name":"Jacobelli, Jordan"},{"first_name":"Olivier","last_name":"Bénichou","full_name":"Bénichou, Olivier"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"},{"last_name":"Piel","full_name":"Piel, Matthieu","first_name":"Matthieu"},{"first_name":"Ana","last_name":"Lennon Duménil","full_name":"Lennon Duménil, Ana"}],"acknowledgement":"M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie).","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Communications","day":"25","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:52:48Z","date_published":"2015-06-25T00:00:00Z","doi":"10.1038/ncomms8526"},{"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:51:39Z","status":"public","type":"journal_article","_id":"1569","ec_funded":1,"issue":"7","volume":112,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 112","month":"02","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/"}],"scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.","lang":"eng"}],"title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","author":[{"full_name":"Doyle, Siamsa","last_name":"Doyle","first_name":"Siamsa"},{"last_name":"Haegera","full_name":"Haegera, Ash","first_name":"Ash"},{"first_name":"Thomas","full_name":"Vain, Thomas","last_name":"Vain"},{"full_name":"Rigala, Adeline","last_name":"Rigala","first_name":"Adeline"},{"last_name":"Viotti","full_name":"Viotti, Corrado","first_name":"Corrado"},{"full_name":"Łangowskaa, Małgorzata","last_name":"Łangowskaa","first_name":"Małgorzata"},{"full_name":"Maa, Qian","last_name":"Maa","first_name":"Qian"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Natasha","full_name":"Raikhel, Natasha","last_name":"Raikhel"},{"first_name":"Glenn","last_name":"Hickse","full_name":"Hickse, Glenn"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"}],"publist_id":"5602","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112.","ista":"Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815.","mla":"Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112.","short":"S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.","ieee":"S. Doyle et al., “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.","ama":"Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112","apa":"Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112"},"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:52:46Z","date_published":"2015-02-17T00:00:00Z","doi":"10.1073/pnas.1424856112","page":"E806 - E815","publication":"PNAS","day":"17","year":"2015","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","acknowledgement":"This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). "},{"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"date_updated":"2021-01-12T06:51:40Z","type":"journal_article","status":"public","_id":"1570","ec_funded":1,"volume":112,"issue":"45","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/","open_access":"1"}],"scopus_import":1,"intvolume":" 112","month":"11","abstract":[{"lang":"eng","text":"Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution."}],"oa_version":"Submitted Version","pmid":1,"external_id":{"pmid":["26504200"]},"publist_id":"5601","author":[{"first_name":"Ralf","full_name":"Der, Ralf","last_name":"Der"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S","last_name":"Martius"}],"title":"Novel plasticity rule can explain the development of sensorimotor intelligence","citation":{"ista":"Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.","chicago":"Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1508400112.","ieee":"R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015.","short":"R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.","apa":"Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1508400112","ama":"Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112","mla":"Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"page":"E6224 - E6232","date_created":"2018-12-11T11:52:47Z","date_published":"2015-11-10T00:00:00Z","doi":"10.1073/pnas.1508400112","year":"2015","publication":"PNAS","day":"10","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences"},{"publication_status":"published","year":"2015","day":"01","language":[{"iso":"eng"}],"publication":"PNAS","page":"14906 - 14911","volume":112,"doi":"10.1073/pnas.1510282112","issue":"48","date_published":"2015-12-01T00:00:00Z","date_created":"2018-12-11T11:52:47Z","abstract":[{"lang":"eng","text":"Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance."}],"oa_version":"None","acknowledgement":"This work is part of the research program of the Foundation for Fundamental Research on Matter, which is part of the Netherlands Organization for Scientific Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences (ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão, J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for discussions and suggestions on the Markov computation. Furthermore, we thank F. J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial version of the manuscript.","quality_controlled":"1","publisher":"National Academy of Sciences","scopus_import":1,"month":"12","intvolume":" 112","citation":{"chicago":"Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510282112.","ista":"de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 112(48), 14906–14911.","mla":"de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11, doi:10.1073/pnas.1510282112.","short":"M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.","ieee":"M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary constraint with a tradeoff ratchet,” PNAS, vol. 112, no. 48. National Academy of Sciences, pp. 14906–14911, 2015.","apa":"de Vos, M., Dawid, A., Šunderlíková, V., & Tans, S. (2015). Breaking evolutionary constraint with a tradeoff ratchet. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510282112","ama":"de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 2015;112(48):14906-14911. doi:10.1073/pnas.1510282112"},"date_updated":"2021-01-12T06:51:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"De Vos, Marjon","last_name":"De Vos","first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dawid, Alexandre","last_name":"Dawid","first_name":"Alexandre"},{"first_name":"Vanda","last_name":"Šunderlíková","full_name":"Šunderlíková, Vanda"},{"full_name":"Tans, Sander","last_name":"Tans","first_name":"Sander"}],"publist_id":"5600","department":[{"_id":"ToBo"}],"title":"Breaking evolutionary constraint with a tradeoff ratchet","_id":"1571","type":"journal_article","status":"public"},{"author":[{"first_name":"Michele","full_name":"Correggi, Michele","last_name":"Correggi"},{"first_name":"Alessandro","last_name":"Giuliani","full_name":"Giuliani, Alessandro"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"publist_id":"5599","title":"Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:51:41Z","citation":{"apa":"Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0","ama":"Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0","short":"M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics 339 (2015) 279–307.","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015.","mla":"Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0.","ista":"Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 339(1), 279–307.","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1572","page":"279 - 307","issue":"1","date_published":"2015-06-23T00:00:00Z","volume":339,"doi":"10.1007/s00220-015-2402-0","date_created":"2018-12-11T11:52:47Z","publication_status":"published","year":"2015","day":"23","language":[{"iso":"eng"}],"publication":"Communications in Mathematical Physics","quality_controlled":"1","scopus_import":1,"publisher":"Springer","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1312.7873","open_access":"1"}],"month":"06","intvolume":" 339","abstract":[{"lang":"eng","text":"We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.\r\n"}],"oa_version":"Preprint"},{"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 68(10), 1845–1884.","chicago":"Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015. https://doi.org/10.1002/cpa.21552.","short":"T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884.","ieee":"T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015.","apa":"Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552","ama":"Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552","mla":"Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics, vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5598","author":[{"full_name":"Chen, Thomas","last_name":"Chen","first_name":"Thomas"},{"first_name":"Christian","full_name":"Hainzl, Christian","last_name":"Hainzl"},{"first_name":"Nataša","full_name":"Pavlović, Nataša","last_name":"Pavlović"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"title":"Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti","quality_controlled":"1","publisher":"Wiley","oa":1,"year":"2015","day":"01","publication":"Communications on Pure and Applied Mathematics","page":"1845 - 1884","doi":"10.1002/cpa.21552","date_published":"2015-10-01T00:00:00Z","date_created":"2018-12-11T11:52:48Z","_id":"1573","type":"journal_article","status":"public","date_updated":"2021-01-12T06:51:41Z","department":[{"_id":"RoSe"}],"abstract":[{"lang":"eng","text":"We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3168"}],"month":"10","intvolume":" 68","publication_status":"published","language":[{"iso":"eng"}],"volume":68,"issue":"10"},{"ddc":["570"],"date_updated":"2021-01-12T06:51:44Z","file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"PeJo"}],"_id":"1580","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_size":5563015,"date_updated":"2020-07-14T12:45:02Z","creator":"dernst","file_name":"2015_Neuroscience_Brenes.pdf","date_created":"2020-05-15T06:50:20Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7849","checksum":"af2c4c994718c7be417eba0dc746aac9"}],"publication_status":"published","volume":311,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs."}],"intvolume":" 311","month":"12","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons,” Neuroscience, vol. 311. Elsevier, pp. 430–443, 2015.","short":"O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience 311 (2015) 430–443.","ama":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 2015;311:430-443. doi:10.1016/j.neuroscience.2015.10.046","apa":"Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., & Ghirardi, M. (2015). Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2015.10.046","mla":"Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience, vol. 311, Elsevier, 2015, pp. 430–43, doi:10.1016/j.neuroscience.2015.10.046.","ista":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 311, 430–443.","chicago":"Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience. Elsevier, 2015. https://doi.org/10.1016/j.neuroscience.2015.10.046."},"title":"Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons","article_processing_charge":"No","author":[{"last_name":"Brenes","full_name":"Brenes, Oscar","first_name":"Oscar"},{"last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emilio","full_name":"Carbone, Emilio","last_name":"Carbone"},{"full_name":"Montarolo, Pier","last_name":"Montarolo","first_name":"Pier"},{"last_name":"Ghirardi","full_name":"Ghirardi, Mirella","first_name":"Mirella"}],"publist_id":"5591","publication":"Neuroscience","day":"17","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:52:50Z","date_published":"2015-12-17T00:00:00Z","doi":"10.1016/j.neuroscience.2015.10.046","page":"430 - 443","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","acknowledgement":"This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript.","page":"12450 - 12455","date_created":"2018-12-11T11:52:49Z","doi":"10.1073/pnas.1516543112","date_published":"2015-10-06T00:00:00Z","year":"2015","publication":"PNAS","day":"06","article_processing_charge":"No","external_id":{"pmid":["26385968"]},"publist_id":"5594","author":[{"first_name":"Antonio","last_name":"Carvalho","full_name":"Carvalho, Antonio"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"full_name":"Russo, Claudia","last_name":"Russo","first_name":"Claudia"},{"first_name":"Bonnielin","full_name":"Swenor, Bonnielin","last_name":"Swenor"},{"first_name":"Andrew","last_name":"Clark","full_name":"Clark, Andrew"}],"title":"Birth of a new gene on the Y chromosome of Drosophila melanogaster","citation":{"chicago":"Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112.","ista":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.","mla":"Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:10.1073/pnas.1516543112.","apa":"Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1516543112","ama":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455. doi:10.1073/pnas.1516543112","ieee":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015.","short":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/","open_access":"1"}],"scopus_import":1,"intvolume":" 112","month":"10","abstract":[{"text":"Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":112,"issue":"40","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"1577","department":[{"_id":"BeVi"}],"date_updated":"2021-01-12T06:51:43Z"},{"status":"public","type":"journal_article","_id":"1579","department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:51:43Z","month":"06","intvolume":" 367","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.4280"}],"oa_version":"Preprint","abstract":[{"text":"We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality.","lang":"eng"}],"issue":"6","volume":367,"language":[{"iso":"eng"}],"publication_status":"published","title":"Galois groups of Schubert problems of lines are at least alternating","publist_id":"5592","author":[{"first_name":"Christopher","last_name":"Brooks","full_name":"Brooks, Christopher"},{"last_name":"Martin Del Campo Sanchez","full_name":"Martin Del Campo Sanchez, Abraham","first_name":"Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sottile","full_name":"Sottile, Frank","first_name":"Frank"}],"article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/S0002-9947-2014-06192-8.","ista":"Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 367(6), 4183–4206.","mla":"Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society, vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8.","ieee":"C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of Schubert problems of lines are at least alternating,” Transactions of the American Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp. 4183–4206, 2015.","short":"C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American Mathematical Society 367 (2015) 4183–4206.","ama":"Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8","apa":"Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8"},"quality_controlled":"1","publisher":"American Mathematical Society","oa":1,"acknowledgement":"This research was supported in part by NSF grant DMS-915211 and the Institut Mittag-Leffler.\r\n","doi":"10.1090/S0002-9947-2014-06192-8","date_published":"2015-06-01T00:00:00Z","date_created":"2018-12-11T11:52:50Z","page":"4183 - 4206","day":"01","publication":"Transactions of the American Mathematical Society","year":"2015"},{"type":"journal_article","status":"public","_id":"1578","author":[{"last_name":"Cao","full_name":"Cao, Thanhtung","first_name":"Thanhtung"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tiowseng","last_name":"Tan","full_name":"Tan, Tiowseng"}],"publist_id":"5593","department":[{"_id":"HeEd"}],"title":"Triangulations from topologically correct digital Voronoi diagrams","date_updated":"2021-01-12T06:51:43Z","citation":{"chicago":"Cao, Thanhtung, Herbert Edelsbrunner, and Tiowseng Tan. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.04.001.","ista":"Cao T, Edelsbrunner H, Tan T. 2015. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 48(7), 507–519.","mla":"Cao, Thanhtung, et al. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry, vol. 48, no. 7, Elsevier, 2015, pp. 507–19, doi:10.1016/j.comgeo.2015.04.001.","apa":"Cao, T., Edelsbrunner, H., & Tan, T. (2015). Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. Elsevier. https://doi.org/10.1016/j.comgeo.2015.04.001","ama":"Cao T, Edelsbrunner H, Tan T. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 2015;48(7):507-519. doi:10.1016/j.comgeo.2015.04.001","short":"T. Cao, H. Edelsbrunner, T. Tan, Computational Geometry 48 (2015) 507–519.","ieee":"T. Cao, H. Edelsbrunner, and T. Tan, “Triangulations from topologically correct digital Voronoi diagrams,” Computational Geometry, vol. 48, no. 7. Elsevier, pp. 507–519, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Elsevier","scopus_import":1,"month":"08","intvolume":" 48","abstract":[{"lang":"eng","text":"We prove that the dual of the digital Voronoi diagram constructed by flooding the plane from the data points gives a geometrically and topologically correct dual triangulation. This provides the proof of correctness for recently developed GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional Delaunay triangulations."}],"oa_version":"None","acknowledgement":"The research of the second author is partially supported by NSF under grant DBI-0820624 and by DARPA under grants HR011-05-1-0057 and HR0011-09-006\r\n","page":"507 - 519","date_published":"2015-08-01T00:00:00Z","doi":"10.1016/j.comgeo.2015.04.001","issue":"7","volume":48,"date_created":"2018-12-11T11:52:49Z","year":"2015","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Computational Geometry"},{"status":"public","type":"journal_article","_id":"1581","department":[{"_id":"ToBo"},{"_id":"CaHe"}],"title":"Gradients are shaping up","author":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"publist_id":"5590","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M.T. Bollenbach, C.-P.J. Heisenberg, Cell 161 (2015) 431–432.","ieee":"M. T. Bollenbach and C.-P. J. Heisenberg, “Gradients are shaping up,” Cell, vol. 161, no. 3. Cell Press, pp. 431–432, 2015.","ama":"Bollenbach MT, Heisenberg C-PJ. Gradients are shaping up. Cell. 2015;161(3):431-432. doi:10.1016/j.cell.2015.04.009","apa":"Bollenbach, M. T., & Heisenberg, C.-P. J. (2015). Gradients are shaping up. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.04.009","mla":"Bollenbach, Mark Tobias, and Carl-Philipp J. Heisenberg. “Gradients Are Shaping Up.” Cell, vol. 161, no. 3, Cell Press, 2015, pp. 431–32, doi:10.1016/j.cell.2015.04.009.","ista":"Bollenbach MT, Heisenberg C-PJ. 2015. Gradients are shaping up. Cell. 161(3), 431–432.","chicago":"Bollenbach, Mark Tobias, and Carl-Philipp J Heisenberg. “Gradients Are Shaping Up.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.04.009."},"date_updated":"2022-08-25T13:56:10Z","month":"04","intvolume":" 161","quality_controlled":"1","scopus_import":"1","publisher":"Cell Press","oa_version":"None","abstract":[{"text":"In animal embryos, morphogen gradients determine tissue patterning and morphogenesis. Shyer et al. provide evidence that, during vertebrate gut formation, tissue folding generates graded activity of signals required for subsequent steps of gut growth and differentiation, thereby revealing an intriguing link between tissue morphogenesis and morphogen gradient formation.","lang":"eng"}],"doi":"10.1016/j.cell.2015.04.009","issue":"3","volume":161,"date_published":"2015-04-23T00:00:00Z","date_created":"2018-12-11T11:52:50Z","page":"431 - 432","day":"23","language":[{"iso":"eng"}],"publication":"Cell","year":"2015","publication_status":"published"},{"volume":5,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:13:49Z","file_name":"IST-2016-472-v1+1_srep18589.pdf","creator":"system","date_updated":"2020-07-14T12:45:03Z","file_size":2771236,"checksum":"927e151674347661ce36eae2818dafdc","file_id":"5036","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","intvolume":" 5","month":"12","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices.","lang":"eng"}],"department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:03Z","ddc":["530","540"],"date_updated":"2021-01-12T06:51:48Z","pubrep_id":"472","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"1589","date_created":"2018-12-11T11:52:53Z","date_published":"2015-12-21T00:00:00Z","doi":"10.1038/srep18589","publication":"Scientific Reports","day":"21","year":"2015","has_accepted_license":"1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","title":"Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system","author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian","last_name":"Altmeyer"},{"full_name":"Do, Younghae","last_name":"Do","first_name":"Younghae"},{"full_name":"Lai, Ying","last_name":"Lai","first_name":"Ying"}],"publist_id":"5582","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports, vol. 5, 18589, Nature Publishing Group, 2015, doi:10.1038/srep18589.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","ama":"Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 2015;5. doi:10.1038/srep18589","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep18589","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep18589.","ista":"Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589."},"article_number":"18589"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.01.004.","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(5), 429–442.","mla":"Biedl, Therese, et al. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 5, Elsevier, 2015, pp. 429–42, doi:10.1016/j.comgeo.2015.01.004.","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Reprint of: Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 5. Elsevier, pp. 429–442, 2015.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 429–442.","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(5):429-442. doi:10.1016/j.comgeo.2015.01.004","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2015.01.004"},"title":"Reprint of: Weighted straight skeletons in the plane","author":[{"full_name":"Biedl, Therese","last_name":"Biedl","first_name":"Therese"},{"first_name":"Martin","last_name":"Held","full_name":"Held, Martin"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Huber","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan"},{"last_name":"Kaaser","full_name":"Kaaser, Dominik","first_name":"Dominik"},{"first_name":"Peter","full_name":"Palfrader, Peter","last_name":"Palfrader"}],"publist_id":"5587","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"01","publication":"Computational Geometry: Theory and Applications","has_accepted_license":"1","year":"2015","date_published":"2015-07-01T00:00:00Z","doi":"10.1016/j.comgeo.2015.01.004","date_created":"2018-12-11T11:52:51Z","page":"429 - 442","_id":"1584","status":"public","pubrep_id":"475","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2023-02-23T10:05:22Z","file_date_updated":"2020-07-14T12:45:03Z","department":[{"_id":"HeEd"}],"oa_version":"Published Version","abstract":[{"text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights.","lang":"eng"}],"month":"07","intvolume":" 48","scopus_import":1,"file":[{"date_created":"2018-12-12T10:17:36Z","file_name":"IST-2016-475-v1+1_1-s2.0-S092577211500005X-main.pdf","date_updated":"2020-07-14T12:45:03Z","file_size":508379,"creator":"system","file_id":"5292","checksum":"5b33719a86f7f4c8e5dc62c1b6893f49","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"other","id":"1582","status":"public"}]},"volume":48,"issue":"5"},{"citation":{"mla":"Biedl, Therese, et al. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 2, Elsevier, 2015, pp. 120–33, doi:10.1016/j.comgeo.2014.08.006.","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(2):120-133. doi:10.1016/j.comgeo.2014.08.006","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.006","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 2. Elsevier, pp. 120–133, 2015.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 120–133.","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.006.","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(2), 120–133."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Biedl, Therese","last_name":"Biedl","first_name":"Therese"},{"first_name":"Martin","full_name":"Held, Martin","last_name":"Held"},{"orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"first_name":"Dominik","full_name":"Kaaser, Dominik","last_name":"Kaaser"},{"first_name":"Peter","full_name":"Palfrader, Peter","last_name":"Palfrader"}],"publist_id":"5589","title":"Weighted straight skeletons in the plane","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2015","has_accepted_license":"1","publication":"Computational Geometry: Theory and Applications","day":"01","page":"120 - 133","date_created":"2018-12-11T11:52:51Z","date_published":"2015-02-01T00:00:00Z","doi":"10.1016/j.comgeo.2014.08.006","_id":"1582","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"474","status":"public","date_updated":"2023-02-23T10:05:27Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"HeEd"}],"abstract":[{"lang":"eng","text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 48","month":"02","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:16:28Z","file_name":"IST-2016-474-v1+1_1-s2.0-S0925772114000807-main.pdf","creator":"system","date_updated":"2020-07-14T12:45:02Z","file_size":505987,"checksum":"c1ef67f6ec925e12f73a96b8fe285ab4","file_id":"5215","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"issue":"2","volume":48,"related_material":{"record":[{"status":"public","id":"1584","relation":"other"}]}},{"author":[{"full_name":"Biedl, Therese","last_name":"Biedl","first_name":"Therese"},{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"full_name":"Kaaser, Dominik","last_name":"Kaaser","first_name":"Dominik"},{"last_name":"Palfrader","full_name":"Palfrader, Peter","first_name":"Peter"}],"publist_id":"5588","title":"A simple algorithm for computing positively weighted straight skeletons of monotone polygons","citation":{"ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 115(2), 243–247.","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.021.","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.021","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 2015;115(2):243-247. doi:10.1016/j.ipl.2014.09.021","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Information Processing Letters 115 (2015) 243–247.","ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “A simple algorithm for computing positively weighted straight skeletons of monotone polygons,” Information Processing Letters, vol. 115, no. 2. Elsevier, pp. 243–247, 2015.","mla":"Biedl, Therese, et al. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters, vol. 115, no. 2, Elsevier, 2015, pp. 243–47, doi:10.1016/j.ipl.2014.09.021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"243 - 247","date_created":"2018-12-11T11:52:51Z","doi":"10.1016/j.ipl.2014.09.021","date_published":"2015-02-01T00:00:00Z","year":"2015","has_accepted_license":"1","publication":"Information Processing Letters","day":"01","oa":1,"publisher":"Elsevier","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:03Z","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:51:45Z","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"473","status":"public","_id":"1583","volume":115,"issue":"2","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:03Z","file_size":270137,"creator":"system","date_created":"2018-12-12T10:18:45Z","file_name":"IST-2016-473-v1+1_1-s2.0-S0020019014001987-main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5367","checksum":"2779a648610c9b5c86d0b51a62816d23"}],"scopus_import":1,"intvolume":" 115","month":"02","abstract":[{"lang":"eng","text":"We study the characteristics of straight skeletons of monotone polygonal chains and use them to devise an algorithm for computing positively weighted straight skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space, where n denotes the number of vertices of the polygon."}],"oa_version":"Published Version"},{"language":[{"iso":"eng"}],"publication_status":"published","issue":"6","volume":92,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme."}],"month":"12","intvolume":" 92","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1511.03585","open_access":"1"}],"date_updated":"2021-01-12T06:51:47Z","department":[{"_id":"MiLe"}],"_id":"1587","status":"public","type":"journal_article","article_type":"original","day":"31","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","year":"2015","doi":"10.1103/PhysRevA.92.062506","date_published":"2015-12-31T00:00:00Z","date_created":"2018-12-11T11:52:53Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R., & Santos, J. (2015). Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.92.062506","ama":"Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 2015;92(6). doi:10.1103/PhysRevA.92.062506","ieee":"P. Amaro et al., “Quantum interference shifts in laser spectroscopy with elliptical polarization,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6. American Physical Society, 2015.","short":"P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 92 (2015).","mla":"Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:10.1103/PhysRevA.92.062506.","ista":"Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J. 2015. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 92(6), 062506.","chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato, Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.062506."},"title":"Quantum interference shifts in laser spectroscopy with elliptical polarization","publist_id":"5584","author":[{"last_name":"Amaro","full_name":"Amaro, Pedro","first_name":"Pedro"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"},{"first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh","last_name":"Safari"},{"first_name":"Aldo","last_name":"Antognini","full_name":"Antognini, Aldo"},{"full_name":"Indelicato, Paul","last_name":"Indelicato","first_name":"Paul"},{"first_name":"Randolf","last_name":"Pohl","full_name":"Pohl, Randolf"},{"full_name":"Santos, José","last_name":"Santos","first_name":"José"}],"article_processing_charge":"No","external_id":{"arxiv":["1511.03585"]},"article_number":"062506","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"issue":"5","volume":92,"date_published":"2015-11-24T00:00:00Z","doi":"10.1103/PhysRevE.92.053018","date_created":"2018-12-11T11:52:53Z","day":"24","publication":"Physical Review E","language":[{"iso":"eng"}],"year":"2015","publication_status":"published","month":"11","intvolume":" 92","publisher":"American Physical Society","quality_controlled":"1","scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"We investigate the Taylor-Couette system where the radius ratio is close to unity. Systematically increasing the Reynolds number, we observe a number of previously known transitions, such as one from the classical Taylor vortex flow (TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence. Prior to the onset of turbulence, we observe intermittent bursting patterns of localized turbulent patches, confirming the experimentally observed pattern of very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds number larger than that for the onset of VSWBs, a new type of intermittently bursting behavior emerges: patterns of azimuthally closed rings of various orders. We call them ring-bursting patterns, which surround the cylinder completely but remain localized and separated in the axial direction through nonturbulent wavy structures. We employ a number of quantitative measures including the cross-flow energy to characterize the ring-bursting patterns and to distinguish them from the background flow. These patterns are interesting because they do not occur in the wide-gap Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly deserves further attention to gain deeper insights into complex flow dynamics in fluids."}],"title":"Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows","department":[{"_id":"BjHo"}],"publist_id":"5583","author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Altmeyer","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203"},{"last_name":"Do","full_name":"Do, Younghae","first_name":"Younghae"},{"first_name":"Ying","last_name":"Lai","full_name":"Lai, Ying"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:47Z","citation":{"short":"S. Altmeyer, Y. Do, Y. Lai, Physical Review E 92 (2015).","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows,” Physical Review E, vol. 92, no. 5. American Physical Society, 2015.","ama":"Altmeyer S, Do Y, Lai Y. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 2015;92(5). doi:10.1103/PhysRevE.92.053018","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2015). Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.92.053018","mla":"Altmeyer, Sebastian, et al. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E, vol. 92, no. 5, 053018, American Physical Society, 2015, doi:10.1103/PhysRevE.92.053018.","ista":"Altmeyer S, Do Y, Lai Y. 2015. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 92(5), 053018.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.92.053018."},"status":"public","type":"journal_article","article_number":"053018","_id":"1588"},{"type":"journal_article","status":"public","_id":"1586","publist_id":"5585","author":[{"last_name":"Angermayr","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"last_name":"Gorchs","full_name":"Gorchs, Aleix","first_name":"Aleix"},{"full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf","first_name":"Klaas"}],"department":[{"_id":"ToBo"}],"title":"Metabolic engineering of cyanobacteria for the synthesis of commodity products","date_updated":"2021-01-12T06:51:46Z","citation":{"mla":"Angermayr, Andreas, et al. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology, vol. 33, no. 6, Elsevier, 2015, pp. 352–61, doi:10.1016/j.tibtech.2015.03.009.","ama":"Angermayr A, Gorchs A, Hellingwerf K. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 2015;33(6):352-361. doi:10.1016/j.tibtech.2015.03.009","apa":"Angermayr, A., Gorchs, A., & Hellingwerf, K. (2015). Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. Elsevier. https://doi.org/10.1016/j.tibtech.2015.03.009","short":"A. Angermayr, A. Gorchs, K. Hellingwerf, Trends in Biotechnology 33 (2015) 352–361.","ieee":"A. Angermayr, A. Gorchs, and K. Hellingwerf, “Metabolic engineering of cyanobacteria for the synthesis of commodity products,” Trends in Biotechnology, vol. 33, no. 6. Elsevier, pp. 352–361, 2015.","chicago":"Angermayr, Andreas, Aleix Gorchs, and Klaas Hellingwerf. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology. Elsevier, 2015. https://doi.org/10.1016/j.tibtech.2015.03.009.","ista":"Angermayr A, Gorchs A, Hellingwerf K. 2015. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 33(6), 352–361."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","scopus_import":1,"quality_controlled":"1","intvolume":" 33","month":"06","abstract":[{"lang":"eng","text":"Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass."}],"oa_version":"None","page":"352 - 361","date_created":"2018-12-11T11:52:52Z","doi":"10.1016/j.tibtech.2015.03.009","issue":"6","date_published":"2015-06-01T00:00:00Z","volume":33,"year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Trends in Biotechnology","day":"01"},{"abstract":[{"lang":"eng","text":"In this paper, we consider the fluctuation of mutual information statistics of a multiple input multiple output channel communication systems without assuming that the entries of the channel matrix have zero pseudovariance. To this end, we also establish a central limit theorem of the linear spectral statistics for sample covariance matrices under general moment conditions by removing the restrictions imposed on the second moment and fourth moment on the matrix entries in Bai and Silverstein (2004)."}],"oa_version":"None","acknowledgement":"G. Pan was supported by MOE Tier 2 under Grant 2014-T2-2-060 and in part by Tier 1 under Grant RG25/14 through the Nanyang Technological University, Singapore. W. Zhou was supported by the National University of Singapore, Singapore, under Grant R-155-000-131-112.\r\n","scopus_import":1,"publisher":"IEEE","quality_controlled":"1","month":"06","intvolume":" 61","publication_status":"published","year":"2015","day":"01","publication":"IEEE Transactions on Information Theory","language":[{"iso":"eng"}],"page":"3413 - 3426","issue":"6","date_published":"2015-06-01T00:00:00Z","doi":"10.1109/TIT.2015.2421894","volume":61,"date_created":"2018-12-11T11:52:52Z","_id":"1585","type":"journal_article","status":"public","citation":{"chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory. IEEE, 2015. https://doi.org/10.1109/TIT.2015.2421894.","ista":"Bao Z, Pan G, Zhou W. 2015. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 61(6), 3413–3426.","mla":"Bao, Zhigang, et al. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory, vol. 61, no. 6, IEEE, 2015, pp. 3413–26, doi:10.1109/TIT.2015.2421894.","apa":"Bao, Z., Pan, G., & Zhou, W. (2015). Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2015.2421894","ama":"Bao Z, Pan G, Zhou W. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 2015;61(6):3413-3426. doi:10.1109/TIT.2015.2421894","short":"Z. Bao, G. Pan, W. Zhou, IEEE Transactions on Information Theory 61 (2015) 3413–3426.","ieee":"Z. Bao, G. Pan, and W. Zhou, “Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices,” IEEE Transactions on Information Theory, vol. 61, no. 6. IEEE, pp. 3413–3426, 2015."},"date_updated":"2021-01-12T06:51:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5586","author":[{"last_name":"Bao","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guangming","full_name":"Pan, Guangming","last_name":"Pan"},{"full_name":"Zhou, Wang","last_name":"Zhou","first_name":"Wang"}],"department":[{"_id":"LaEr"}],"title":"Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices"},{"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis"}],"publist_id":"5578","author":[{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"full_name":"Smet, Dajo","last_name":"Smet","first_name":"Dajo"},{"id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","first_name":"Qiang","last_name":"Zhu","full_name":"Zhu, Qiang"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Strategies of seedlings to overcome their sessile nature: Auxin in mobility control","citation":{"ista":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 6(4).","chicago":"Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fpls.2015.00218.","ieee":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies of seedlings to overcome their sessile nature: Auxin in mobility control,” Frontiers in Plant Science, vol. 6, no. 4. Frontiers Research Foundation, 2015.","short":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers in Plant Science 6 (2015).","apa":"Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., & Benková, E. (2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.00218","ama":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 2015;6(4). doi:10.3389/fpls.2015.00218","mla":"Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science, vol. 6, no. 4, Frontiers Research Foundation, 2015, doi:10.3389/fpls.2015.00218."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Frontiers Research Foundation","quality_controlled":"1","oa":1,"doi":"10.3389/fpls.2015.00218","date_published":"2015-04-14T00:00:00Z","date_created":"2018-12-11T11:52:55Z","has_accepted_license":"1","year":"2015","day":"14","publication":"Frontiers in Plant Science","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"471","_id":"1593","file_date_updated":"2020-07-14T12:45:03Z","department":[{"_id":"EvBe"}],"date_updated":"2021-01-12T06:51:50Z","ddc":["570"],"scopus_import":1,"month":"04","intvolume":" 6","abstract":[{"text":"Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.","lang":"eng"}],"oa_version":"Published Version","issue":"4","volume":6,"ec_funded":1,"publication_status":"published","file":[{"date_created":"2018-12-12T10:15:23Z","file_name":"IST-2016-471-v1+1_fpls-06-00218.pdf","date_updated":"2020-07-14T12:45:03Z","file_size":965690,"creator":"system","file_id":"5142","checksum":"c454d642e18dfa86820b97a86cd6d3cc","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}]},{"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4697","checksum":"685f91bd077a951ba067d42cce75409e","date_updated":"2020-07-14T12:45:03Z","file_size":330135,"creator":"system","date_created":"2018-12-12T10:08:36Z","file_name":"IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":9411,"related_material":{"record":[{"relation":"later_version","id":"1113","status":"public"},{"relation":"later_version","id":"1164","status":"public"}]},"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth."}],"month":"11","intvolume":" 9411","alternative_title":["LNCS"],"scopus_import":1,"ddc":["510"],"date_updated":"2023-02-21T16:23:36Z","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:03Z","_id":"1595","status":"public","pubrep_id":"594","type":"conference","conference":{"location":"Los Angeles, CA, USA","end_date":"2015-09-26","start_date":"2015-09-24","name":"GD: Graph Drawing and Network Visualization"},"day":"27","has_accepted_license":"1","year":"2015","doi":"10.1007/978-3-319-27261-0_9","date_published":"2015-11-27T00:00:00Z","date_created":"2018-12-11T11:52:55Z","page":"99 - 110","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].","publisher":"Springer","quality_controlled":"1","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110.","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA, 2015, vol. 9411, pp. 99–110.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol 9411. Springer; 2015:99-110. doi:10.1007/978-3-319-27261-0_9","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2015). Hanani-Tutte for radial planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA: Springer. https://doi.org/10.1007/978-3-319-27261-0_9","mla":"Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity. Vol. 9411, Springer, 2015, pp. 99–110, doi:10.1007/978-3-319-27261-0_9.","ista":"Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity,” 9411:99–110. Springer, 2015. https://doi.org/10.1007/978-3-319-27261-0_9."},"title":"Hanani-Tutte for radial planarity","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Pelsmajer, Michael","last_name":"Pelsmajer","first_name":"Michael"},{"last_name":"Schaefer","full_name":"Schaefer, Marcus","first_name":"Marcus"}],"publist_id":"5576","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2018-12-11T11:52:54Z","date_published":"2015-11-27T00:00:00Z","doi":"10.1007/978-3-319-27261-0_28","page":"335 - 347","publication":"Graph Drawing and Network Visualization","day":"27","year":"2015","title":"Representing directed trees as straight skeletons","article_processing_charge":"No","publist_id":"5581","author":[{"first_name":"Oswin","full_name":"Aichholzer, Oswin","last_name":"Aichholzer"},{"full_name":"Biedl, Therese","last_name":"Biedl","first_name":"Therese"},{"first_name":"Thomas","full_name":"Hackl, Thomas","last_name":"Hackl"},{"last_name":"Held","full_name":"Held, Martin","first_name":"Martin"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"O. Aichholzer, T. Biedl, T. Hackl, M. Held, S. Huber, P. Palfrader, B. Vogtenhuber, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 335–347.","ieee":"O. Aichholzer et al., “Representing directed trees as straight skeletons,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–347.","apa":"Aichholzer, O., Biedl, T., Hackl, T., Held, M., Huber, S., Palfrader, P., & Vogtenhuber, B. (2015). Representing directed trees as straight skeletons. In Graph Drawing and Network Visualization (Vol. 9411, pp. 335–347). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_28","ama":"Aichholzer O, Biedl T, Hackl T, et al. Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:335-347. doi:10.1007/978-3-319-27261-0_28","mla":"Aichholzer, Oswin, et al. “Representing Directed Trees as Straight Skeletons.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–47, doi:10.1007/978-3-319-27261-0_28.","ista":"Aichholzer O, Biedl T, Hackl T, Held M, Huber S, Palfrader P, Vogtenhuber B. 2015.Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 335–347.","chicago":"Aichholzer, Oswin, Therese Biedl, Thomas Hackl, Martin Held, Stefan Huber, Peter Palfrader, and Birgit Vogtenhuber. “Representing Directed Trees as Straight Skeletons.” In Graph Drawing and Network Visualization, 9411:335–47. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_28."},"intvolume":" 9411","month":"11","main_file_link":[{"url":"http://arxiv.org/abs/1508.01076","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The straight skeleton of a polygon is the geometric graph obtained by tracing the vertices during a mitered offsetting process. It is known that the straight skeleton of a simple polygon is a tree, and one can naturally derive directions on the edges of the tree from the propagation of the shrinking process. In this paper, we ask the reverse question: Given a tree with directed edges, can it be the straight skeleton of a polygon? And if so, can we find a suitable simple polygon? We answer these questions for all directed trees where the order of edges around each node is fixed."}],"volume":9411,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-319-27260-3"],"eisbn":["978-3-319-27261-0"]},"status":"public","conference":{"start_date":"2015-09-24","end_date":"2015-09-26","location":"Los Angeles, CA, United States","name":"GD: International Symposium on Graph Drawing"},"type":"book_chapter","_id":"1590","department":[{"_id":"HeEd"}],"date_updated":"2022-01-28T09:10:37Z"},{"day":"22","year":"2015","date_created":"2018-12-11T11:52:55Z","date_published":"2015-11-22T00:00:00Z","doi":"10.1007/978-3-662-48899-7_12","page":"162 - 177","acknowledgement":"This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the Czech Science Foundation under grant agreement P202/12/G061, by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the CDZ project 1023 (CAP), by the CAS/SAFEA International Partnership Program for Creative Research Teams, by the EPSRC grant EP/M023656/1, by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734, by the Austrian Science Fund (FWF) S11407-N23 (RiSE/SHiNE), and by the ERC Start Grant (279307: Graph Games).\r\n","publisher":"Springer","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Forejt V, Krčál J, Kretinsky J. 2015. Controller synthesis for MDPs and frequency LTL\\GU. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 9450, 162–177.","chicago":"Forejt, Vojtěch, Jan Krčál, and Jan Kretinsky. “Controller Synthesis for MDPs and Frequency LTL\\GU,” 9450:162–77. Springer, 2015. https://doi.org/10.1007/978-3-662-48899-7_12.","ama":"Forejt V, Krčál J, Kretinsky J. Controller synthesis for MDPs and frequency LTL\\GU. In: Vol 9450. Springer; 2015:162-177. doi:10.1007/978-3-662-48899-7_12","apa":"Forejt, V., Krčál, J., & Kretinsky, J. (2015). Controller synthesis for MDPs and frequency LTL\\GU (Vol. 9450, pp. 162–177). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji: Springer. https://doi.org/10.1007/978-3-662-48899-7_12","ieee":"V. Forejt, J. Krčál, and J. Kretinsky, “Controller synthesis for MDPs and frequency LTL\\GU,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji, 2015, vol. 9450, pp. 162–177.","short":"V. Forejt, J. Krčál, J. Kretinsky, in:, Springer, 2015, pp. 162–177.","mla":"Forejt, Vojtěch, et al. Controller Synthesis for MDPs and Frequency LTL\\GU. Vol. 9450, Springer, 2015, pp. 162–77, doi:10.1007/978-3-662-48899-7_12."},"title":"Controller synthesis for MDPs and frequency LTL\\GU","author":[{"first_name":"Vojtěch","full_name":"Forejt, Vojtěch","last_name":"Forejt"},{"last_name":"Krčál","full_name":"Krčál, Jan","first_name":"Jan"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky"}],"publist_id":"5577","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":9450,"oa_version":"None","abstract":[{"lang":"eng","text":"Quantitative extensions of temporal logics have recently attracted significant attention. In this work, we study frequency LTL (fLTL), an extension of LTL which allows to speak about frequencies of events along an execution. Such an extension is particularly useful for probabilistic systems that often cannot fulfil strict qualitative guarantees on the behaviour. It has been recently shown that controller synthesis for Markov decision processes and fLTL is decidable when all the bounds on frequencies are 1. As a step towards a complete quantitative solution, we show that the problem is decidable for the fragment fLTL\\GU, where U does not occur in the scope of G (but still F can). Our solution is based on a novel translation of such quantitative formulae into equivalent deterministic automata."}],"intvolume":" 9450","month":"11","scopus_import":1,"alternative_title":["LNCS"],"date_updated":"2021-01-12T06:51:50Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"_id":"1594","status":"public","conference":{"location":"Suva, Fiji","end_date":"2015-11-28","start_date":"2015-11-24","name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning"},"type":"conference"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"full_name":"Radoičić, Radoš","last_name":"Radoičić","first_name":"Radoš"}],"publist_id":"5575","article_processing_charge":"No","title":"Vertical visibility among parallel polygons in three dimensions","citation":{"ama":"Fulek R, Radoičić R. Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:373-379. doi:10.1007/978-3-319-27261-0_31","apa":"Fulek, R., & Radoičić, R. (2015). Vertical visibility among parallel polygons in three dimensions. In Graph Drawing and Network Visualization (Vol. 9411, pp. 373–379). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_31","short":"R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 373–379.","ieee":"R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in three dimensions,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–379.","mla":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–79, doi:10.1007/978-3-319-27261-0_31.","ista":"Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 373–379.","chicago":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” In Graph Drawing and Network Visualization, 9411:373–79. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_31."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Springer Nature","quality_controlled":"1","oa":1,"page":"373 - 379","date_published":"2015-11-27T00:00:00Z","doi":"10.1007/978-3-319-27261-0_31","date_created":"2018-12-11T11:52:56Z","has_accepted_license":"1","year":"2015","day":"27","publication":"Graph Drawing and Network Visualization","type":"book_chapter","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2015-09-26","location":"Los Angeles, CA, United States","start_date":"2015-09-24"},"status":"public","pubrep_id":"595","_id":"1596","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:04Z","date_updated":"2022-01-28T09:20:50Z","ddc":["510"],"alternative_title":["LNCS"],"scopus_import":"1","month":"11","intvolume":" 9411","abstract":[{"text":"Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon in the plane with the stacking order. The collection C forms a visibility clique if for everyi < j the intersection Ci and (Ci ∩ Cj)\\⋃i<l<jCl =∅.elements that are stacked between them, i.e., We show that if C forms a visibility clique its size is bounded from above by O(k4) thereby improving the upper bound of 22k from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the size of a visibility clique for homothetes of a convex (not necessarily regular) k-gon.","lang":"eng"}],"oa_version":"Submitted Version","volume":9411,"ec_funded":1,"publication_identifier":{"isbn":["978-3-319-27260-3"]},"publication_status":"published","file":[{"file_name":"IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf","date_created":"2018-12-12T10:17:06Z","file_size":312992,"date_updated":"2020-07-14T12:45:04Z","creator":"system","checksum":"eec04f86c5921d04f025d5791db9b965","file_id":"5258","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}]},{"title":"The Hanoi omega-automata format","article_processing_charge":"No","publist_id":"5566","author":[{"first_name":"Tomáš","last_name":"Babiak","full_name":"Babiak, Tomáš"},{"first_name":"František","full_name":"Blahoudek, František","last_name":"Blahoudek"},{"first_name":"Alexandre","full_name":"Duret Lutz, Alexandre","last_name":"Duret Lutz"},{"last_name":"Klein","full_name":"Klein, Joachim","first_name":"Joachim"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky"},{"first_name":"Daniel","full_name":"Mueller, Daniel","last_name":"Mueller"},{"full_name":"Parker, David","last_name":"Parker","first_name":"David"},{"last_name":"Strejček","full_name":"Strejček, Jan","first_name":"Jan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller, D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486.","ieee":"T. Babiak et al., “The Hanoi omega-automata format,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 479–486.","apa":"Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller, D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_31","ama":"Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format. In: Vol 9206. Springer; 2015:479-486. doi:10.1007/978-3-319-21690-4_31","mla":"Babiak, Tomáš, et al. The Hanoi Omega-Automata Format. Vol. 9206, Springer, 2015, pp. 479–86, doi:10.1007/978-3-319-21690-4_31.","ista":"Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification, LNCS, vol. 9206, 479–486.","chicago":"Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein, Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata Format,” 9206:479–86. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_31."},"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"date_created":"2018-12-11T11:52:57Z","date_published":"2015-07-16T00:00:00Z","doi":"10.1007/978-3-319-21690-4_31","page":"479 - 486","day":"16","year":"2015","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:04Z","ddc":["000"],"date_updated":"2021-01-12T06:51:54Z","status":"public","conference":{"start_date":"2015-07-18","location":"San Francisco, CA, United States","end_date":"2015-07-24","name":"CAV: Computer Aided Verification"},"type":"conference","_id":"1601","ec_funded":1,"volume":9206,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5885236fa88a439baba9ac6f3e801e93","file_id":"7850","date_updated":"2020-07-14T12:45:04Z","file_size":1651779,"creator":"dernst","date_created":"2020-05-15T08:38:12Z","file_name":"2015_CAV_Babiak.pdf"}],"publication_status":"published","intvolume":" 9206","month":"07","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata."}]},{"volume":9434,"ec_funded":1,"publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:05Z","file_size":1053207,"creator":"dernst","date_created":"2020-05-15T08:43:19Z","file_name":"2015_LNCS_Bogomolov.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7851","checksum":"3aab260f3f34641d622030ba22645b3e"}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":1,"month":"11","intvolume":" 9434","abstract":[{"text":"Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:05Z","date_updated":"2021-01-12T06:51:56Z","ddc":["000"],"type":"conference","conference":{"name":"HVC: Haifa Verification Conference","start_date":"2015-11-17","end_date":"2015-11-19","location":"Haifa, Israel"},"status":"public","_id":"1605","page":"19 - 35","doi":"10.1007/978-3-319-26287-1_2","date_published":"2015-11-28T00:00:00Z","date_created":"2018-12-11T11:52:59Z","has_accepted_license":"1","year":"2015","day":"28","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"This work was partly supported by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS, http://www.avacs.org/).","author":[{"last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"first_name":"Grégory","last_name":"Batt","full_name":"Batt, Grégory"},{"full_name":"Kong, Hui","orcid":"0000-0002-3066-6941","last_name":"Kong","first_name":"Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"publist_id":"5561","article_processing_charge":"No","title":"Abstraction-based parameter synthesis for multiaffine systems","citation":{"mla":"Bogomolov, Sergiy, et al. Abstraction-Based Parameter Synthesis for Multiaffine Systems. Vol. 9434, Springer, 2015, pp. 19–35, doi:10.1007/978-3-319-26287-1_2.","short":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:, Springer, 2015, pp. 19–35.","ieee":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu, “Abstraction-based parameter synthesis for multiaffine systems,” presented at the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.","apa":"Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., & Grosu, R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol. 9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_2","ama":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35. doi:10.1007/978-3-319-26287-1_2","chicago":"Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,” 9434:19–35. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_2.","ista":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference, LNCS, vol. 9434, 19–35."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}]},{"_id":"1606","status":"public","conference":{"name":"RV: Runtime Verification","location":"Vienna, Austria","end_date":"2015-09-25","start_date":"2015-09-22"},"type":"conference","date_updated":"2022-02-01T14:52:59Z","department":[{"_id":"ToHe"}],"oa_version":"None","abstract":[{"lang":"eng","text":"In this paper, we present the first steps toward a runtime verification framework for monitoring hybrid and cyber-physical systems (CPS) development tools based on randomized differential testing. The development tools include hybrid systems reachability analysis tools, model-based development environments like Simulink/Stateflow (SLSF), etc. First, hybrid automaton models are randomly generated. Next, these hybrid automaton models are translated to a number of different tools (currently, SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using the HyST source transformation and translation tool. Then, the hybrid automaton models are executed in the different tools and their outputs are parsed. The final step is the differential comparison: the outputs of the different tools are compared. If the results do not agree (in the sense that an analysis or verification result from one tool does not match that of another tool, ignoring timeouts, etc.), a candidate bug is flagged and the model is saved for future analysis by the user. The process then repeats and the monitoring continues until the user terminates the process. We present preliminary results that have been useful in identifying a few bugs in the analysis methods of different development tools, and in an earlier version of HyST."}],"intvolume":" 9333","month":"11","scopus_import":"1","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-319-23819-7"]},"ec_funded":1,"volume":9333,"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Runtime verification for hybrid analysis tools. 6th International Conference. RV: Runtime Verification, LNCS, vol. 9333, 281–286.","chicago":"Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson. “Runtime Verification for Hybrid Analysis Tools.” In 6th International Conference, 9333:281–86. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-23820-3_19.","ieee":"L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, “Runtime verification for hybrid analysis tools,” in 6th International Conference, Vienna, Austria, 2015, vol. 9333, pp. 281–286.","short":"L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, in:, 6th International Conference, Springer Nature, 2015, pp. 281–286.","ama":"Nguyen L, Schilling C, Bogomolov S, Johnson T. Runtime verification for hybrid analysis tools. In: 6th International Conference. Vol 9333. Springer Nature; 2015:281-286. doi:10.1007/978-3-319-23820-3_19","apa":"Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Runtime verification for hybrid analysis tools. In 6th International Conference (Vol. 9333, pp. 281–286). Vienna, Austria: Springer Nature. https://doi.org/10.1007/978-3-319-23820-3_19","mla":"Nguyen, Luan, et al. “Runtime Verification for Hybrid Analysis Tools.” 6th International Conference, vol. 9333, Springer Nature, 2015, pp. 281–86, doi:10.1007/978-3-319-23820-3_19."},"title":"Runtime verification for hybrid analysis tools","article_processing_charge":"No","publist_id":"5562","author":[{"last_name":"Nguyen","full_name":"Nguyen, Luan","first_name":"Luan"},{"last_name":"Schilling","full_name":"Schilling, Christian","first_name":"Christian"},{"orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"first_name":"Taylor","full_name":"Johnson, Taylor","last_name":"Johnson"}],"quality_controlled":"1","publisher":"Springer Nature","publication":"6th International Conference","day":"15","year":"2015","date_created":"2018-12-11T11:52:59Z","doi":"10.1007/978-3-319-23820-3_19","date_published":"2015-11-15T00:00:00Z","page":"281 - 286"},{"date_updated":"2022-02-01T15:04:44Z","department":[{"_id":"KrCh"}],"_id":"1609","status":"public","conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2015-07-06","end_date":"2015-07-10","location":"Kyoto, Japan"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-662-47665-9"]},"ec_funded":1,"volume":9135,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound."}],"intvolume":" 9135","month":"06","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.04844"}],"scopus_import":"1","alternative_title":["LNCS"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity of Synthesis from Probabilistic Components.” In 42nd International Colloquium, 9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9.","ista":"Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic components. 42nd International Colloquium. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 108–120.","mla":"Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic Components.” 42nd International Colloquium, vol. 9135, Springer Nature, 2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9.","ama":"Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic components. In: 42nd International Colloquium. Vol 9135. Springer Nature; 2015:108-120. doi:10.1007/978-3-662-47666-6_9","apa":"Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis from probabilistic components. In 42nd International Colloquium (Vol. 9135, pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9","short":"K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 108–120.","ieee":"K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol. 9135, pp. 108–120."},"title":"The complexity of synthesis from probabilistic components","article_processing_charge":"No","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"first_name":"Moshe","last_name":"Vardi","full_name":"Vardi, Moshe"}],"publist_id":"5557","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"publication":"42nd International Colloquium","day":"20","year":"2015","date_created":"2018-12-11T11:53:00Z","date_published":"2015-06-20T00:00:00Z","doi":"10.1007/978-3-662-47666-6_9","page":"108 - 120","acknowledgement":"This research was supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"abstract":[{"lang":"eng","text":"Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 13","month":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5005","checksum":"44d30fbb543774b076b4938bd36af9d7","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf","date_created":"2018-12-12T10:13:23Z","file_size":2314406,"date_updated":"2020-07-14T12:45:07Z","creator":"system"}],"issue":"3","volume":13,"_id":"1615","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"470","status":"public","date_updated":"2021-01-12T06:52:01Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"PeJo"}],"acknowledgement":"This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry.","oa":1,"quality_controlled":"1","publisher":"Cell Press","year":"2015","has_accepted_license":"1","publication":"Cell Reports","day":"20","page":"516 - 523","date_created":"2018-12-11T11:53:02Z","doi":"10.1016/j.celrep.2015.09.011","date_published":"2015-10-20T00:00:00Z","citation":{"chicago":"Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011.","ista":"Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523.","mla":"Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011.","ama":"Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011","apa":"Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2015.09.011","short":"M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523.","ieee":"M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13, no. 3. Cell Press, pp. 516–523, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5551","author":[{"full_name":"Hammer, Matthieu","last_name":"Hammer","first_name":"Matthieu"},{"first_name":"Dilja","full_name":"Krueger Burg, Dilja","last_name":"Krueger Burg"},{"first_name":"Liam","last_name":"Tuffy","full_name":"Tuffy, Liam"},{"last_name":"Cooper","full_name":"Cooper, Benjamin","first_name":"Benjamin"},{"last_name":"Taschenberger","full_name":"Taschenberger, Holger","first_name":"Holger"},{"last_name":"Goswami","full_name":"Goswami, Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","first_name":"Sarit"},{"first_name":"Hannelore","last_name":"Ehrenreich","full_name":"Ehrenreich, Hannelore"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"full_name":"Varoqueaux, Frederique","last_name":"Varoqueaux","first_name":"Frederique"},{"full_name":"Rhee, Jeong","last_name":"Rhee","first_name":"Jeong"},{"first_name":"Nils","last_name":"Brose","full_name":"Brose, Nils"}],"title":"Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism"},{"publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"day":"27","publication":"PNAS","has_accepted_license":"1","year":"2015","doi":"10.1073/pnas.1412996112","date_published":"2015-01-27T00:00:00Z","date_created":"2018-12-11T11:53:02Z","page":"1220 - 1225","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 112(4), 1220–1225.","chicago":"Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112.","apa":"Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112","ama":"Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 2015;112(4):1220-1225. doi:10.1073/pnas.1412996112","short":"M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.","ieee":"M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells,” PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.","mla":"Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112, no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112."},"title":"Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells","publist_id":"5552","author":[{"first_name":"Michael","last_name":"Strüber","full_name":"Strüber, Michael"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"}],"external_id":{"pmid":["25583495"]},"pmid":1,"oa_version":"Published Version","abstract":[{"text":"GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. ","lang":"eng"}],"month":"01","intvolume":" 112","scopus_import":1,"file":[{"date_created":"2019-01-17T07:52:40Z","file_name":"2015_PNAS_Strueber.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:07Z","file_size":1280860,"file_id":"5838","checksum":"6703309a1f58493cf5a704211fb6ebed","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":112,"ec_funded":1,"_id":"1614","status":"public","type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:52:01Z","file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"PeJo"}]},{"intvolume":" 24","month":"09","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/"}],"scopus_import":1,"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue."}],"volume":24,"issue":"9","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"1611","department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T06:52:00Z","oa":1,"quality_controlled":"1","publisher":"Wiley","date_created":"2018-12-11T11:53:01Z","date_published":"2015-09-01T00:00:00Z","doi":"10.1002/pro.2721","page":"1412 - 1422","publication":"Protein Science","day":"01","year":"2015","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"title":"Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction","external_id":{"pmid":["26061224"]},"author":[{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"first_name":"Michel","full_name":"Herde, Michel","last_name":"Herde"},{"first_name":"Ben","last_name":"Clifton","full_name":"Clifton, Ben"},{"first_name":"Johanna","last_name":"Radziejewski","full_name":"Radziejewski, Johanna"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"publist_id":"5555","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no. 9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721.","apa":"Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak, H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721","ama":"Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 2015;24(9):1412-1422. doi:10.1002/pro.2721","short":"J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak, C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.","ieee":"J. Whitfield et al., “Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction,” Protein Science, vol. 24, no. 9. Wiley, pp. 1412–1422, 2015.","chicago":"Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski, Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721.","ista":"Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422."}},{"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:07Z","date_updated":"2021-01-12T06:52:05Z","ddc":["000"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"466","_id":"1624","volume":5,"ec_funded":1,"publication_status":"published","file":[{"file_name":"IST-2016-466-v1+1_srep17147.pdf","date_created":"2018-12-12T10:12:29Z","creator":"system","file_size":1021931,"date_updated":"2020-07-14T12:45:07Z","checksum":"38e06d8310d2087cae5f6d4d4bfe082b","file_id":"4947","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"11","intvolume":" 5","abstract":[{"text":"Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an extremely strong amplifier of cooperation in a one dimensional spatial model. For the shift update rule, an individual is chosen for reproduction proportional to fecundity; the offspring is placed next to the parent; a random individual dies. Subsequently, the population is rearranged (shifted) until all individual cells are again evenly spaced out. For large population size and a one dimensional population structure, the shift update rule favors cooperation for any benefit-to-cost ratio greater than one. But every attempt to generalize shift updating to higher dimensions while maintaining its strong effect has failed. The reason is that in two dimensions the clusters are fragmented by the movements caused by rearranging the cells. Here we introduce the natural phenomenon of a repulsive force between cells of different types. After a birth and death event, the cells are being rearranged minimizing the overall energy expenditure. If the repulsive force is sufficiently high, shift becomes a strong promoter of cooperation in two dimensions.","lang":"eng"}],"oa_version":"Published Version","publist_id":"5536","author":[{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Adlam","full_name":"Adlam, Ben","first_name":"Ben"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"title":"Cellular cooperation with shift updating and repulsion","citation":{"mla":"Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports, vol. 5, 17147, Nature Publishing Group, 2015, doi:10.1038/srep17147.","ama":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift updating and repulsion. Scientific Reports. 2015;5. doi:10.1038/srep17147","apa":"Pavlogiannis, A., Chatterjee, K., Adlam, B., & Nowak, M. (2015). Cellular cooperation with shift updating and repulsion. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep17147","short":"A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5 (2015).","ieee":"A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation with shift updating and repulsion,” Scientific Reports, vol. 5. Nature Publishing Group, 2015.","chicago":"Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep17147.","ista":"Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation with shift updating and repulsion. Scientific Reports. 5, 17147."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"article_number":"17147","doi":"10.1038/srep17147","date_published":"2015-11-25T00:00:00Z","date_created":"2018-12-11T11:53:06Z","has_accepted_license":"1","year":"2015","day":"25","publication":"Scientific Reports","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"acknowledgement":"The research was supported by the Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton foundation is gratefully acknowledged."},{"department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:45:07Z","ddc":["570"],"date_updated":"2021-01-12T06:52:04Z","status":"public","pubrep_id":"467","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1623","issue":"1","volume":8,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"172b0b6f4eb2e5c22b7cec1d57dc0107","file_id":"4796","creator":"system","date_updated":"2020-07-14T12:45:07Z","file_size":2914089,"date_created":"2018-12-12T10:10:11Z","file_name":"IST-2016-467-v1+1_s13068-015-0380-2.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"11","intvolume":" 8","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Background\r\nPhotosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.\r\n","lang":"eng"}],"title":"Single-cell screening of photosynthetic growth and lactate production by cyanobacteria","author":[{"last_name":"Hammar","full_name":"Hammar, Petter","first_name":"Petter"},{"full_name":"Angermayr, Andreas","orcid":"0000-0001-8619-2223","last_name":"Angermayr","first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Staffan","last_name":"Sjostrom","full_name":"Sjostrom, Staffan"},{"full_name":"Van Der Meer, Josefin","last_name":"Van Der Meer","first_name":"Josefin"},{"last_name":"Hellingwerf","full_name":"Hellingwerf, Klaas","first_name":"Klaas"},{"first_name":"Elton","full_name":"Hudson, Elton","last_name":"Hudson"},{"full_name":"Joensson, Hakaan","last_name":"Joensson","first_name":"Hakaan"}],"publist_id":"5537","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer, Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels. BioMed Central, 2015. https://doi.org/10.1186/s13068-015-0380-2.","ista":"Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E, Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 8(1), 193.","mla":"Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels, vol. 8, no. 1, 193, BioMed Central, 2015, doi:10.1186/s13068-015-0380-2.","ieee":"P. Hammar et al., “Single-cell screening of photosynthetic growth and lactate production by cyanobacteria,” Biotechnology for Biofuels, vol. 8, no. 1. BioMed Central, 2015.","short":"P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E. Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015).","ama":"Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 2015;8(1). doi:10.1186/s13068-015-0380-2","apa":"Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K., Hudson, E., & Joensson, H. (2015). Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. BioMed Central. https://doi.org/10.1186/s13068-015-0380-2"},"article_number":"193","date_published":"2015-11-25T00:00:00Z","doi":"10.1186/s13068-015-0380-2","date_created":"2018-12-11T11:53:05Z","day":"25","publication":"Biotechnology for Biofuels","has_accepted_license":"1","year":"2015","publisher":"BioMed Central","quality_controlled":"1","oa":1}]