[{"_id":"6877","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-27T23:30:40Z","department":[{"_id":"MiSi"}],"pmid":1,"oa_version":"None","scopus_import":"1","intvolume":" 179","month":"09","publication_status":"published","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"language":[{"iso":"eng"}],"volume":179,"issue":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"6891","status":"public"}]},"citation":{"mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047.","apa":"Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047","ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell. 2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047.","ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000486618500011"],"pmid":["31539498"]},"article_processing_charge":"No","author":[{"full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","last_name":"Kopf","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"title":"The neural crest pitches in to remove apoptotic debris","publisher":"Elsevier","quality_controlled":"1","year":"2019","isi":1,"publication":"Cell","day":"19","page":"51-53","date_created":"2019-09-15T22:00:46Z","date_published":"2019-09-19T00:00:00Z","doi":"10.1016/j.cell.2019.08.047"},{"title":"Memo1 tiles the radial glial cell grid","article_processing_charge":"No","external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"author":[{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021","apa":"Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021."},"date_created":"2019-08-25T22:00:50Z","date_published":"2019-09-04T00:00:00Z","doi":"10.1016/j.neuron.2019.08.021","page":"750-752","publication":"Neuron","day":"04","year":"2019","isi":1,"oa":1,"quality_controlled":"1","publisher":"Elsevier","department":[{"_id":"SiHi"}],"date_updated":"2024-03-27T23:30:41Z","status":"public","article_type":"letter_note","type":"journal_article","_id":"6830","issue":"5","related_material":{"record":[{"status":"public","id":"7902","relation":"part_of_dissertation"}]},"volume":103,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"intvolume":" 103","month":"09","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.021","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","pmid":1},{"author":[{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"Yes","external_id":{"isi":["000477041100221"],"pmid":["31284661"]},"title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","citation":{"mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337","ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337.","ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_number":"3337","date_published":"2019-07-07T00:00:00Z","doi":"10.3390/ijms20133337","date_created":"2019-07-11T12:00:32Z","isi":1,"has_accepted_license":"1","year":"2019","day":"07","publication":"International Journal of Molecular Sciences","quality_controlled":"1","publisher":"MDPI","oa":1,"file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"JiFr"}],"date_updated":"2024-03-27T23:30:43Z","ddc":["580"],"article_type":"original","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":"6627","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"volume":20,"issue":"13","ec_funded":1,"publication_identifier":{"eissn":["1422-0067"]},"publication_status":"published","file":[{"file_name":"2019_JournalMolecularScience_Adamowski.pdf","date_created":"2019-07-17T06:17:15Z","creator":"dernst","file_size":3330291,"date_updated":"2020-07-14T12:47:34Z","checksum":"dd9d1cbb933a72ceb666c9667890ac51","file_id":"6645","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 20","abstract":[{"text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation.","lang":"eng"}],"oa_version":"Published Version","pmid":1},{"project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"157","external_id":{"isi":["000498397300007"]},"article_processing_charge":"No","author":[{"last_name":"Hafner","full_name":"Hafner, Christian","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schumacher, Christian","last_name":"Schumacher","first_name":"Christian"},{"last_name":"Knoop","full_name":"Knoop, Espen","first_name":"Espen"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bächer","full_name":"Bächer, Moritz","first_name":"Moritz"}],"title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","citation":{"chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576.","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"ACM","date_created":"2019-11-26T14:22:09Z","date_published":"2019-11-06T00:00:00Z","doi":"10.1145/3355089.3356576","year":"2019","isi":1,"has_accepted_license":"1","publication":"ACM Transactions on Graphics","day":"06","type":"journal_article","article_type":"original","status":"public","_id":"7117","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:47:49Z","date_updated":"2024-03-27T23:30:46Z","ddc":["000"],"scopus_import":"1","intvolume":" 38","month":"11","abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"related_material":{"record":[{"status":"public","id":"12897","relation":"dissertation_contains"}]},"volume":38,"issue":"6","publication_status":"published","publication_identifier":{"issn":["0730-0301"]},"language":[{"iso":"eng"}],"file":[{"file_name":"xcad_sup_mat_siga19.pdf","title":"X-CAD Supplemental Material","date_created":"2019-11-26T14:24:26Z","file_size":1673176,"date_updated":"2020-07-14T12:47:49Z","creator":"bbickel","checksum":"56a2fb019adcb556d2b022f5e5acb68c","file_id":"7119","content_type":"application/pdf","relation":"supplementary_material","access_level":"open_access"},{"file_name":"XCAD_authors_version.pdf","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","date_created":"2019-11-26T14:24:27Z","file_size":14563618,"date_updated":"2020-07-14T12:47:49Z","creator":"bbickel","checksum":"5f29d76aceb5102e766cbab9b17d776e","file_id":"7120","content_type":"application/pdf","description":"This is the author's version of the work.","relation":"main_file","access_level":"open_access"},{"file_name":"XCAD_video.mp4","date_created":"2019-11-26T14:27:37Z","creator":"bbickel","file_size":259979129,"date_updated":"2020-07-14T12:47:49Z","checksum":"0d31e123286cbec9e28b2001c2bb0d55","file_id":"7121","relation":"main_file","access_level":"open_access","content_type":"video/mp4"}]},{"status":"public","type":"journal_article","_id":"6189","department":[{"_id":"BjHo"}],"date_updated":"2024-03-27T23:30:47Z","intvolume":" 122","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1809.06358","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"9728","status":"public"}]},"issue":"11","volume":122,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"article_number":"114502","title":"Transition to turbulence in particle laden flows","article_processing_charge":"No","external_id":{"isi":["000461922000006"],"arxiv":["1809.06358"]},"author":[{"full_name":"Agrawal, Nishchal","last_name":"Agrawal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","first_name":"Nishchal"},{"first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H","last_name":"Choueiri"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502.","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019)."},"oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_created":"2019-03-31T21:59:12Z","doi":"10.1103/PhysRevLett.122.114502","date_published":"2019-03-22T00:00:00Z","publication":"Physical Review Letters","day":"22","year":"2019","isi":1},{"status":"public","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"type":"dissertation","_id":"6371","department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:13Z","ddc":["576","579"],"supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"date_updated":"2024-02-21T13:45:52Z","month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n","lang":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"67"},{"id":"5585","status":"public","relation":"popular_science"}]},"file":[{"file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","date_created":"2019-05-03T11:54:52Z","creator":"cigler","file_size":12597663,"date_updated":"2021-02-11T11:17:13Z","embargo":"2020-05-02","file_id":"6373","checksum":"c0085d47c58c9cbcab1b0a783480f6da","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"6374","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","file_size":34644426,"date_updated":"2020-07-14T12:47:28Z","creator":"cigler","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","date_created":"2019-05-03T11:54:54Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","author":[{"id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","full_name":"Igler, Claudia","last_name":"Igler"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371."},"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2019-05-03T00:00:00Z","doi":"10.15479/AT:ISTA:6371","date_created":"2019-05-03T11:55:51Z","page":"152","day":"03","has_accepted_license":"1","year":"2019"},{"volume":2018,"issue":"3","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10289","checksum":"b816b848f046c48a8357700d9305dce5","creator":"cchlebak","file_size":955755,"date_updated":"2021-11-15T10:27:29Z","file_name":"2018_IACR_Allini.pdf","date_created":"2021-11-15T10:27:29Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2569-2925"]},"publication_status":"published","month":"01","intvolume":" 2018","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied.","lang":"eng"}],"department":[{"_id":"KrPi"}],"file_date_updated":"2021-11-15T10:27:29Z","ddc":["000"],"date_updated":"2021-11-15T10:48:49Z","status":"public","article_type":"original","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":"10286","doi":"10.13154/tches.v2018.i3.214-242","date_published":"2018-01-01T00:00:00Z","date_created":"2021-11-14T23:01:25Z","page":"214-242","day":"01","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","has_accepted_license":"1","year":"2018","quality_controlled":"1","publisher":"International Association for Cryptologic Research","oa":1,"title":"Evaluation and monitoring of free running oscillators serving as source of randomness","author":[{"first_name":"Elie Noumon","last_name":"Allini","full_name":"Allini, Elie Noumon"},{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","full_name":"Skórski, Maciej","last_name":"Skórski"},{"first_name":"Oto","last_name":"Petura","full_name":"Petura, Oto"},{"first_name":"Florent","last_name":"Bernard","full_name":"Bernard, Florent"},{"full_name":"Laban, Marek","last_name":"Laban","first_name":"Marek"},{"first_name":"Viktor","last_name":"Fischer","full_name":"Fischer, Viktor"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242."}},{"project":[{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Dvořák, Wolfgang","last_name":"Dvořák","first_name":"Wolfgang"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"last_name":"Svozil","full_name":"Svozil, Alexander","first_name":"Alexander"}],"external_id":{"arxiv":["1909.04983"]},"article_processing_charge":"No","title":"Quasipolynomial set-based symbolic algorithms for parity games","citation":{"apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k.","ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","quality_controlled":"1","publisher":"EasyChair","oa":1,"acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","page":"233-253","doi":"10.29007/5z5k","date_published":"2018-10-23T00:00:00Z","date_created":"2022-03-18T12:46:32Z","has_accepted_license":"1","year":"2018","day":"23","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","type":"conference","conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","start_date":"2018-11-17","end_date":"2018-11-21","location":"Awassa, Ethiopia"},"status":"public","_id":"10883","file_date_updated":"2022-05-17T07:51:08Z","department":[{"_id":"KrCh"}],"date_updated":"2022-07-29T09:24:31Z","ddc":["000"],"scopus_import":"1","alternative_title":["EPiC Series in Computing"],"month":"10","intvolume":" 57","abstract":[{"text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.","lang":"eng"}],"oa_version":"Published Version","volume":57,"ec_funded":1,"publication_identifier":{"issn":["2398-7340"]},"publication_status":"published","file":[{"creator":"dernst","file_size":720893,"date_updated":"2022-05-17T07:51:08Z","file_name":"2018_EPiCs_Chatterjee.pdf","date_created":"2022-05-17T07:51:08Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"11392","checksum":"1229aa8640bd6db610c85decf2265480"}],"language":[{"iso":"eng"}]},{"oa_version":"Preprint","abstract":[{"text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm.","lang":"eng"}],"month":"10","intvolume":" 270","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1806.10843","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":270,"ec_funded":1,"_id":"11","status":"public","type":"conference","conference":{"name":"MaLiQS: Macroscopic Limits of Quantum Systems","start_date":"2017-03-30","location":"Munich, Germany","end_date":"2017-04-01"},"date_updated":"2021-01-12T06:48:16Z","department":[{"_id":"RoSe"}],"quality_controlled":"1","publisher":"Springer","oa":1,"day":"27","year":"2018","doi":"10.1007/978-3-030-01602-9_9","date_published":"2018-10-27T00:00:00Z","date_created":"2018-12-11T11:44:08Z","page":"185 - 214","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214."},"title":"Mean-field limits of particles in interaction with quantised radiation fields","author":[{"orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","last_name":"Leopold","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"}],"publist_id":"8045","external_id":{"arxiv":["1806.10843"]}},{"abstract":[{"lang":"eng","text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus."}],"oa_version":"Published Version","scopus_import":1,"month":"06","intvolume":" 31","publication_status":"published","file":[{"file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","date_created":"2018-12-12T10:17:13Z","creator":"system","file_size":671125,"date_updated":"2020-07-14T12:44:39Z","checksum":"47686d58ec21c164540f1a980ff2163f","file_id":"5266","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"2","volume":31,"_id":"1215","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":"712","date_updated":"2021-01-12T06:49:09Z","ddc":["519"],"department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:44:39Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA.","publisher":"Springer","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Journal of Theoretical Probability","page":"789-826","date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s10959-016-0724-2","date_created":"2018-12-11T11:50:45Z","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"citation":{"mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2.","ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” Journal of Theoretical Probability, vol. 31, no. 2. Springer, pp. 789–826, 2018.","short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826.","ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826. doi:10.1007/s10959-016-0724-2","apa":"Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. Springer. https://doi.org/10.1007/s10959-016-0724-2","chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2.","ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6119","author":[{"first_name":"Franco","last_name":"Flandoli","full_name":"Flandoli, Franco"},{"first_name":"Francesco","last_name":"Russo","full_name":"Russo, Francesco"},{"first_name":"Giovanni A","id":"47491882-F248-11E8-B48F-1D18A9856A87","full_name":"Zanco, Giovanni A","last_name":"Zanco"}],"article_processing_charge":"Yes (via OA deal)","title":"Infinite-dimensional calculus under weak spatial regularity of the processes"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"day":"01","has_accepted_license":"1","year":"2018","date_published":"2018-01-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.39","date_created":"2018-12-11T11:45:04Z","article_number":"39","project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39.","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","apa":"Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.39","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39","mla":"Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39."},"title":"Hanani-Tutte for approximating maps of graphs","publist_id":"7735","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"}],"oa_version":"Published Version","abstract":[{"text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint "pipes" corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.","lang":"eng"}],"month":"01","intvolume":" 99","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"file":[{"date_updated":"2020-07-14T12:45:19Z","file_size":718857,"creator":"dernst","date_created":"2018-12-17T12:33:52Z","file_name":"2018_LIPIcs_Fulek.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","file_id":"5701"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-95977-066-8"]},"publication_status":"published","volume":99,"_id":"185","status":"public","type":"conference","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":{"start_date":"2018-06-11","end_date":"2018-06-14","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"ddc":["510"],"date_updated":"2021-01-12T06:53:36Z","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"UlWa"}]},{"project":[{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"citation":{"chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","mla":"Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35.","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Virk","full_name":"Virk, Ziga","first_name":"Ziga"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Hubert"}],"publist_id":"7733","title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","has_accepted_license":"1","day":"11","page":"35:1 - 35:13","date_created":"2018-12-11T11:45:05Z","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.35","_id":"188","conference":{"location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11","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)"},"type":"conference","status":"public","date_updated":"2021-01-12T06:53:48Z","ddc":["000"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:20Z","abstract":[{"text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"intvolume":" 99","month":"06","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5724","checksum":"7509403803b3ac1aee94bbc2ad293d21","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_LIPIcs_Edelsbrunner.pdf","date_created":"2018-12-17T16:31:31Z","file_size":489080,"date_updated":"2020-07-14T12:45:20Z","creator":"dernst"}],"volume":99},{"article_number":"e00596","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596.","chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018.","ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596","apa":"De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596","mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Andrea","last_name":"De Martino","full_name":"De Martino, Andrea"},{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"}],"title":"An introduction to the maximum entropy approach and its application to inference problems in biology","oa":1,"quality_controlled":"1","publisher":"Elsevier","year":"2018","has_accepted_license":"1","publication":"Heliyon","day":"01","date_created":"2018-12-11T11:45:44Z","doi":"10.1016/j.heliyon.2018.e00596","date_published":"2018-04-01T00:00:00Z","_id":"306","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","status":"public","date_updated":"2021-01-12T07:40:46Z","ddc":["530"],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:59Z","abstract":[{"lang":"eng","text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 4","month":"04","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-06T07:36:24Z","file_name":"2018_Heliyon_DeMartino.pdf","date_updated":"2020-07-14T12:45:59Z","file_size":994490,"creator":"dernst","file_id":"5929","checksum":"67010cf5e3b3e0637c659371714a715a","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"ec_funded":1,"issue":"4","volume":4},{"citation":{"mla":"Clarke, Edmund M., et al. Handbook of Model Checking. 1st ed., Springer Nature, 2018, doi:10.1007/978-3-319-10575-8.","ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model Checking, 1st ed. Cham: Springer Nature, 2018.","short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. Handbook of Model Checking. 1st ed. Cham: Springer Nature; 2018. doi:10.1007/978-3-319-10575-8","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., & Bloem, R. (2018). Handbook of Model Checking (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-10575-8","chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. Handbook of Model Checking. 1st ed. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-10575-8.","ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p."},"date_updated":"2021-12-21T10:49:36Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"last_name":"Clarke","full_name":"Clarke, Edmund M.","first_name":"Edmund M."},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"},{"full_name":"Bloem, Roderick","last_name":"Bloem","first_name":"Roderick"}],"publist_id":"3340","title":"Handbook of Model Checking","department":[{"_id":"ToHe"}],"_id":"3300","type":"book","status":"public","publication_status":"published","year":"2018","publication_identifier":{"eisbn":["978-3-319-10575-8"],"isbn":["978-3-319-10574-1"]},"language":[{"iso":"eng"}],"day":"08","page":"XLVIII, 1212","date_created":"2018-12-11T12:02:32Z","date_published":"2018-06-08T00:00:00Z","doi":"10.1007/978-3-319-10575-8","abstract":[{"lang":"eng","text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools."}],"oa_version":"None","edition":"1","scopus_import":"1","publisher":"Springer Nature","quality_controlled":"1","month":"06","place":"Cham"},{"series_title":"MIMB","_id":"37","status":"public","type":"book_chapter","ddc":["570"],"date_updated":"2021-01-12T07:49:03Z","department":[{"_id":"AnKi"}],"file_date_updated":"2020-10-13T14:20:37Z","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube."}],"month":"10","intvolume":" 1863","scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"file":[{"file_name":"2018_MIMB_Zagorski.pdf","date_created":"2020-10-13T14:20:37Z","creator":"dernst","file_size":4906815,"date_updated":"2020-10-13T14:20:37Z","success":1,"file_id":"8656","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-4939-8771-9"]},"publication_status":"published","volume":1863,"ec_funded":1,"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4.","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63.","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4."},"title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","author":[{"last_name":"Zagórski","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"}],"publist_id":"8018","article_processing_charge":"No","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"16","publication":"Morphogen Gradients ","has_accepted_license":"1","year":"2018","doi":"10.1007/978-1-4939-8772-6_4","date_published":"2018-10-16T00:00:00Z","date_created":"2018-12-11T11:44:17Z","page":"47 - 63"},{"oa_version":"None","abstract":[{"text":"The hanging-drop network (HDN) is a technology platform based on a completely open microfluidic network at the bottom of an inverted, surface-patterned substrate. The platform is predominantly used for the formation, culturing, and interaction of self-assembled spherical microtissues (spheroids) under precisely controlled flow conditions. Here, we describe design, fabrication, and operation of microfluidic hanging-drop networks.","lang":"eng"}],"intvolume":" 1771","month":"01","scopus_import":1,"alternative_title":["MIMB"],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":1771,"_id":"305","status":"public","type":"journal_article","date_updated":"2021-01-12T07:40:42Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"acknowledgement":"This work was financially supported by FP7 of the EU through the project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS” (contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss National Science Foundation for Olivier Frey. The research leading to these results also 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]. We would like to thank Alexander Stettler, ETH Zurich for his expertise and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE, ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members of the Guet and Tkačik groups, IST Austria, for valuable comments and support.","publisher":"Springer","quality_controlled":"1","publication":"Methods in Molecular Biology","day":"01","year":"2018","date_created":"2018-12-11T11:45:43Z","date_published":"2018-01-01T00:00:00Z","doi":"10.1007/978-1-4939-7792-5_15","page":"183 - 202","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771. Springer, pp. 183–202, 2018.","short":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.","apa":"Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-4939-7792-5_15","ama":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15","mla":"Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp. 183–202, doi:10.1007/978-1-4939-7792-5_15.","ista":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.","chicago":"Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15."},"title":"Fabrication and operation of microfluidic hanging drop networks","publist_id":"7574","author":[{"first_name":"Patrick","last_name":"Misun","full_name":"Misun, Patrick"},{"first_name":"Axel","full_name":"Birchler, Axel","last_name":"Birchler"},{"last_name":"Lang","full_name":"Lang, Moritz","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hierlemann, Andreas","last_name":"Hierlemann","first_name":"Andreas"},{"first_name":"Olivier","last_name":"Frey","full_name":"Frey, Olivier"}]},{"article_number":"34","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122.","ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","mla":"Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM, 2018, doi:10.1145/3158122.","apa":"Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/3158122","ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:10.1145/3158122","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Sheshansh","full_name":"Agrawal, Sheshansh","last_name":"Agrawal"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Novotny, Petr","last_name":"Novotny","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7540","external_id":{"arxiv":["1709.04037"]},"title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","quality_controlled":"1","publisher":"ACM","oa":1,"year":"2018","day":"01","date_published":"2018-01-01T00:00:00Z","doi":"10.1145/3158122","date_created":"2018-12-11T11:45:50Z","_id":"325","type":"conference","conference":{"start_date":"2018-01-07","location":"Los Angeles, CA, USA","end_date":"2018-01-13","name":"POPL: Principles of Programming Languages"},"status":"public","date_updated":"2021-01-12T07:42:07Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1709.04037","open_access":"1"}],"month":"01","intvolume":" 2","publication_status":"published","language":[{"iso":"eng"}],"issue":"POPL","volume":2},{"volume":1761,"publication_status":"published","publication_identifier":{"issn":["1064-3745"]},"language":[{"iso":"eng"}],"alternative_title":["MIMB"],"scopus_import":"1","intvolume":" 1761","month":"03","abstract":[{"lang":"eng","text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings."}],"oa_version":"None","pmid":1,"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T07:54:21Z","type":"book_chapter","status":"public","_id":"408","page":"95 - 102","date_created":"2018-12-11T11:46:18Z","date_published":"2018-03-01T00:00:00Z","doi":"10.1007/978-1-4939-7747-5_7","year":"2018","publication":"Root Development ","day":"01","publisher":"Springer Nature","quality_controlled":"1","article_processing_charge":"No","external_id":{"pmid":["29525951"]},"publist_id":"7421","author":[{"first_name":"Hoang","last_name":"Trinh","full_name":"Trinh, Hoang"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Geelen","full_name":"Geelen, Danny","first_name":"Danny"}],"title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","citation":{"chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7.","ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.","mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7.","apa":"Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102.","short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:54:34Z","citation":{"mla":"Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10.","ieee":"M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.","short":"M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.","apa":"Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10","ama":"Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10","chicago":"Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10.","ista":"Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143."},"title":"Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia","editor":[{"last_name":"Ristova","full_name":"Ristova, Daniela","first_name":"Daniela"},{"last_name":"Barbez","full_name":"Barbez, Elke","first_name":"Elke"}],"department":[{"_id":"JiFr"}],"publist_id":"7418","author":[{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"}],"_id":"411","series_title":"MIMB","status":"public","type":"book_chapter","language":[{"iso":"eng"}],"publication":"Root Development. Methods and Protocols","day":"11","publication_status":"published","year":"2018","date_created":"2018-12-11T11:46:20Z","doi":"10.1007/978-1-4939-7747-5_10","volume":1761,"date_published":"2018-03-11T00:00:00Z","page":"131 - 143","oa_version":"None","abstract":[{"lang":"eng","text":"Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins."}],"intvolume":" 1761","month":"03","quality_controlled":"1","publisher":"Springer","alternative_title":["Methods in Molecular Biology"],"scopus_import":1},{"date_created":"2018-12-11T11:46:34Z","volume":10,"doi":"10.1126/scitranslmed.aar7514","issue":"423","date_published":"2018-01-10T00:00:00Z","publication_status":"published","year":"2018","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","day":"10","publisher":"American Association for the Advancement of Science","scopus_import":1,"quality_controlled":"1","intvolume":" 10","month":"01","abstract":[{"lang":"eng","text":"Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. "}],"oa_version":"None","publist_id":"7365","author":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"}],"title":"Zika-associated microcephaly: Reduce the stress and race for the treatment","department":[{"_id":"GaNo"}],"citation":{"mla":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine, vol. 10, no. 423, eaar7514, American Association for the Advancement of Science, 2018, doi:10.1126/scitranslmed.aar7514.","short":"G. Novarino, Science Translational Medicine 10 (2018).","ieee":"G. Novarino, “Zika-associated microcephaly: Reduce the stress and race for the treatment,” Science Translational Medicine, vol. 10, no. 423. American Association for the Advancement of Science, 2018.","ama":"Novarino G. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 2018;10(423). doi:10.1126/scitranslmed.aar7514","apa":"Novarino, G. (2018). Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aar7514","chicago":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/scitranslmed.aar7514.","ista":"Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 10(423), eaar7514."},"date_updated":"2021-01-12T07:59:42Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"456","article_number":"eaar7514"}]