[{"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_created":"2019-04-30T11:56:10Z","date_published":"2019-04-30T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"PeJo"}],"page":"140","related_material":{"record":[{"id":"21","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-15T12:03:48Z","year":"2019","alternative_title":["ISTA Thesis"],"oa":1,"article_processing_charge":"No","has_accepted_license":"1","file":[{"file_id":"6389","date_created":"2019-05-07T16:00:39Z","embargo":"2020-05-09","file_name":"Espinozathesis_all2.pdf","file_size":13966891,"creator":"cespinoza","relation":"main_file","date_updated":"2021-02-11T11:17:15Z","access_level":"open_access","content_type":"application/pdf","checksum":"77c6c05cfe8b58c8abcf1b854375d084"},{"date_created":"2019-05-07T16:00:48Z","file_id":"6390","embargo_to":"open_access","relation":"source_file","file_size":11159900,"creator":"cespinoza","file_name":"Espinoza_Thesis.docx","date_updated":"2020-07-14T12:47:28Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"f6aa819f127691a2b0fc21c76eb09746","access_level":"closed"}],"degree_awarded":"PhD","oa_version":"Published Version","file_date_updated":"2021-02-11T11:17:15Z","ddc":["570"],"month":"04","citation":{"apa":"Espinoza Martinez, C. (2019). <i>Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>","ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019.","ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","mla":"Espinoza Martinez, Claudia. <i>Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>.","chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>."},"day":"30","status":"public","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-000-8"]},"doi":"10.15479/AT:ISTA:6363","abstract":[{"lang":"eng","text":"Distinguishing  between  similar  experiences  is  achieved  by  the  brain  in  a  process called  pattern  separation.  In  the  hippocampus,  pattern  separation  reduces  the interference of memories and increases the storage capacity by decorrelating similar inputs  patterns  of  neuronal  activity  into  non-overlapping output  firing  patterns. Winners-take-all  (WTA)  mechanism  is  a  theoretical  model  for  pattern  separation  in which  a  \"winner\"  cell  suppresses  the  activity  of  the  neighboring  neurons  through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of  feedback  inhibition  in  which  a  GC  inhibits  other  GCs  but  not  itself  through  the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron  connectivity  was  more  spatially  confined  but  less  abundant  than  PV+interneurons–GC  connectivity,  leading  to  an  asymmetrical  distribution  of  excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the  primary  mechanism.  This  process  relied  on  lateral  inhibition,  fast-signaling properties  of  PV+interneurons  and  the  asymmetrical  distribution  of  excitatory  and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in  vivoleads  to  acute  deficits  in  discrimination  between  similar  environments, suggesting  that  PV+interneuron  networks  are  necessary  for  behavioral  relevant computations.  Our   results   demonstrate   that   PV+interneurons  possess  unique connectivity  and  fast  signaling  properties  that confer  to  the  dentate  gyrus  network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n"}],"_id":"6363","supervisor":[{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","author":[{"orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia ","full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez"}]},{"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"publication_status":"published","status":"public","title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","author":[{"last_name":"Bellstaedt","full_name":"Bellstaedt, Julia","first_name":"Julia"},{"first_name":"Jana","full_name":"Trenner, Jana","last_name":"Trenner"},{"last_name":"Lippmann","full_name":"Lippmann, Rebecca","first_name":"Rebecca"},{"first_name":"Yvonne","full_name":"Poeschl, Yvonne","last_name":"Poeschl"},{"first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"Marcel","full_name":"Quint, Marcel","last_name":"Quint"},{"full_name":"Delker, Carolin","last_name":"Delker","first_name":"Carolin"}],"_id":"6366","abstract":[{"lang":"eng","text":"Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl."}],"issue":"2","doi":"10.1104/pp.18.01377","volume":180,"article_processing_charge":"No","citation":{"ama":"Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. 2019;180(2):757-766. doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>","ista":"Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766.","short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","ieee":"J. Bellstaedt <i>et al.</i>, “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” <i>Plant Physiology</i>, vol. 180, no. 2. ASPB, pp. 757–766, 2019.","apa":"Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>","mla":"Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>.","chicago":"Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>."},"day":"01","month":"06","pmid":1,"oa_version":"Published Version","publication":"Plant Physiology","date_updated":"2023-09-05T12:25:19Z","page":"757-766","article_type":"original","oa":1,"year":"2019","publisher":"ASPB","intvolume":"       180","main_file_link":[{"url":"www.doi.org/10.1104/pp.18.01377","open_access":"1"}],"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"JiFr"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-06-01T00:00:00Z","external_id":{"isi":["000470086100019"],"pmid":["31000634"]},"date_created":"2019-04-30T15:24:22Z","scopus_import":"1"},{"date_updated":"2024-02-21T13:45:52Z","page":"152","related_material":{"record":[{"id":"67","status":"public","relation":"part_of_dissertation"},{"relation":"popular_science","status":"public","id":"5585"}]},"oa":1,"keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"alternative_title":["ISTA Thesis"],"year":"2019","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"CaGu"}],"date_created":"2019-05-03T11:55:51Z","date_published":"2019-05-03T00:00:00Z","project":[{"grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","status":"public","_id":"6371","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","supervisor":[{"orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"author":[{"last_name":"Igler","full_name":"Igler, Claudia","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:6371","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"}],"file":[{"date_created":"2019-05-03T11:54:52Z","file_id":"6373","date_updated":"2021-02-11T11:17:13Z","content_type":"application/pdf","checksum":"c0085d47c58c9cbcab1b0a783480f6da","access_level":"open_access","embargo":"2020-05-02","relation":"main_file","creator":"cigler","file_size":12597663,"file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf"},{"file_id":"6374","date_created":"2019-05-03T11:54:54Z","embargo_to":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","relation":"source_file","creator":"cigler","file_size":34644426,"date_updated":"2020-07-14T12:47:28Z","access_level":"closed","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","month":"05","file_date_updated":"2021-02-11T11:17:13Z","ddc":["576","579"],"citation":{"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.","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>","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.","apa":"Igler, C. (2019). <i>On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>","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. <i>On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>.","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. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>."},"day":"03","oa_version":"Published Version"},{"publication_status":"published","status":"public","publication_identifier":{"issn":["15524450"],"eissn":["15524469"]},"doi":"10.1038/s41589-019-0262-1","issue":"6","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acutely and reversibly perturb CME, the few chemical CME inhibitors that have been applied to plants are either ineffective or show undesirable side effects. Here, we identify the previously described endosidin9 (ES9) as an inhibitor of clathrin heavy chain (CHC) function in both Arabidopsis and human cells through affinity-based target isolation, in vitro binding studies and X-ray crystallography. Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the undesirable side effects of ES9 while retaining the ability to target CHC. ES9 and ES9-17 have expanded the chemical toolbox used to probe CHC function, and present chemical scaffolds for further design of more specific and potent CHC inhibitors across different systems."}],"_id":"6377","author":[{"full_name":"Dejonghe, Wim","last_name":"Dejonghe","first_name":"Wim"},{"first_name":"Isha","last_name":"Sharma","full_name":"Sharma, Isha"},{"last_name":"Denoo","full_name":"Denoo, Bram","first_name":"Bram"},{"first_name":"Steven","last_name":"De Munck","full_name":"De Munck, Steven"},{"first_name":"Qing","last_name":"Lu","full_name":"Lu, Qing"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"full_name":"Bulut, Haydar","last_name":"Bulut","first_name":"Haydar"},{"first_name":"Evelien","last_name":"Mylle","full_name":"Mylle, Evelien"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"first_name":"Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","full_name":"Vasileva, Mina K"},{"last_name":"Savatin","full_name":"Savatin, Daniel V.","first_name":"Daniel V."},{"first_name":"Wim","last_name":"Nerinckx","full_name":"Nerinckx, Wim"},{"first_name":"An","last_name":"Staes","full_name":"Staes, An"},{"first_name":"Andrzej","full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki"},{"first_name":"Dominique","last_name":"Audenaert","full_name":"Audenaert, Dominique"},{"first_name":"Klaas","last_name":"Yperman","full_name":"Yperman, Klaas"},{"first_name":"Annemieke","last_name":"Madder","full_name":"Madder, Annemieke"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Daniël","full_name":"Van Damme, Daniël","last_name":"Van Damme"},{"full_name":"Gevaert, Kris","last_name":"Gevaert","first_name":"Kris"},{"full_name":"Haucke, Volker","last_name":"Haucke","first_name":"Volker"},{"first_name":"Savvas N.","last_name":"Savvides","full_name":"Savvides, Savvas N."},{"full_name":"Winne, Johan","last_name":"Winne","first_name":"Johan"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"}],"title":"Disruption of endocytosis through chemical inhibition of clathrin heavy chain function","volume":15,"article_processing_charge":"No","oa_version":"None","month":"06","day":"01","citation":{"mla":"Dejonghe, Wim, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” <i>Nature Chemical Biology</i>, vol. 15, no. 6, Springer Nature, 2019, pp. 641–649, doi:<a href=\"https://doi.org/10.1038/s41589-019-0262-1\">10.1038/s41589-019-0262-1</a>.","chicago":"Dejonghe, Wim, Isha Sharma, Bram Denoo, Steven De Munck, Qing Lu, Kiril Mishev, Haydar Bulut, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” <i>Nature Chemical Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41589-019-0262-1\">https://doi.org/10.1038/s41589-019-0262-1</a>.","ieee":"W. Dejonghe <i>et al.</i>, “Disruption of endocytosis through chemical inhibition of clathrin heavy chain function,” <i>Nature Chemical Biology</i>, vol. 15, no. 6. Springer Nature, pp. 641–649, 2019.","apa":"Dejonghe, W., Sharma, I., Denoo, B., De Munck, S., Lu, Q., Mishev, K., … Russinova, E. (2019). Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. <i>Nature Chemical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41589-019-0262-1\">https://doi.org/10.1038/s41589-019-0262-1</a>","short":"W. Dejonghe, I. Sharma, B. Denoo, S. De Munck, Q. Lu, K. Mishev, H. Bulut, E. Mylle, R. De Rycke, M.K. Vasileva, D.V. Savatin, W. Nerinckx, A. Staes, A. Drozdzecki, D. Audenaert, K. Yperman, A. Madder, J. Friml, D. Van Damme, K. Gevaert, V. Haucke, S.N. Savvides, J. Winne, E. Russinova, Nature Chemical Biology 15 (2019) 641–649.","ista":"Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle E, De Rycke R, Vasileva MK, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN, Winne J, Russinova E. 2019. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. 15(6), 641–649.","ama":"Dejonghe W, Sharma I, Denoo B, et al. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. <i>Nature Chemical Biology</i>. 2019;15(6):641–649. doi:<a href=\"https://doi.org/10.1038/s41589-019-0262-1\">10.1038/s41589-019-0262-1</a>"},"article_type":"original","page":"641–649","related_material":{"record":[{"id":"7172","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-09-07T12:54:35Z","publication":"Nature Chemical Biology","year":"2019","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"intvolume":"        15","publisher":"Springer Nature","scopus_import":"1","date_created":"2019-05-05T21:59:11Z","date_published":"2019-06-01T00:00:00Z","external_id":{"isi":["000468195600018"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}]},{"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"publication_identifier":{"isbn":["9781450359337"]},"ec_funded":1,"publication_status":"published","status":"public","_id":"6378","title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584"},{"first_name":"Arash","full_name":"Pourdamghani, Arash","last_name":"Pourdamghani"}],"doi":"10.1145/3297280.3297319","abstract":[{"text":"In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin.","lang":"eng"}],"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"fbfbcd5a0c7a743862bfc3045539a614","date_updated":"2020-07-14T12:47:29Z","file_name":"2019_ACM_Chatterjee.pdf","relation":"main_file","file_size":1023934,"creator":"dernst","file_id":"6379","date_created":"2019-05-06T12:09:27Z"}],"volume":"Part F147772","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:29Z","ddc":["004"],"month":"04","pubrep_id":"1069","citation":{"ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. Proceedings of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing vol. Part F147772, 374–381.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In: <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>. Vol Part F147772. ACM; 2019:374-381. doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving,” in <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Limassol, Cyprus, 2019, vol. Part F147772, pp. 374–381.","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pourdamghani, A. (2019). Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i> (Vol. Part F147772, pp. 374–381). Limassol, Cyprus: ACM. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Part F147772:374–81. ACM, 2019. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>.","mla":"Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, vol. Part F147772, ACM, 2019, pp. 374–81, doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>."},"day":"01","oa_version":"Submitted Version","conference":{"location":"Limassol, Cyprus","start_date":"2019-04-08","end_date":"2019-04-12","name":"ACM Symposium on Applied Computing"},"date_updated":"2025-06-02T08:53:46Z","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","page":"374-381","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"oa":1,"year":"2019","publisher":"ACM","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"KrCh"}],"date_created":"2019-05-06T12:11:36Z","scopus_import":"1","external_id":{"isi":["000474685800049"]},"date_published":"2019-04-01T00:00:00Z"},{"ec_funded":1,"publication_status":"published","status":"public","project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"publication_identifier":{"issn":["2475-1421"]},"doi":"10.1145/3290366","abstract":[{"lang":"eng","text":"There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses. "}],"issue":"POPL","_id":"6380","title":"Efficient parameterized algorithms for data packing","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-1702-6584","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Okati","full_name":"Okati, Nastaran","first_name":"Nastaran"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"volume":3,"has_accepted_license":"1","file":[{"file_name":"2019_ACM_POPL_Chatterjee.pdf","file_size":1294962,"relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:47:29Z","access_level":"open_access","checksum":"c157752f96877b36685ad7063ada4524","content_type":"application/pdf","file_id":"6381","date_created":"2019-05-06T12:23:11Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","ddc":["004"],"file_date_updated":"2020-07-14T12:47:29Z","month":"01","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>.","mla":"Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL, 53, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>.","apa":"Chatterjee, K., Goharshady, A. K., Okati, N., &#38; Pavlogiannis, A. (2019). Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. ACM. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>","ieee":"K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient parameterized algorithms for data packing,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL. ACM, 2019.","short":"K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 3 (2019).","ama":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. 2019;3(POPL). doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>","ista":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 3(POPL), 53."},"pubrep_id":"1056","day":"01","article_number":"53","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-25T23:30:18Z","publication":"Proceedings of the ACM on Programming Languages","year":"2019","oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"ACM","intvolume":"         3","date_created":"2019-05-06T12:18:17Z","date_published":"2019-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}]},{"status":"public","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-001-5"],"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6392","abstract":[{"lang":"eng","text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes.  \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. "}],"_id":"6392","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","supervisor":[{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"author":[{"last_name":"Lukacisin","full_name":"Lukacisin, Martin","first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177"}],"has_accepted_license":"1","file":[{"file_name":"Thesis_Draft_v3.4Final.docx","file_size":43740796,"relation":"hidden","creator":"mlukacisin","access_level":"closed","checksum":"829bda074444857c7935171237bb7c0c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:47:29Z","embargo_to":"open_access","file_id":"6409","date_created":"2019-05-10T13:51:49Z"},{"file_name":"Thesis_Draft_v3.4FinalA.pdf","relation":"main_file","creator":"mlukacisin","file_size":35228388,"embargo":"2020-04-17","access_level":"open_access","content_type":"application/pdf","checksum":"56cb5e97f5f8fc41692401b53832d8e0","date_updated":"2021-02-11T11:17:16Z","file_id":"6410","date_created":"2019-05-10T14:13:42Z"}],"oa_version":"Published Version","month":"05","file_date_updated":"2021-02-11T11:17:16Z","ddc":["570"],"citation":{"mla":"Lukacisin, Martin. <i>Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory</i>. IST Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>.","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>.","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","apa":"Lukacisin, M. (2019). <i>Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>"},"day":"09","page":"103","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1029"}]},"date_updated":"2023-09-22T09:19:41Z","alternative_title":["IST Austria Thesis"],"year":"2019","oa":1,"language":[{"iso":"eng"}],"type":"dissertation","publisher":"IST Austria","date_created":"2019-05-09T19:53:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"date_published":"2019-05-09T00:00:00Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToBo"}]},{"oa":1,"year":"2019","date_updated":"2023-08-25T10:31:56Z","publication":"Nature Communications","article_number":"1931","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SaSi"}],"scopus_import":"1","date_created":"2019-05-13T07:58:35Z","date_published":"2019-04-29T00:00:00Z","external_id":{"isi":["000466118700002"]},"intvolume":"        10","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"_id":"6412","author":[{"first_name":"Hagar F.","full_name":"Moussa, Hagar F.","last_name":"Moussa"},{"first_name":"Daniel","full_name":"Bsteh, Daniel","last_name":"Bsteh"},{"first_name":"Ramesh","full_name":"Yelagandula, Ramesh","last_name":"Yelagandula"},{"full_name":"Pribitzer, Carina","last_name":"Pribitzer","first_name":"Carina"},{"first_name":"Karin","last_name":"Stecher","full_name":"Stecher, Karin"},{"first_name":"Katarina","id":"4D883232-F248-11E8-B48F-1D18A9856A87","last_name":"Bartalska","full_name":"Bartalska, Katarina"},{"first_name":"Luca","full_name":"Michetti, Luca","last_name":"Michetti"},{"first_name":"Jingkui","last_name":"Wang","full_name":"Wang, Jingkui"},{"full_name":"Zepeda-Martinez, Jorge A.","last_name":"Zepeda-Martinez","first_name":"Jorge A."},{"first_name":"Ulrich","full_name":"Elling, Ulrich","last_name":"Elling"},{"first_name":"Jacob I.","full_name":"Stuckey, Jacob I.","last_name":"Stuckey"},{"first_name":"Lindsey I.","full_name":"James, Lindsey I.","last_name":"James"},{"full_name":"Frye, Stephen V.","last_name":"Frye","first_name":"Stephen V."},{"last_name":"Bell","full_name":"Bell, Oliver","first_name":"Oliver"}],"title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","doi":"10.1038/s41467-019-09628-6","issue":"1","abstract":[{"lang":"eng","text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates."}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","status":"public","file_date_updated":"2020-07-14T12:47:29Z","month":"04","ddc":["570"],"day":"29","citation":{"chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>.","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>.","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. 2019;10(1). doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","ieee":"H. F. Moussa <i>et al.</i>, “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” <i>Nature Communications</i>, vol. 10, no. 1. Springer Nature, 2019.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"6448","date_created":"2019-05-14T08:45:51Z","file_name":"2019_NatureComm_Moussa.pdf","file_size":1223647,"relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:47:29Z","access_level":"open_access","content_type":"application/pdf","checksum":"6550a328335396c856db4cbdda7d2994"}],"article_processing_charge":"No","volume":10,"has_accepted_license":"1"},{"arxiv":1,"article_processing_charge":"No","volume":117,"month":"08","citation":{"chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>.","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>, vol. 117, Elsevier, 2019, pp. 14–24, doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>.","apa":"Song, B., Plana, C., Lopez Alonso, J. M., &#38; Avila, M. (2019). Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” <i>International Journal of Multiphase Flow</i>, vol. 117. Elsevier, pp. 14–24, 2019.","ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. 2019;117:14-24. doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24."},"day":"01","oa_version":"Preprint","publication_identifier":{"issn":["03019322"]},"publication_status":"published","status":"public","_id":"6413","title":"Phase-field simulation of core-annular pipe flow","author":[{"first_name":"Baofang","full_name":"Song, Baofang","last_name":"Song"},{"full_name":"Plana, Carlos","last_name":"Plana","first_name":"Carlos"},{"first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"}],"doi":"10.1016/j.ijmultiphaseflow.2019.04.027","abstract":[{"text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase.","lang":"eng"}],"publisher":"Elsevier","main_file_link":[{"url":"https://arxiv.org/abs/1902.07351","open_access":"1"}],"intvolume":"       117","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BjHo"}],"date_created":"2019-05-13T07:58:35Z","scopus_import":"1","external_id":{"isi":["000474496000002"],"arxiv":["1902.07351"]},"date_published":"2019-08-01T00:00:00Z","date_updated":"2023-08-25T10:19:55Z","publication":"International Journal of Multiphase Flow","page":"14-24","article_type":"original","oa":1,"year":"2019"},{"scopus_import":"1","oa_version":"None","date_created":"2019-05-13T07:58:36Z","date_published":"2019-06-01T00:00:00Z","external_id":{"isi":["000477666000012"]},"month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","department":[{"_id":"SyCr"}],"citation":{"apa":"Cremer, S. (2019). Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>","ieee":"S. Cremer, “Pathogens and disease defense of invasive ants,” <i>Current Opinion in Insect Science</i>, vol. 33. Elsevier, pp. 63–68, 2019.","ama":"Cremer S. Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. 2019;33:63-68. doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>","ista":"Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68.","short":"S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.","mla":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>, vol. 33, Elsevier, 2019, pp. 63–68, doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>.","chicago":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>."},"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":33,"isi":1,"intvolume":"        33","publisher":"Elsevier","doi":"10.1016/j.cois.2019.03.011","year":"2019","abstract":[{"text":"Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success.","lang":"eng"}],"_id":"6415","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"title":"Pathogens and disease defense of invasive ants","page":"63-68","status":"public","publication_status":"published","date_updated":"2023-08-25T10:31:31Z","publication":"Current Opinion in Insect Science","publication_identifier":{"issn":["22145745"],"eissn":["22145753"]}},{"intvolume":"        11","publisher":"Oxford University Press","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"BeVi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000476569800003"]},"date_published":"2019-04-01T00:00:00Z","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2019-05-13T07:58:38Z","publication":"Genome biology and evolution","date_updated":"2024-02-21T12:45:41Z","related_material":{"record":[{"status":"public","relation":"popular_science","id":"6060"}]},"page":"1033-1044","oa":1,"year":"2019","file":[{"file_id":"6446","date_created":"2019-05-14T08:29:38Z","access_level":"open_access","content_type":"application/pdf","checksum":"7d0ede297b6741f3dc89cd59017c7642","date_updated":"2020-07-14T12:47:29Z","file_name":"2019_GBE_Huylmans.pdf","file_size":1256303,"creator":"dernst","relation":"main_file"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":11,"day":"01","citation":{"apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>.","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>."},"ddc":["570"],"month":"04","file_date_updated":"2020-07-14T12:47:29Z","oa_version":"Published Version","publication_identifier":{"eissn":["1759-6653"]},"project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"publication_status":"published","status":"public","ec_funded":1,"author":[{"last_name":"Huylmans","full_name":"Huylmans, Ann K","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961"},{"orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A","last_name":"Toups"},{"full_name":"Macon, Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger","full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","_id":"6418","issue":"4","abstract":[{"text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.","lang":"eng"}],"doi":"10.1093/gbe/evz053"},{"_id":"6419","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","author":[{"last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X"},{"full_name":"Usmanova, Dinara R.","last_name":"Usmanova","first_name":"Dinara R."},{"full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva","first_name":"Ekaterina V."},{"last_name":"Espinar","full_name":"Espinar, Lorena","first_name":"Lorena"},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","full_name":"Sarkisyan, Karen","last_name":"Sarkisyan","orcid":"0000-0002-5375-6341"},{"last_name":"Mishin","full_name":"Mishin, Alexander S.","first_name":"Alexander S."},{"full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva","first_name":"Natalya S."},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya","first_name":"Inna S."},{"first_name":"Guillaume J.","full_name":"Filion, Guillaume J.","last_name":"Filion"},{"first_name":"Lucas B.","full_name":"Carey, Lucas B.","last_name":"Carey"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"}],"doi":"10.1371/journal.pgen.1008079","abstract":[{"lang":"eng","text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible."}],"issue":"4","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"publication_identifier":{"eissn":["15537404"]},"ec_funded":1,"publication_status":"published","status":"public","month":"04","ddc":["570"],"file_date_updated":"2020-07-14T12:47:30Z","citation":{"ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. <i>PLoS Genetics</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079\">10.1371/journal.pgen.1008079</a>","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","ieee":"V. Pokusaeva <i>et al.</i>, “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” <i>PLoS Genetics</i>, vol. 15, no. 4. Public Library of Science, 2019.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1008079\">https://doi.org/10.1371/journal.pgen.1008079</a>","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” <i>PLoS Genetics</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pgen.1008079\">https://doi.org/10.1371/journal.pgen.1008079</a>.","mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” <i>PLoS Genetics</i>, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079\">10.1371/journal.pgen.1008079</a>."},"day":"10","oa_version":"Published Version","file":[{"date_created":"2019-05-14T08:26:08Z","file_id":"6445","checksum":"cf3889c8a8a16053dacf9c3776cbe217","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:30Z","creator":"dernst","relation":"main_file","file_size":3726017,"file_name":"2019_PLOSGenetics_Pokusaeva.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","volume":15,"has_accepted_license":"1","oa":1,"year":"2019","date_updated":"2023-08-25T10:30:37Z","publication":"PLoS Genetics","article_number":"e1008079","related_material":{"record":[{"id":"9789","relation":"research_data","status":"public"},{"id":"9790","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9797"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"FyKo"}],"date_created":"2019-05-13T07:58:38Z","scopus_import":"1","date_published":"2019-04-10T00:00:00Z","external_id":{"isi":["000466866000029"]},"publisher":"Public Library of Science","intvolume":"        15","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1},{"page":"57-66","publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","date_updated":"2023-08-25T10:19:23Z","year":"2019","oa":1,"isi":1,"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"ACM","external_id":{"isi":["000516713900007"]},"date_published":"2019-04-16T00:00:00Z","scopus_import":"1","date_created":"2019-05-13T08:13:46Z","department":[{"_id":"ToHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_status":"published","publication_identifier":{"isbn":["9781450362825"]},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system.","lang":"eng"}],"doi":"10.1145/3302504.3311800","author":[{"last_name":"Ferrere","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","full_name":"Nickovic, Dejan","last_name":"Nickovic"},{"first_name":"Alexandre","full_name":"Donzé, Alexandre","last_name":"Donzé"},{"first_name":"Hisahiro","last_name":"Ito","full_name":"Ito, Hisahiro"},{"last_name":"Kapinski","full_name":"Kapinski, James","first_name":"James"}],"title":"Interface-aware signal temporal logic","_id":"6428","has_accepted_license":"1","article_processing_charge":"No","file":[{"file_name":"2019_ACM_Ferrere.pdf","creator":"dernst","relation":"main_file","file_size":1055421,"success":1,"date_updated":"2020-10-08T17:25:45Z","access_level":"open_access","content_type":"application/pdf","checksum":"b8e967081e051d1c55ca5d18fb187890","file_id":"8633","date_created":"2020-10-08T17:25:45Z"}],"conference":{"name":"HSCC: Hybrid Systems Computation and Control","location":"Montreal, Canada","start_date":"2019-04-16","end_date":"2019-04-18"},"oa_version":"Submitted Version","day":"16","citation":{"apa":"Ferrere, T., Nickovic, D., Donzé, A., Ito, H., &#38; Kapinski, J. (2019). Interface-aware signal temporal logic. In <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i> (pp. 57–66). Montreal, Canada: ACM. <a href=\"https://doi.org/10.1145/3302504.3311800\">https://doi.org/10.1145/3302504.3311800</a>","ieee":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>, Montreal, Canada, 2019, pp. 57–66.","short":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66.","ista":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66.","ama":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>. ACM; 2019:57-66. doi:<a href=\"https://doi.org/10.1145/3302504.3311800\">10.1145/3302504.3311800</a>","chicago":"Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>, 57–66. ACM, 2019. <a href=\"https://doi.org/10.1145/3302504.3311800\">https://doi.org/10.1145/3302504.3311800</a>.","mla":"Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>, ACM, 2019, pp. 57–66, doi:<a href=\"https://doi.org/10.1145/3302504.3311800\">10.1145/3302504.3311800</a>."},"ddc":["000"],"month":"04","file_date_updated":"2020-10-08T17:25:45Z"},{"project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["03029743"],"isbn":["9783030172589"],"eissn":["16113349"]},"ec_funded":1,"status":"public","publication_status":"published","_id":"6430","author":[{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan"},{"last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"title":"Adaptively secure proxy re-encryption","doi":"10.1007/978-3-030-17259-6_11","abstract":[{"lang":"eng","text":"A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key 𝑝𝑘′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under 𝑝𝑘′ without having to know the underlying message, while transformations from 𝑝𝑘′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure.\r\n\r\nAll existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in  Open image in new window , rendering the result meaningless already for moderate Open image in new window .\r\n\r\nJafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications.\r\n\r\nOur results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14)."}],"volume":11443,"article_processing_charge":"No","month":"04","day":"06","citation":{"ista":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. 2019. Adaptively secure proxy re-encryption. PKC: Public-Key Cryptograhy, LNCS, vol. 11443, 317–346.","short":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, Springer Nature, 2019, pp. 317–346.","ama":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. Adaptively secure proxy re-encryption. In: Vol 11443. Springer Nature; 2019:317-346. doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>","apa":"Fuchsbauer, G., Kamath Hosdurg, C., Klein, K., &#38; Pietrzak, K. Z. (2019). Adaptively secure proxy re-encryption (Vol. 11443, pp. 317–346). Presented at the PKC: Public-Key Cryptograhy, Beijing, China: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>","ieee":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “Adaptively secure proxy re-encryption,” presented at the PKC: Public-Key Cryptograhy, Beijing, China, 2019, vol. 11443, pp. 317–346.","chicago":"Fuchsbauer, Georg, Chethan Kamath Hosdurg, Karen Klein, and Krzysztof Z Pietrzak. “Adaptively Secure Proxy Re-Encryption,” 11443:317–46. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>.","mla":"Fuchsbauer, Georg, et al. <i>Adaptively Secure Proxy Re-Encryption</i>. Vol. 11443, Springer Nature, 2019, pp. 317–46, doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>."},"conference":{"name":"PKC: Public-Key Cryptograhy","location":"Beijing, China","start_date":"2019-04-14","end_date":"2019-04-17"},"oa_version":"Preprint","date_updated":"2023-09-08T11:33:20Z","page":"317-346","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10035"}]},"oa":1,"year":"2019","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/426"}],"intvolume":"     11443","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrPi"}],"scopus_import":"1","date_created":"2019-05-13T08:13:46Z","date_published":"2019-04-06T00:00:00Z"},{"file_date_updated":"2021-02-11T11:17:15Z","month":"05","ddc":["570","006","578","592"],"citation":{"mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria."},"day":"07","oa_version":"Published Version","file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","date_updated":"2021-02-11T11:17:15Z","file_name":"tesisDoctoradoBC.pdf","creator":"casillas","relation":"main_file","file_size":3895187,"embargo":"2020-05-08","file_id":"6438","date_created":"2019-05-13T09:16:20Z"},{"embargo_to":"open_access","file_id":"6439","date_created":"2019-05-13T09:16:20Z","file_name":"tesisDoctoradoBC.zip","creator":"casillas","file_size":7365118,"relation":"source_file","access_level":"closed","content_type":"application/zip","checksum":"3d221aaff7559a7060230a1ff610594f","date_updated":"2020-07-14T12:47:30Z"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","_id":"6435","title":"Collective defenses of garden ants against a fungal pathogen","supervisor":[{"orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia M","first_name":"Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"author":[{"last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:6435","abstract":[{"text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour.","lang":"eng"}],"project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","call_identifier":"H2020"}],"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"status":"public","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"SyCr"}],"date_created":"2019-05-13T08:58:35Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"date_published":"2019-05-07T00:00:00Z","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","oa":1,"keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"alternative_title":["ISTA Thesis"],"year":"2019","date_updated":"2023-09-07T12:57:04Z","page":"183","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1999"}]}},{"has_accepted_license":"1","volume":38,"article_processing_charge":"No","file":[{"file_id":"6443","date_created":"2019-05-14T07:03:55Z","access_level":"open_access","content_type":"application/pdf","checksum":"1b737dfe3e051aba8f3f4ab1dceda673","date_updated":"2020-07-14T12:47:30Z","file_name":"2019_ACM_Schreck.pdf","file_size":44328918,"relation":"main_file","creator":"dernst"}],"oa_version":"Submitted Version","citation":{"ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130.","ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","apa":"Schreck, C., Hafner, C., &#38; Wojtan, C. (2019). Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.","mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 130, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>.","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>."},"day":"01","ddc":["000","005"],"file_date_updated":"2020-07-14T12:47:30Z","month":"07","publication_status":"published","status":"public","ec_funded":1,"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples."}],"issue":"4","doi":"10.1145/3306346.3323002","title":"Fundamental solutions for water wave animation","author":[{"full_name":"Schreck, Camille","last_name":"Schreck","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille"},{"last_name":"Hafner","full_name":"Hafner, Christian","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546"}],"_id":"6442","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"ACM","intvolume":"        38","external_id":{"isi":["000475740600104"]},"date_published":"2019-07-01T00:00:00Z","date_created":"2019-05-14T07:04:06Z","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"ChWo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/","description":"News on IST Homepage","relation":"press_release"}]},"article_number":"130","publication":"ACM Transactions on Graphics","date_updated":"2023-08-25T10:18:46Z","year":"2019","oa":1},{"date_published":"2019-05-31T00:00:00Z","external_id":{"isi":["000470104600022"]},"date_created":"2019-05-14T11:47:40Z","department":[{"_id":"SiHi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Elsevier","intvolume":"        15","year":"2019","oa":1,"page":"243-256","publication":"iScience","date_updated":"2023-09-08T11:38:04Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","citation":{"ista":"Amberg N, Sotiropoulou PA, Heller G, Lichtenberger BM, Holcmann M, Camurdanoglu B, Baykuscheva-Gentscheva T, Blanpain C, Sibilia M. 2019. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 15, 243–256.","ama":"Amberg N, Sotiropoulou PA, Heller G, et al. EGFR controls hair shaft differentiation in a p53-independent manner. <i>iScience</i>. 2019;15:243-256. doi:<a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">10.1016/j.isci.2019.04.018</a>","short":"N. Amberg, P.A. Sotiropoulou, G. Heller, B.M. Lichtenberger, M. Holcmann, B. Camurdanoglu, T. Baykuscheva-Gentscheva, C. Blanpain, M. Sibilia, IScience 15 (2019) 243–256.","ieee":"N. Amberg <i>et al.</i>, “EGFR controls hair shaft differentiation in a p53-independent manner,” <i>iScience</i>, vol. 15. Elsevier, pp. 243–256, 2019.","apa":"Amberg, N., Sotiropoulou, P. A., Heller, G., Lichtenberger, B. M., Holcmann, M., Camurdanoglu, B., … Sibilia, M. (2019). EGFR controls hair shaft differentiation in a p53-independent manner. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">https://doi.org/10.1016/j.isci.2019.04.018</a>","mla":"Amberg, Nicole, et al. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” <i>IScience</i>, vol. 15, Elsevier, 2019, pp. 243–56, doi:<a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">10.1016/j.isci.2019.04.018</a>.","chicago":"Amberg, Nicole, Panagiota A. Sotiropoulou, Gerwin Heller, Beate M. Lichtenberger, Martin Holcmann, Bahar Camurdanoglu, Temenuschka Baykuscheva-Gentscheva, Cedric Blanpain, and Maria Sibilia. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” <i>IScience</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">https://doi.org/10.1016/j.isci.2019.04.018</a>."},"day":"31","file_date_updated":"2020-07-14T12:47:30Z","month":"05","ddc":["570"],"has_accepted_license":"1","volume":15,"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:47:30Z","checksum":"a9ad2296726c9474ad5860c9c2f53622","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_size":8365970,"relation":"main_file","file_name":"2019_iScience_Amberg.pdf","date_created":"2019-05-14T11:51:51Z","file_id":"6452"}],"abstract":[{"lang":"eng","text":"Epidermal growth factor receptor (EGFR) signaling controls skin development and homeostasis inmice and humans, and its deficiency causes severe skin inflammation, which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle stem cells. Expression and alternative splicing analysisof RNA sequencing data from interfollicular epidermis and outer root sheath indicate that EGFR con-trols genes involved in epidermal differentiation and also in centrosome function, DNA damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions in proliferative epidermal compartments, aswell asp53-independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1 protein specifically in the innermost epithelial hair layers, resulting in disorganizationof medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomousEGFR functions in the epidermis."}],"doi":"10.1016/j.isci.2019.04.018","title":"EGFR controls hair shaft differentiation in a p53-independent manner","author":[{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207"},{"full_name":"Sotiropoulou, Panagiota A.","last_name":"Sotiropoulou","first_name":"Panagiota A."},{"last_name":"Heller","full_name":"Heller, Gerwin","first_name":"Gerwin"},{"first_name":"Beate M.","last_name":"Lichtenberger","full_name":"Lichtenberger, Beate M."},{"first_name":"Martin","full_name":"Holcmann, Martin","last_name":"Holcmann"},{"full_name":"Camurdanoglu, Bahar","last_name":"Camurdanoglu","first_name":"Bahar"},{"last_name":"Baykuscheva-Gentscheva","full_name":"Baykuscheva-Gentscheva, Temenuschka","first_name":"Temenuschka"},{"last_name":"Blanpain","full_name":"Blanpain, Cedric","first_name":"Cedric"},{"full_name":"Sibilia, Maria","last_name":"Sibilia","first_name":"Maria"}],"_id":"6451","status":"public","publication_status":"published","publication_identifier":{"issn":["2589-0042"]}},{"year":"2019","oa":1,"page":"159-172.e7","publication":"Neuron","date_updated":"2023-09-05T13:02:21Z","external_id":{"pmid":["30824354"],"isi":["000463337900018"]},"date_published":"2019-04-03T00:00:00Z","date_created":"2019-05-14T13:06:30Z","scopus_import":"1","department":[{"_id":"SiHi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Elsevier","intvolume":"       102","abstract":[{"lang":"eng","text":"Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells."}],"issue":"1","doi":"10.1016/j.neuron.2019.01.051","title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","author":[{"first_name":"G","last_name":"Ortiz-Álvarez","full_name":"Ortiz-Álvarez, G"},{"full_name":"Daclin, M","last_name":"Daclin","first_name":"M"},{"first_name":"A","last_name":"Shihavuddin","full_name":"Shihavuddin, A"},{"last_name":"Lansade","full_name":"Lansade, P","first_name":"P"},{"first_name":"A","full_name":"Fortoul, A","last_name":"Fortoul"},{"last_name":"Faucourt","full_name":"Faucourt, M","first_name":"M"},{"first_name":"S","last_name":"Clavreul","full_name":"Clavreul, S"},{"first_name":"ME","full_name":"Lalioti, ME","last_name":"Lalioti"},{"first_name":"S","full_name":"Taraviras, S","last_name":"Taraviras"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Livet","full_name":"Livet, J","first_name":"J"},{"first_name":"A","last_name":"Meunier","full_name":"Meunier, A"},{"first_name":"A","full_name":"Genovesio, A","last_name":"Genovesio"},{"last_name":"Spassky","full_name":"Spassky, N","first_name":"N"}],"_id":"6454","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"oa_version":"Published Version","citation":{"chicago":"Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt, S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">https://doi.org/10.1016/j.neuron.2019.01.051</a>.","mla":"Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” <i>Neuron</i>, vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">10.1016/j.neuron.2019.01.051</a>.","ieee":"G. Ortiz-Álvarez <i>et al.</i>, “Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members,” <i>Neuron</i>, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019.","apa":"Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt, M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">https://doi.org/10.1016/j.neuron.2019.01.051</a>","short":"G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt, S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A. Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7.","ama":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. <i>Neuron</i>. 2019;102(1):159-172.e7. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">10.1016/j.neuron.2019.01.051</a>","ista":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 102(1), 159–172.e7."},"day":"03","ddc":["570"],"file_date_updated":"2020-07-14T12:47:30Z","pmid":1,"month":"04","has_accepted_license":"1","volume":102,"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"date_created":"2019-05-15T09:28:41Z","file_id":"6457","relation":"main_file","file_size":7288572,"creator":"dernst","file_name":"2019_Neuron_Ortiz.pdf","content_type":"application/pdf","checksum":"1fb6e195c583eb0c5cabf26f69ff6675","access_level":"open_access","date_updated":"2020-07-14T12:47:30Z"}]},{"external_id":{"isi":["000467631800034"],"pmid":["31073041"]},"date_published":"2019-05-10T00:00:00Z","scopus_import":"1","date_created":"2019-05-14T13:07:47Z","department":[{"_id":"SiHi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf","open_access":"1"}],"intvolume":"       364","publisher":"AAAS","year":"2019","oa":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/","description":"News on IST Homepage"}]},"article_type":"original","article_number":"eaav2522","publication":"Science","date_updated":"2023-09-05T11:51:09Z","oa_version":"Published Version","day":"10","citation":{"ieee":"L. Telley <i>et al.</i>, “Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex,” <i>Science</i>, vol. 364, no. 6440. AAAS, 2019.","apa":"Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., … Jabaudon, D. (2019). Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aav2522\">https://doi.org/10.1126/science.aav2522</a>","ama":"Telley L, Agirman G, Prados J, et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. <i>Science</i>. 2019;364(6440). doi:<a href=\"https://doi.org/10.1126/science.aav2522\">10.1126/science.aav2522</a>","ista":"Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G, Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. 2019. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 364(6440), eaav2522.","short":"L. Telley, G. Agirman, J. Prados, N. Amberg, S. Fièvre, P. Oberst, G. Bartolini, I. Vitali, C. Cadilhac, S. Hippenmeyer, L. Nguyen, A. Dayer, D. Jabaudon, Science 364 (2019).","mla":"Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” <i>Science</i>, vol. 364, no. 6440, eaav2522, AAAS, 2019, doi:<a href=\"https://doi.org/10.1126/science.aav2522\">10.1126/science.aav2522</a>.","chicago":"Telley, L, G Agirman, J Prados, Nicole Amberg, S Fièvre, P Oberst, G Bartolini, et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” <i>Science</i>. AAAS, 2019. <a href=\"https://doi.org/10.1126/science.aav2522\">https://doi.org/10.1126/science.aav2522</a>."},"month":"05","pmid":1,"article_processing_charge":"No","volume":364,"issue":"6440","abstract":[{"lang":"eng","text":"During corticogenesis, distinct subtypes of neurons are sequentially born from ventricular zone progenitors. How these cells are molecularly temporally patterned is poorly understood. We used single-cell RNA sequencing at high temporal resolution to trace the lineage of the molecular identities of successive generations of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified a core set of evolutionarily conserved, temporally patterned genes that drive APs from internally driven to more exteroceptive states. We found that the Polycomb repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic age–dependent AP molecular states are transmitted to their progeny as successive ground states, onto which essentially conserved early postmitotic differentiation programs are applied, and are complemented by later-occurring environment-dependent signals. Thus, epigenetically regulated temporal molecular birthmarks present in progenitors act in their postmitotic progeny to seed adult neuronal diversity."}],"doi":"10.1126/science.aav2522","author":[{"first_name":"L","last_name":"Telley","full_name":"Telley, L"},{"first_name":"G","last_name":"Agirman","full_name":"Agirman, G"},{"full_name":"Prados, J","last_name":"Prados","first_name":"J"},{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207"},{"first_name":"S","full_name":"Fièvre, S","last_name":"Fièvre"},{"last_name":"Oberst","full_name":"Oberst, P","first_name":"P"},{"first_name":"G","full_name":"Bartolini, G","last_name":"Bartolini"},{"first_name":"I","last_name":"Vitali","full_name":"Vitali, I"},{"first_name":"C","full_name":"Cadilhac, C","last_name":"Cadilhac"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"full_name":"Nguyen, L","last_name":"Nguyen","first_name":"L"},{"last_name":"Dayer","full_name":"Dayer, A","first_name":"A"},{"full_name":"Jabaudon, D","last_name":"Jabaudon","first_name":"D"}],"title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","_id":"6455","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression"}]},{"oa_version":"Published Version","conference":{"name":"CAV: Computer Aided Verification","end_date":"2019-07-18","location":"New York, NY, United States","start_date":"2019-07-13"},"citation":{"short":"G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 630–649.","ama":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: <i>31st International Conference on Computer-Aided Verification</i>. Vol 11561. Springer; 2019:630-649. doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">10.1007/978-3-030-25540-4_36</a>","ista":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019. Run-time optimization for learned controllers through quantitative games. 31st International Conference on Computer-Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 11561, 630–649.","ieee":"G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger, “Run-time optimization for learned controllers through quantitative games,” in <i>31st International Conference on Computer-Aided Verification</i>, New York, NY, United States, 2019, vol. 11561, pp. 630–649.","apa":"Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., &#38; Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In <i>31st International Conference on Computer-Aided Verification</i> (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">https://doi.org/10.1007/978-3-030-25540-4_36</a>","mla":"Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” <i>31st International Conference on Computer-Aided Verification</i>, vol. 11561, Springer, 2019, pp. 630–49, doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">10.1007/978-3-030-25540-4_36</a>.","chicago":"Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers through Quantitative Games.” In <i>31st International Conference on Computer-Aided Verification</i>, 11561:630–49. Springer, 2019. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">https://doi.org/10.1007/978-3-030-25540-4_36</a>."},"day":"12","file_date_updated":"2020-07-14T12:47:31Z","month":"07","ddc":["000"],"has_accepted_license":"1","volume":11561,"article_processing_charge":"No","file":[{"date_updated":"2020-07-14T12:47:31Z","checksum":"c231579f2485c6fd4df17c9443a4d80b","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":659766,"file_name":"2019_CAV_Avni.pdf","date_created":"2019-08-14T09:35:24Z","file_id":"6816"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive  synthesis.  First,  we  abstract  the  plant  by  building  a  stochastic  model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles.","lang":"eng"}],"doi":"10.1007/978-3-030-25540-4_36","title":"Run-time optimization for learned controllers through quantitative games","author":[{"last_name":"Avni","full_name":"Avni, Guy","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"full_name":"Bloem, Roderick","last_name":"Bloem","first_name":"Roderick"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"full_name":"Konighofer, Bettina","last_name":"Konighofer","first_name":"Bettina"},{"first_name":"Stefan","last_name":"Pranger","full_name":"Pranger, Stefan"}],"_id":"6462","status":"public","publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030255398"]},"project":[{"_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"external_id":{"isi":["000491468000036"]},"date_published":"2019-07-12T00:00:00Z","date_created":"2019-05-16T11:22:30Z","scopus_import":"1","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"publisher":"Springer","intvolume":"     11561","year":"2019","alternative_title":["LNCS"],"oa":1,"page":"630-649","publication":"31st International Conference on Computer-Aided Verification","date_updated":"2023-08-25T10:33:27Z"}]