[{"month":"08","type":"dissertation","date_created":"2018-12-11T11:50:18Z","citation":{"ama":"Rieckh G. Studying the complexities of transcriptional regulation. 2016.","mla":"Rieckh, Georg. <i>Studying the Complexities of Transcriptional Regulation</i>. Institute of Science and Technology Austria, 2016.","apa":"Rieckh, G. (2016). <i>Studying the complexities of transcriptional regulation</i>. Institute of Science and Technology Austria.","ieee":"G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.","short":"G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.","ista":"Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","chicago":"Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016."},"oa_version":"Published Version","degree_awarded":"PhD","oa":1,"day":"01","date_published":"2016-08-01T00:00:00Z","status":"public","author":[{"last_name":"Rieckh","full_name":"Rieckh, Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"}],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The process of gene expression is central to the modern understanding of how cellular systems\r\nfunction. In this process, a special kind of regulatory proteins, called transcription factors,\r\nare important to determine how much protein is produced from a given gene. As biological\r\ninformation is transmitted from transcription factor concentration to mRNA levels to amounts of\r\nprotein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical\r\ndescription of complex promoters responsible for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information processing the cell faces due to the interference from multiple\r\nfluctuating signals, (iii) how the presence of gene expression noise influences the evolution\r\nof regulatory sequences, (iv) and tools for the experimental study of origins and consequences\r\nof cell-cell heterogeneity, including an application to bacterial stress response systems."}],"file":[{"file_name":"Thesis_Georg_Rieckh_w_signature_page.pdf","date_updated":"2019-08-13T11:46:25Z","checksum":"ec453918c3bf8e6f460fd1156ef7b493","content_type":"application/pdf","access_level":"closed","creator":"dernst","file_id":"6815","relation":"main_file","file_size":2614660,"date_created":"2019-08-13T11:46:25Z"},{"file_name":"Thesis_Georg_Rieckh.pdf","date_updated":"2020-09-21T11:30:40Z","checksum":"51ae398166370d18fd22478b6365c4da","success":1,"file_size":6096178,"date_created":"2020-09-21T11:30:40Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"8542","relation":"main_file"}],"date_updated":"2023-09-07T11:44:34Z","article_processing_charge":"No","has_accepted_license":"1","year":"2016","title":"Studying the complexities of transcriptional regulation","page":"114","supervisor":[{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455"}],"department":[{"_id":"GaTk"}],"alternative_title":["ISTA Thesis"],"_id":"1128","publist_id":"6232","publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-09-21T11:30:40Z","publication_status":"published","ddc":["570"]},{"oa":1,"day":"01","status":"public","date_published":"2016-07-01T00:00:00Z","acknowledgement":"First, I would like to thank Michael Sixt for being a great supervisor, mentor and\r\nscientist. I highly appreciate his guidance and continued support. Furthermore, I\r\nam very grateful that he gave me the exceptional opportunity to pursue many\r\nideas of which some managed to be included in this thesis.\r\nI owe sincere thanks to the members of my PhD thesis committee, Daria\r\nSiekhaus, Daniel Legler and Harald Janovjak. Especially I would like to thank\r\nDaria for her advice and encouragement during our regular progress meetings.\r\nI also want to thank the team and fellows of the Boehringer Ingelheim Fond\r\n(BIF) PhD Fellowship for amazing and inspiring meetings and the BIF for\r\nfinancial support.\r\nImportant factors for the success of this thesis were the warm, creative\r\nand helpful atmosphere as well as the team spirit of the whole Sixt Lab.\r\nTherefore I would like to thank my current and former colleagues Frank Assen,\r\nMarkus Brown, Ingrid de Vries, Michelle Duggan, Alexander Eichner, Miroslav\r\nHons, Eva Kiermaier, Aglaja Kopf, Alexander Leithner, Christine Moussion, Jan\r\nMüller, Maria Nemethova, Jörg Renkawitz, Anne Reversat, Kari Vaahtomeri,\r\nMichele Weber and Stefan Wieser. We had an amazing time with many\r\nlegendary evenings and events. Along these lines I want to thank the in vitro\r\ncrew of the lab, Jörg, Anne and Alex, for lots of ideas and productive\r\ndiscussions. I am sure, some day we will reveal the secret of the ‘splodge’.\r\nI want to thank the members of the Heisenberg Lab for a great time and\r\nthrilling kicker matches. In this regard I especially want to thank Maurizio\r\n‘Gnocci’ Monti, Gabriel Krens, Alex Eichner, Martin Behrndt, Vanessa Barone,Philipp Schmalhorst, Michael Smutny, Daniel Capek, Anne Reversat, Eva\r\nKiermaier, Frank Assen and Jan Müller for wonderful after-lunch matches.\r\nI would not have been able to analyze the thousands of cell trajectories\r\nand probably hundreds of thousands of mouse clicks without the productive\r\ncollaboration with Veronika Bierbaum and Tobias Bollenbach. Thanks Vroni for\r\ncountless meetings, discussions and graphs and of course for proofreading and\r\nadvice for this thesis. For proofreading I also want to thank Evi, Jörg, Jack and\r\nAnne.\r\nI would like to acknowledge Matthias Mehling for a very productive\r\ncollaboration and for introducing me into the wild world of microfluidics. Jack\r\nMerrin, for countless wafers, PDMS coated coverslips and help with anything\r\nmicro-fabrication related. And Maria Nemethova for establishing the ‘click’\r\npatterning approach with me. Without her it still would be just one of the ideas…\r\nMany thanks to Ekaterina Papusheva, Robert Hauschild, Doreen Milius\r\nand Nasser Darwish from the Bioimaging Facility as well as the Preclinical and\r\nthe Life Science facilities of IST Austria for excellent technical support. At this\r\npoint I especially want to thank Robert for countless image analyses and\r\ntechnical ideas. Always interested and creative he played an essential role in all\r\nof my projects.\r\nAdditionally I want to thank Ingrid and Gabby for welcoming me warmly\r\nwhen I first started at IST, for scientific and especially mental support in all\r\nthose years, countless coffee sessions and Heurigen evenings. #BioimagingFacility #LifeScienceFacility #PreClinicalFacility","month":"07","citation":{"chicago":"Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute of Science and Technology Austria, 2016.","ista":"Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria.","short":"J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute of Science and Technology Austria, 2016.","ieee":"J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute of Science and Technology Austria, 2016.","apa":"Schwarz, J. (2016). <i>Quantitative analysis of haptotactic cell migration</i>. Institute of Science and Technology Austria.","mla":"Schwarz, Jan. <i>Quantitative Analysis of Haptotactic Cell Migration</i>. Institute of Science and Technology Austria, 2016.","ama":"Schwarz J. Quantitative analysis of haptotactic cell migration. 2016."},"oa_version":"Published Version","date_created":"2018-12-11T11:50:18Z","degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"department":[{"_id":"MiSi"}],"page":"178","title":"Quantitative analysis of haptotactic cell migration","supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"ddc":["570"],"file_date_updated":"2021-02-22T11:43:14Z","publication_status":"published","_id":"1129","publisher":"Institute of Science and Technology Austria","publist_id":"6231","abstract":[{"lang":"eng","text":"Directed cell migration is a hallmark feature, present in almost all multi-cellular\r\norganisms. Despite its importance, basic questions regarding force transduction\r\nor directional sensing are still heavily investigated. Directed migration of cells\r\nguided by immobilized guidance cues - haptotaxis - occurs in key-processes,\r\nsuch as embryonic development and immunity (Middleton et al., 1997; Nguyen\r\net al., 2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues\r\ncomprise adhesive ligands, such as collagen and fibronectin (Barczyk et al.,\r\n2009), or chemokines - the main guidance cues for migratory leukocytes\r\n(Middleton et al., 1997; Weber et al., 2013). While adhesive ligands serve as\r\nattachment sites guiding cell migration (Carter, 1965), chemokines instruct\r\nhaptotactic migration by inducing adhesion to adhesive ligands and directional\r\nguidance (Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis\r\nof the cellular response to immobilized guidance cues requires in vitro assays\r\nthat foster cell migration, offer accurate control of the immobilized cues on a\r\nsubcellular scale and in the ideal case closely reproduce in vivo conditions. The\r\nexploration of haptotactic cell migration through design and employment of such\r\nassays represents the main focus of this work.\r\nDendritic cells (DCs) are leukocytes, which after encountering danger\r\nsignals such as pathogens in peripheral organs instruct naïve T-cells and\r\nconsequently the adaptive immune response in the lymph node (Mellman and\r\nSteinman, 2001). To reach the lymph node from the periphery, DCs follow\r\nhaptotactic gradients of the chemokine CCL21 towards lymphatic vessels\r\n(Weber et al., 2013). Questions about how DCs interpret haptotactic CCL21\r\ngradients have not yet been addressed. The main reason for this is the lack of\r\nan assay that offers diverse haptotactic environments, hence allowing the study\r\nof DC migration as a response to different signals of immobilized guidance cue.\r\nIn this work, we developed an in vitro assay that enables us to\r\nquantitatively assess DC haptotaxis, by combining precisely controllable\r\nchemokine photo-patterning with physically confining migration conditions. With this tool at hand, we studied the influence of CCL21 gradient properties and\r\nconcentration on DC haptotaxis. We found that haptotactic gradient sensing\r\ndepends on the absolute CCL21 concentration in combination with the local\r\nsteepness of the gradient. Our analysis suggests that the directionality of\r\nmigrating DCs is governed by the signal-to-noise ratio of CCL21 binding to its\r\nreceptor CCR7. Moreover, the haptotactic CCL21 gradient formed in vivo\r\nprovides an optimal shape for DCs to recognize haptotactic guidance cue.\r\nBy reconstitution of the CCL21 gradient in vitro we were also able to\r\nstudy the influence of CCR7 signal termination on DC haptotaxis. To this end,\r\nwe used DCs lacking the G-protein coupled receptor kinase GRK6, which is\r\nresponsible for CCL21 induced CCR7 receptor phosphorylation and\r\ndesensitization (Zidar et al., 2009). We found that CCR7 desensitization by\r\nGRK6 is crucial for maintenance of haptotactic CCL21 gradient sensing in vitro\r\nand confirm those observations in vivo.\r\nIn the context of the organism, immobilized haptotactic guidance cues\r\noften coincide and compete with soluble chemotactic guidance cues. During\r\nwound healing, fibroblasts are exposed and influenced by adhesive cues and\r\nsoluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,\r\nmigrating DCs are exposed to both, soluble chemokines (CCL19 and truncated\r\nCCL21) inducing chemotactic behavior as well as the immobilized CCL21. To\r\nquantitatively assess these complex coinciding immobilized and soluble\r\nguidance cues, we implemented our chemokine photo-patterning technique in a\r\nmicrofluidic system allowing for chemotactic gradient generation. To validate\r\nthe assay, we observed DC migration in competing CCL19/CCL21\r\nenvironments.\r\nAdhesiveness guided haptotaxis has been studied intensively over the\r\nlast century. However, quantitative studies leading to conceptual models are\r\nlargely missing, again due to the lack of a precisely controllable in vitro assay. A\r\nrequirement for such an in vitro assay is that it must prevent any uncontrolled\r\ncell adhesion. This can be accomplished by stable passivation of the surface. In\r\naddition, controlled adhesion must be sustainable, quantifiable and dose\r\ndependent in order to create homogenous gradients. Therefore, we developed a novel covalent photo-patterning technique satisfying all these needs. In\r\ncombination with a sustainable poly-vinyl alcohol (PVA) surface coating we\r\nwere able to generate gradients of adhesive cue to direct cell migration. This\r\napproach allowed us to characterize the haptotactic migratory behavior of\r\nzebrafish keratocytes in vitro. Furthermore, defined patterns of adhesive cue\r\nallowed us to control for cell shape and growth on a subcellular scale."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-07T11:54:33Z","file":[{"file_name":"Thesis_JSchwarz_final.pdf","date_updated":"2019-08-13T10:55:35Z","checksum":"e3cd6b28f9c5cccb8891855565a2dade","content_type":"application/pdf","access_level":"closed","creator":"dernst","file_id":"6813","relation":"main_file","file_size":32044069,"date_created":"2019-08-13T10:55:35Z"},{"creator":"dernst","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9181","date_created":"2021-02-22T11:43:14Z","file_size":8396717,"success":1,"date_updated":"2021-02-22T11:43:14Z","file_name":"2016_Thesis_JSchwarz.pdf","checksum":"c3dbe219acf87eed2f46d21d5cca00de"}],"publication_identifier":{"issn":["2663-337X"]},"author":[{"last_name":"Schwarz","full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"year":"2016","has_accepted_license":"1"},{"ec_funded":1,"_id":"1130","publisher":"Institute of Science and Technology Austria","publist_id":"6230","ddc":["000"],"file_date_updated":"2021-11-17T13:46:55Z","publication_status":"published","title":"Automatic synthesis of synchronisation primitives for concurrent programs","page":"151","supervisor":[{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"has_accepted_license":"1","year":"2016","author":[{"orcid":"0000-0003-4409-8487","first_name":"Thorsten","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tarrach, Thorsten"}],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"abstract":[{"text":"In this thesis we present a computer-aided programming approach to concurrency. Our approach helps the programmer by automatically fixing concurrency-related bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are program behaviours that are incorrect w.r.t. a specification. We consider both user-provided explicit specifications in the form of assertion\r\nstatements in the code as well as an implicit specification. The implicit specification is inferred from the non-preemptive behaviour. Let us consider sequences of calls that the program makes to an external interface. The implicit specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We consider several semantics-preserving fixes that go beyond atomic sections typically explored in the synchronisation synthesis literature. Our synthesis is able to place locks, barriers and wait-signal statements and last, but not least reorder independent statements. The latter may be useful if a thread is released to early, e.g., before some initialisation is completed. We guarantee that our synthesis does not introduce deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective function. We dub our solution trace-based synchronisation synthesis and it is loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis works by discovering a trace that is incorrect w.r.t. the specification and identifying ordering constraints crucial to trigger the specification violation. Synchronisation may be placed immediately (greedy approach) or delayed until all incorrect traces are found (non-greedy approach). For the non-greedy approach we construct a set of global constraints over synchronisation placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronisation placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronisation solution. We evaluate our approach on a number of realistic (albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions of the drivers with known concurrency-related bugs. For the experiments with an explicit specification we added assertions that would detect the bugs in the experiments. Device drivers lend themselves to implicit specification, where the device and the operating system are the external interfaces. Our experiments demonstrate that our synthesis method is precise and efficient. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronisation placements are produced for our experiments, favouring e.g. a minimal number of synchronisation operations or maximum concurrency.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-07T11:57:01Z","file":[{"success":1,"file_name":"2016_Tarrach_Thesis.pdf","date_updated":"2021-02-22T11:39:32Z","checksum":"319a506831650327e85376db41fc1094","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"9179","relation":"main_file","file_size":1523935,"date_created":"2021-02-22T11:39:32Z"},{"checksum":"39efcd789f0ad859ff15652cb7afc412","file_name":"2016_Tarrach_Thesispdfa.pdf","date_updated":"2021-11-17T13:46:55Z","file_size":1306068,"date_created":"2021-11-16T14:14:38Z","file_id":"10296","relation":"main_file","access_level":"closed","content_type":"application/pdf","creator":"cchlebak"}],"doi":"10.15479/at:ista:1130","date_published":"2016-07-07T00:00:00Z","related_material":{"record":[{"status":"public","id":"1729","relation":"part_of_dissertation"},{"status":"public","id":"2218","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"2445"}]},"status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf"}],"day":"07","type":"dissertation","oa_version":"Published Version","citation":{"chicago":"Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for Concurrent Programs.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>.","ista":"Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent programs. Institute of Science and Technology Austria.","ieee":"T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent programs,” Institute of Science and Technology Austria, 2016.","short":"T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent Programs, Institute of Science and Technology Austria, 2016.","mla":"Tarrach, Thorsten. <i>Automatic Synthesis of Synchronisation Primitives for Concurrent Programs</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>.","apa":"Tarrach, T. (2016). <i>Automatic synthesis of synchronisation primitives for concurrent programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>","ama":"Tarrach T. Automatic synthesis of synchronisation primitives for concurrent programs. 2016. doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>"},"date_created":"2018-12-11T11:50:19Z","degree_awarded":"PhD","month":"07"},{"month":"07","acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","type":"dissertation","citation":{"ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria."},"oa_version":"Published Version","date_created":"2018-12-11T11:50:19Z","degree_awarded":"PhD","oa":1,"day":"01","date_published":"2016-07-01T00:00:00Z","related_material":{"record":[{"id":"5554","relation":"research_data","status":"public"},{"status":"public","id":"1666","relation":"part_of_dissertation"}]},"status":"public","publication_identifier":{"issn":["2663-337X"]},"author":[{"last_name":"Tugrul","full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat","orcid":"0000-0002-8523-0758"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","file":[{"file_id":"6810","relation":"main_file","content_type":"application/pdf","access_level":"closed","creator":"dernst","file_size":3695257,"date_created":"2019-08-13T08:53:52Z","checksum":"66cb61a59943e4fb7447c6a86be5ef51","file_name":"Tugrul_thesis_w_signature_page.pdf","date_updated":"2019-08-13T08:53:52Z"},{"file_size":3880811,"date_created":"2021-02-22T11:45:20Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_id":"9182","relation":"main_file","file_name":"2016_Tugrul_Thesis.pdf","date_updated":"2021-02-22T11:45:20Z","checksum":"293e388d70563760f6b24c3e66283dda","success":1}],"date_updated":"2025-05-28T11:57:04Z","has_accepted_license":"1","year":"2016","title":"Evolution of transcriptional regulatory sequences","page":"89","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"NiBa"}],"_id":"1131","publisher":"Institute of Science and Technology Austria","publist_id":"6229","publication_status":"published","file_date_updated":"2021-02-22T11:45:20Z","ddc":["576"]},{"oa":1,"day":"01","article_number":"26","date_published":"2016-10-01T00:00:00Z","doi":"10.1145/2968478.2968499","status":"public","month":"10","pubrep_id":"644","quality_controlled":"1","type":"conference","date_created":"2018-12-11T11:50:20Z","oa_version":"Submitted Version","citation":{"ista":"Avni G, Guha S, Rodríguez Navas G. 2016. Synthesizing time triggered schedules for switched networks with faulty links. Proceedings of the 13th International Conference on Embedded Software . EMSOFT: Embedded Software , 26.","chicago":"Avni, Guy, Shibashis Guha, and Guillermo Rodríguez Navas. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” In <i>Proceedings of the 13th International Conference on Embedded Software </i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2968478.2968499\">https://doi.org/10.1145/2968478.2968499</a>.","short":"G. Avni, S. Guha, G. Rodríguez Navas, in:, Proceedings of the 13th International Conference on Embedded Software , ACM, 2016.","ieee":"G. Avni, S. Guha, and G. Rodríguez Navas, “Synthesizing time triggered schedules for switched networks with faulty links,” in <i>Proceedings of the 13th International Conference on Embedded Software </i>, Pittsburgh, PA, USA, 2016.","apa":"Avni, G., Guha, S., &#38; Rodríguez Navas, G. (2016). Synthesizing time triggered schedules for switched networks with faulty links. In <i>Proceedings of the 13th International Conference on Embedded Software </i>. Pittsburgh, PA, USA: ACM. <a href=\"https://doi.org/10.1145/2968478.2968499\">https://doi.org/10.1145/2968478.2968499</a>","mla":"Avni, Guy, et al. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” <i>Proceedings of the 13th International Conference on Embedded Software </i>, 26, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2968478.2968499\">10.1145/2968478.2968499</a>.","ama":"Avni G, Guha S, Rodríguez Navas G. Synthesizing time triggered schedules for switched networks with faulty links. In: <i>Proceedings of the 13th International Conference on Embedded Software </i>. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2968478.2968499\">10.1145/2968478.2968499</a>"},"publication":"Proceedings of the 13th International Conference on Embedded Software ","title":"Synthesizing time triggered schedules for switched networks with faulty links","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"department":[{"_id":"ToHe"}],"_id":"1135","ec_funded":1,"publist_id":"6223","publisher":"ACM","file_date_updated":"2018-12-12T10:09:31Z","ddc":["000"],"publication_status":"published","conference":{"end_date":"2016-10-07","start_date":"2016-10-01","location":"Pittsburgh, PA, USA","name":"EMSOFT: Embedded Software "},"author":[{"first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"last_name":"Rodríguez Navas","full_name":"Rodríguez Navas, Guillermo","first_name":"Guillermo"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Time-triggered (TT) switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. These networks rely on the notion of globally discretized time (i.e. time slots) and a static TT schedule that prescribes which message is sent through which link at every time slot, such that all messages reach their destination before a global timeout. These schedules are generated offline, assuming a static network with fault-free links, and entrusting all error-handling functions to the end user. Assuming the network is static is an over-optimistic view, and indeed links tend to fail in practice. We study synthesis of TT schedules on a network in which links fail over time and we assume the switches run a very simple error-recovery protocol once they detect a crashed link. We address the problem of finding a pk; qresistant schedule; namely, one that, assuming the switches run a fixed error-recovery protocol, guarantees that the number of messages that arrive at their destination by the timeout is at least no matter what sequence of at most k links fail. Thus, we maintain the simplicity of the switches while giving a guarantee on the number of messages that meet the timeout. We show how a pk; q-resistant schedule can be obtained using a CEGAR-like approach: find a schedule, decide whether it is pk; q-resistant, and if it is not, use the witnessing fault sequence to generate a constraint that is added to the program. The newly added constraint disallows the schedule to be regenerated in a future iteration while also eliminating several other schedules that are not pk; q-resistant. We illustrate the applicability of our approach using an SMT-based implementation. © 2016 ACM.","lang":"eng"}],"date_updated":"2021-01-12T06:48:33Z","file":[{"file_id":"4755","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","file_size":279240,"date_created":"2018-12-12T10:09:31Z","file_name":"IST-2016-644-v1+1_emsoft-no-format.pdf","date_updated":"2018-12-12T10:09:31Z"}],"has_accepted_license":"1","year":"2016","scopus_import":1},{"article_number":"2994261","date_published":"2016-10-10T00:00:00Z","doi":"10.1145/2994258.2994261","status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01367181"}],"day":"10","type":"conference","citation":{"ama":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. Space-time sculpting of liquid animation. In: <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>","apa":"Manteaux, P., Vimont, U., Wojtan, C., Rohmer, D., &#38; Cani, M. (2016). Space-time sculpting of liquid animation. In <i>Proceedings of the 9th International Conference on Motion in Games </i>. San Francisco, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>","mla":"Manteaux, Pierre, et al. “Space-Time Sculpting of Liquid Animation.” <i>Proceedings of the 9th International Conference on Motion in Games </i>, 2994261, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>.","short":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of the 9th International Conference on Motion in Games , ACM, 2016.","ieee":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, and M. Cani, “Space-time sculpting of liquid animation,” in <i>Proceedings of the 9th International Conference on Motion in Games </i>, San Francisco, CA, USA, 2016.","ista":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. 2016. Space-time sculpting of liquid animation. Proceedings of the 9th International Conference on Motion in Games . MIG: Motion in Games, 2994261.","chicago":"Manteaux, Pierre, Ulysse Vimont, Chris Wojtan, Damien Rohmer, and Marie Cani. “Space-Time Sculpting of Liquid Animation.” In <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>."},"oa_version":"Submitted Version","date_created":"2018-12-11T11:50:20Z","publication":"Proceedings of the 9th International Conference on Motion in Games ","month":"10","acknowledgement":"This work was partly supported by the starting grant BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2014-StG 638176 , and ERC-2011-ADG 20110209).","quality_controlled":"1","ec_funded":1,"_id":"1136","publisher":"ACM","publist_id":"6222","publication_status":"published","ddc":["004"],"title":"Space-time sculpting of liquid animation","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"department":[{"_id":"ChWo"}],"has_accepted_license":"1","scopus_import":"1","year":"2016","author":[{"first_name":"Pierre","full_name":"Manteaux, Pierre","last_name":"Manteaux"},{"first_name":"Ulysse","last_name":"Vimont","full_name":"Vimont, Ulysse"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J"},{"first_name":"Damien","full_name":"Rohmer, Damien","last_name":"Rohmer"},{"first_name":"Marie","full_name":"Cani, Marie","last_name":"Cani"}],"conference":{"name":"MIG: Motion in Games","location":"San Francisco, CA, USA","start_date":"2016-10-10","end_date":"2016-10-12"},"language":[{"iso":"eng"}],"abstract":[{"text":"We propose an interactive sculpting system for seamlessly editing pre-computed animations of liquid, without the need for any resimulation. The input is a sequence of meshes without correspondences representing the liquid surface over time. Our method enables the efficient selection of consistent space-time parts of this animation, such as moving waves or droplets, which we call space-time features. Once selected, a feature can be copied, edited, or duplicated and then pasted back anywhere in space and time in the same or in another liquid animation sequence. Our method circumvents tedious user interactions by automatically computing the spatial and temporal ranges of the selected feature. We also provide space-time shape editing tools for non-uniform scaling, rotation, trajectory changes, and temporal editing to locally speed up or slow down motion. Using our tools, the user can edit and progressively refine any input simulation result, possibly using a library of precomputed space-time features extracted from other animations. In contrast to the trial-and-error loop usually required to edit animation results through the tuning of indirect simulation parameters, our method gives the user full control over the edited space-time behaviors. © 2016 Copyright held by the owner/author(s).","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2023-02-21T09:49:49Z"},{"citation":{"ama":"Salzer E, Çaǧdaş D, Hons M, et al. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. 2016;17(12):1352-1360. doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>","mla":"Salzer, Elisabeth, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1352–60, doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>.","apa":"Salzer, E., Çaǧdaş, D., Hons, M., Mace, E., Garncarz, W., Petronczki, O., … Boztug, K. (2016). RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>","short":"E. Salzer, D. Çaǧdaş, M. Hons, E. Mace, W. Garncarz, O. Petronczki, R. Platzer, L. Pfajfer, I. Bilic, S. Ban, K. Willmann, M. Mukherjee, V. Supper, H. Hsu, P. Banerjee, P. Sinha, F. Mcclanahan, G. Zlabinger, W. Pickl, J. Gribben, H. Stockinger, K. Bennett, J. Huppa, L. Dupré, Ö. Sanal, U. Jäger, M.K. Sixt, I. Tezcan, J. Orange, K. Boztug, Nature Immunology 17 (2016) 1352–1360.","ieee":"E. Salzer <i>et al.</i>, “RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1352–1360, 2016.","ista":"Salzer E, Çaǧdaş D, Hons M, Mace E, Garncarz W, Petronczki O, Platzer R, Pfajfer L, Bilic I, Ban S, Willmann K, Mukherjee M, Supper V, Hsu H, Banerjee P, Sinha P, Mcclanahan F, Zlabinger G, Pickl W, Gribben J, Stockinger H, Bennett K, Huppa J, Dupré L, Sanal Ö, Jäger U, Sixt MK, Tezcan I, Orange J, Boztug K. 2016. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. 17(12), 1352–1360.","chicago":"Salzer, Elisabeth, Deniz Çaǧdaş, Miroslav Hons, Emily Mace, Wojciech Garncarz, Oezlem Petronczki, René Platzer, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>."},"oa_version":"Submitted Version","date_created":"2018-12-11T11:50:21Z","publication":"Nature Immunology","type":"journal_article","quality_controlled":"1","month":"12","status":"public","date_published":"2016-12-01T00:00:00Z","doi":"10.1038/ni.3575","intvolume":"        17","oa":1,"external_id":{"pmid":["27776107"]},"day":"01","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263","open_access":"1"}],"issue":"12","scopus_import":1,"year":"2016","volume":17,"abstract":[{"lang":"eng","text":"RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency also resulted in defective proliferation, activation and motility of T cells and B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity with defective granule convergence and actin accumulation. Interaction proteomics identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed the migration and activation defects of RASGRP1-deficient lymphocytes."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2021-01-12T06:48:33Z","author":[{"first_name":"Elisabeth","full_name":"Salzer, Elisabeth","last_name":"Salzer"},{"first_name":"Deniz","full_name":"Çaǧdaş, Deniz","last_name":"Çaǧdaş"},{"first_name":"Miroslav","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348"},{"last_name":"Mace","full_name":"Mace, Emily","first_name":"Emily"},{"last_name":"Garncarz","full_name":"Garncarz, Wojciech","first_name":"Wojciech"},{"full_name":"Petronczki, Oezlem","last_name":"Petronczki","first_name":"Oezlem"},{"first_name":"René","last_name":"Platzer","full_name":"Platzer, René"},{"last_name":"Pfajfer","full_name":"Pfajfer, Laurène","first_name":"Laurène"},{"last_name":"Bilic","full_name":"Bilic, Ivan","first_name":"Ivan"},{"full_name":"Ban, Sol","last_name":"Ban","first_name":"Sol"},{"last_name":"Willmann","full_name":"Willmann, Katharina","first_name":"Katharina"},{"full_name":"Mukherjee, Malini","last_name":"Mukherjee","first_name":"Malini"},{"full_name":"Supper, Verena","last_name":"Supper","first_name":"Verena"},{"last_name":"Hsu","full_name":"Hsu, Hsiangting","first_name":"Hsiangting"},{"last_name":"Banerjee","full_name":"Banerjee, Pinaki","first_name":"Pinaki"},{"first_name":"Papiya","full_name":"Sinha, Papiya","last_name":"Sinha"},{"last_name":"Mcclanahan","full_name":"Mcclanahan, Fabienne","first_name":"Fabienne"},{"first_name":"Gerhard","full_name":"Zlabinger, Gerhard","last_name":"Zlabinger"},{"full_name":"Pickl, Winfried","last_name":"Pickl","first_name":"Winfried"},{"first_name":"John","last_name":"Gribben","full_name":"Gribben, John"},{"last_name":"Stockinger","full_name":"Stockinger, Hannes","first_name":"Hannes"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"full_name":"Huppa, Johannes","last_name":"Huppa","first_name":"Johannes"},{"last_name":"Dupré","full_name":"Dupré, Loï̈C","first_name":"Loï̈C"},{"last_name":"Sanal","full_name":"Sanal, Özden","first_name":"Özden"},{"first_name":"Ulrich","last_name":"Jäger","full_name":"Jäger, Ulrich"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ilhan","last_name":"Tezcan","full_name":"Tezcan, Ilhan"},{"full_name":"Orange, Jordan","last_name":"Orange","first_name":"Jordan"},{"first_name":"Kaan","full_name":"Boztug, Kaan","last_name":"Boztug"}],"pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","_id":"1137","publisher":"Nature Publishing Group","article_type":"original","publist_id":"6221","department":[{"_id":"MiSi"}],"title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","page":"1352 - 1360"},{"page":"76 - 85","title":"Quantitative automata under probabilistic semantics","project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"1138","ec_funded":1,"publist_id":"6220","publisher":"IEEE","publication_status":"published","conference":{"start_date":"2016-07-05","name":"LICS: Logic in Computer Science","location":"New York, NY, USA","end_date":"2016-07-08"},"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider. © 2016 ACM."}],"date_updated":"2021-01-12T06:48:34Z","year":"2016","scopus_import":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"day":"05","external_id":{"arxiv":["1604.06764"]},"doi":"10.1145/2933575.2933588","date_published":"2016-07-05T00:00:00Z","status":"public","month":"07","arxiv":1,"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S114","quality_controlled":"1","type":"conference","date_created":"2018-12-11T11:50:21Z","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic semantics. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>. IEEE; 2016:76-85. doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Quantitative automata under probabilistic semantics. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i> (pp. 76–85). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>","mla":"Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, IEEE, 2016, pp. 76–85, doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under probabilistic semantics,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, New York, NY, USA, 2016, pp. 76–85.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 76–85.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Automata under Probabilistic Semantics.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, 76–85. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>."},"oa_version":"Preprint","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium"},{"status":"public","date_published":"2016-07-05T00:00:00Z","doi":"10.1145/2933575.2935304","oa":1,"day":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02670"}],"external_id":{"arxiv":["1602.02670"]},"date_created":"2018-12-11T11:50:22Z","oa_version":"Preprint","citation":{"short":"K. Chatterjee, W. Dvoák, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206.","ieee":"K. Chatterjee, W. Dvoák, M. H. Henzinger, and V. Loitzenbauer, “Model and objective separation with conditional lower bounds: disjunction is harder than conjunction,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, New York, NY, USA, 2016, pp. 197–206.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvoák, Monika H Henzinger, and Veronika Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 197–206. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>.","ista":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. 2016. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, , 197–206.","ama":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>. IEEE; 2016:197-206. doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>","mla":"Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, IEEE, 2016, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>.","apa":"Chatterjee, K., Dvoák, W., Henzinger, M. H., &#38; Loitzenbauer, V. (2016). Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 197–206). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>"},"publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","type":"conference","acknowledgement":"K.  C.,  M.  H.,  and  W.  D.  are  partially  supported  by  the  Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK. C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H., and V. L. the research\r\nleading to these results has received funding from the European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme (FP/2007-2013) / ERC Grant Agreement no. 340506.","quality_controlled":"1","month":"07","arxiv":1,"publication_status":"published","_id":"1140","publist_id":"6219","publisher":"IEEE","department":[{"_id":"KrCh"}],"alternative_title":["Proceedings Symposium on Logic in Computer Science"],"title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","page":"197 - 206","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"year":"2016","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental -regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical -regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. © 2016 ACM."}],"date_updated":"2025-06-02T08:53:44Z","article_processing_charge":"No","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Wolfgang","last_name":"Dvoák","full_name":"Dvoák, Wolfgang"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"}],"conference":{"end_date":"2016-07-08","start_date":"2016-07-05","location":"New York, NY, USA","name":"LICS: Logic in Computer Science"},"language":[{"iso":"eng"}]},{"department":[{"_id":"MiSi"},{"_id":"PeJo"}],"page":"1361 - 1372","title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","publication_status":"published","_id":"1142","publisher":"Nature Publishing Group","publist_id":"6216","abstract":[{"text":"Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:36Z","author":[{"full_name":"Martins, Rui","last_name":"Martins","first_name":"Rui"},{"first_name":"Julia","last_name":"Maier","full_name":"Maier, Julia"},{"first_name":"Anna","full_name":"Gorki, Anna","last_name":"Gorki"},{"first_name":"Kilian","last_name":"Huber","full_name":"Huber, Kilian"},{"first_name":"Omar","full_name":"Sharif, Omar","last_name":"Sharif"},{"first_name":"Philipp","full_name":"Starkl, Philipp","last_name":"Starkl"},{"first_name":"Simona","full_name":"Saluzzo, Simona","last_name":"Saluzzo"},{"full_name":"Quattrone, Federica","last_name":"Quattrone","first_name":"Federica"},{"first_name":"Riem","full_name":"Gawish, Riem","last_name":"Gawish"},{"first_name":"Karin","last_name":"Lakovits","full_name":"Lakovits, Karin"},{"first_name":"Michael","last_name":"Aichinger","full_name":"Aichinger, Michael"},{"last_name":"Radic Sarikas","full_name":"Radic Sarikas, Branka","first_name":"Branka"},{"last_name":"Lardeau","full_name":"Lardeau, Charles","first_name":"Charles"},{"first_name":"Anastasiya","last_name":"Hladik","full_name":"Hladik, Anastasiya"},{"full_name":"Korosec, Ana","last_name":"Korosec","first_name":"Ana"},{"first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","first_name":"Kari"},{"last_name":"Duggan","id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","full_name":"Duggan, Michelle","first_name":"Michelle"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"},{"first_name":"Harald","full_name":"Esterbauer, Harald","last_name":"Esterbauer"},{"first_name":"Jacques","last_name":"Colinge","full_name":"Colinge, Jacques"},{"full_name":"Eisenbarth, Stephanie","last_name":"Eisenbarth","first_name":"Stephanie"},{"first_name":"Thomas","last_name":"Decker","full_name":"Decker, Thomas"},{"first_name":"Keiryn","last_name":"Bennett","full_name":"Bennett, Keiryn"},{"last_name":"Kubicek","full_name":"Kubicek, Stefan","first_name":"Stefan"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"first_name":"Giulio","full_name":"Superti Furga, Giulio","last_name":"Superti Furga"},{"first_name":"Sylvia","last_name":"Knapp","full_name":"Knapp, Sylvia"}],"language":[{"iso":"eng"}],"scopus_import":1,"issue":"12","year":"2016","volume":17,"oa":1,"day":"01","main_file_link":[{"open_access":"1","url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d"}],"status":"public","date_published":"2016-12-01T00:00:00Z","doi":"10.1038/ni.3590","intvolume":"        17","acknowledgement":"Y. Fukui (Medical Institute of Bioregulation, Kyushu University) and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children's Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct. pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding retrovirus was kindly provided by A. Leithner (Institute of Science and Technology Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research, National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent technical support (Core imaging facility, Medical University of Vienna). We thank D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was supported by the Austrian Academy of Sciences, the Science Fund of the Austrian National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA framework (to S.Knapp).","quality_controlled":"1","month":"12","citation":{"short":"R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo, F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau, A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer, J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.","ieee":"R. Martins <i>et al.</i>, “Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.","chicago":"Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>.","ista":"Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 17(12), 1361–1372.","ama":"Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. 2016;17(12):1361-1372. doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>","mla":"Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1361–72, doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>.","apa":"Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp, S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>"},"oa_version":"Submitted Version","date_created":"2018-12-11T11:50:22Z","publication":"Nature Immunology","type":"journal_article"},{"department":[{"_id":"RoSe"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","page":"459 - 485","publication_status":"published","publisher":"Mathematical Sciences Publishers","publist_id":"6215","ec_funded":1,"_id":"1143","date_updated":"2021-01-12T06:48:36Z","abstract":[{"lang":"eng","text":"We study the ground state of a dilute Bose gas in a scaling limit where the Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger functional whose quartic term is proportional to the scattering length of the interparticle interaction potential. We propose a new derivation of this limit problem, with a method that bypasses some of the technical difficulties that previous derivations had to face. The new method is based on a combination of Dyson\\'s lemma, the quantum de Finetti theorem and a second moment estimate for ground states of the effective Dyson Hamiltonian. It applies equally well to the case where magnetic fields or rotation are present."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"first_name":"Phan","full_name":"Nam, Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rougerie, Nicolas","last_name":"Rougerie","first_name":"Nicolas"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"issue":"2","scopus_import":1,"year":"2016","volume":9,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1503.07061"}],"day":"24","oa":1,"status":"public","doi":"10.2140/apde.2016.9.459","date_published":"2016-03-24T00:00:00Z","intvolume":"         9","quality_controlled":"1","month":"03","publication":"Analysis and PDE","oa_version":"Preprint","citation":{"short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","ieee":"P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems: The gross Pitaevskii limit revisited,” <i>Analysis and PDE</i>, vol. 9, no. 2. Mathematical Sciences Publishers, pp. 459–485, 2016.","ista":"Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485.","chicago":"Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>. Mathematical Sciences Publishers, 2016. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>.","ama":"Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. 2016;9(2):459-485. doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>","mla":"Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>, vol. 9, no. 2, Mathematical Sciences Publishers, 2016, pp. 459–85, doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>.","apa":"Nam, P., Rougerie, N., &#38; Seiringer, R. (2016). Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>"},"date_created":"2018-12-11T11:50:23Z","type":"journal_article"},{"acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","quality_controlled":"1","pubrep_id":"746","month":"11","date_created":"2018-12-11T11:50:23Z","oa_version":"Published Version","citation":{"ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. 2016;9(11):1504-1519. doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>","apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., &#38; Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>","mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>.","short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” <i>Molecular Plant</i>, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519.","chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>."},"publication":"Molecular Plant","type":"journal_article","oa":1,"day":"07","status":"public","intvolume":"         9","doi":"10.1016/j.molp.2016.08.010","date_published":"2016-11-07T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors"}],"file":[{"file_id":"5004","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system","file_size":5005876,"date_created":"2018-12-12T10:13:22Z","file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","date_updated":"2018-12-12T10:13:22Z"}],"date_updated":"2021-01-12T06:48:37Z","author":[{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"language":[{"iso":"eng"}],"year":"2016","scopus_import":1,"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"issue":"11","has_accepted_license":"1","volume":9,"department":[{"_id":"JiFr"}],"page":"1504 - 1519","title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"publication_status":"published","file_date_updated":"2018-12-12T10:13:22Z","ddc":["581"],"_id":"1145","ec_funded":1,"publist_id":"6213","publisher":"Cell Press"},{"status":"public","intvolume":"         6","doi":"10.1038/srep35955","date_published":"2016-11-08T00:00:00Z","article_number":"35955","day":"08","oa":1,"publication":"Scientific Reports","date_created":"2018-12-11T11:50:24Z","citation":{"mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>, vol. 6, 35955, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>.","apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., &#38; Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955.","chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>.","ieee":"J. Balla <i>et al.</i>, “Auxin flow mediated competition between axillary buds to restore apical dominance,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016)."},"oa_version":"Published Version","type":"journal_article","quality_controlled":"1","acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).","license":"https://creativecommons.org/licenses/by/4.0/","month":"11","pubrep_id":"745","file_date_updated":"2018-12-12T10:09:28Z","publication_status":"published","ddc":["581"],"publist_id":"6211","publisher":"Nature Publishing Group","_id":"1147","department":[{"_id":"JiFr"}],"title":"Auxin flow mediated competition between axillary buds to restore apical dominance","year":"2016","scopus_import":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":6,"has_accepted_license":"1","file":[{"relation":"main_file","file_id":"4752","creator":"system","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:09:28Z","file_size":1587544,"date_updated":"2018-12-12T10:09:28Z","file_name":"IST-2017-745-v1+1_srep35955.pdf"}],"date_updated":"2021-01-12T06:48:38Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016."}],"language":[{"iso":"eng"}],"author":[{"last_name":"Balla","full_name":"Balla, Jozef","first_name":"Jozef"},{"first_name":"Zuzana","full_name":"Medved'Ová, Zuzana","last_name":"Medved'Ová"},{"first_name":"Petr","full_name":"Kalousek, Petr","last_name":"Kalousek"},{"last_name":"Matiješčuková","full_name":"Matiješčuková, Natálie","first_name":"Natálie"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí"},{"first_name":"Vilém","last_name":"Reinöhl","full_name":"Reinöhl, Vilém"},{"first_name":"Stanislav","last_name":"Procházka","full_name":"Procházka, Stanislav"}]},{"intvolume":"        30","date_published":"2016-10-15T00:00:00Z","doi":"10.1101/gad.285361.116","status":"public","day":"15","external_id":{"pmid":["27898393"]},"oa":1,"type":"journal_article","publication":"Genes and Development","date_created":"2018-12-11T11:50:25Z","citation":{"ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. <i>Genes and Development</i>. 2016;30(20):2286-2296. doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>","mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” <i>Genes and Development</i>, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>.","apa":"Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>","ieee":"S. Simonini <i>et al.</i>, “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” <i>Genes and Development</i>, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296.","chicago":"Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2016. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>.","ista":"Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20), 2286–2296."},"oa_version":"Published Version","month":"10","quality_controlled":"1","acknowledgement":"We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford, Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt, Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds; Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1 (Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1) to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. ","publist_id":"6207","publisher":"Cold Spring Harbor Laboratory Press","_id":"1151","publication_status":"published","ddc":["570"],"file_date_updated":"2019-01-25T09:32:55Z","page":"2286 - 2296","title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","department":[{"_id":"JiFr"}],"volume":30,"has_accepted_license":"1","year":"2016","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"20","scopus_import":1,"language":[{"iso":"eng"}],"pmid":1,"author":[{"last_name":"Simonini","full_name":"Simonini, Sara","first_name":"Sara"},{"last_name":"Deb","full_name":"Deb, Joyita","first_name":"Joyita"},{"last_name":"Moubayidin","full_name":"Moubayidin, Laila","first_name":"Laila"},{"full_name":"Stephenson, Pauline","last_name":"Stephenson","first_name":"Pauline"},{"full_name":"Valluru, Manoj","last_name":"Valluru","first_name":"Manoj"},{"first_name":"Alejandra","full_name":"Freire Rios, Alejandra","last_name":"Freire Rios"},{"full_name":"Sorefan, Karim","last_name":"Sorefan","first_name":"Karim"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Lars","last_name":"Östergaard","full_name":"Östergaard, Lars"}],"file":[{"file_size":1419263,"date_created":"2019-01-25T09:32:55Z","file_id":"5882","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_name":"2016_GeneDev_Simonini.pdf","date_updated":"2019-01-25T09:32:55Z","success":1}],"date_updated":"2021-01-12T06:48:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al."}]},{"scopus_import":1,"issue":"10","year":"2016","volume":28,"date_updated":"2021-01-12T06:48:40Z","abstract":[{"text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"first_name":"Marçal","full_name":"Gallemí, Marçal","last_name":"Gallemí"},{"last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique","first_name":"Dominique"},{"first_name":"Richard","full_name":"Smith, Richard","last_name":"Smith"},{"first_name":"Dirk","full_name":"Inze, Dirk","last_name":"Inze"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Przemysław","full_name":"Prusinkiewicz, Przemysław","last_name":"Prusinkiewicz"},{"first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"publication_status":"published","publisher":"American Society of Plant Biologists","publist_id":"6205","ec_funded":1,"_id":"1153","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"title":"A model of differential growth guided apical hook formation in plants","page":"2464 - 2477","publication":"Plant Cell","citation":{"ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. 2016;28(10):2464-2477. doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>","mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>.","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>","ieee":"P. Žádníková <i>et al.</i>, “A model of differential growth guided apical hook formation in plants,” <i>Plant Cell</i>, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477.","chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>.","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477."},"oa_version":"Submitted Version","date_created":"2018-12-11T11:50:26Z","type":"journal_article","quality_controlled":"1","acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","month":"10","status":"public","date_published":"2016-10-01T00:00:00Z","doi":"10.1105/tpc.15.00569","intvolume":"        28","day":"01","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/"}],"oa":1},{"type":"journal_article","oa_version":"Published Version","citation":{"apa":"Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach, M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>","mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>, vol. 6, 36440, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>.","ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>","ista":"Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 6, 36440.","chicago":"Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild, Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>.","ieee":"J. Schwarz <i>et al.</i>, “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","short":"J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach, S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016)."},"date_created":"2018-12-11T11:50:27Z","publication":"Scientific Reports","month":"11","pubrep_id":"744","acknowledgement":"This work was supported by the Swiss National Science Foundation (Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society (research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF) to J.S., the European Research Council (grant ERC GA 281556) and a START award from the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility","quality_controlled":"1","article_number":"36440","doi":"10.1038/srep36440","date_published":"2016-11-07T00:00:00Z","intvolume":"         6","status":"public","oa":1,"day":"07","has_accepted_license":"1","volume":6,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"year":"2016","author":[{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","last_name":"Schwarz","first_name":"Jan"},{"id":"3FD04378-F248-11E8-B48F-1D18A9856A87","last_name":"Bierbaum","full_name":"Bierbaum, Veronika","first_name":"Veronika"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tino","last_name":"Frank","full_name":"Frank, Tino"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"},{"last_name":"Tay","full_name":"Tay, Savaş","first_name":"Savaş"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"},{"last_name":"Mehling","full_name":"Mehling, Matthias","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","orcid":"0000-0001-8599-1226"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. \r\n"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2017-744-v1+1_srep36440.pdf","date_updated":"2018-12-12T10:09:32Z","file_size":2353456,"date_created":"2018-12-12T10:09:32Z","content_type":"application/pdf","access_level":"open_access","creator":"system","file_id":"4756","relation":"main_file"}],"date_updated":"2021-01-12T06:48:41Z","ec_funded":1,"_id":"1154","publisher":"Nature Publishing Group","publist_id":"6204","publication_status":"published","file_date_updated":"2018-12-12T10:09:32Z","ddc":["579"],"title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12"}],"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay.","lang":"eng"}],"date_updated":"2021-01-12T06:48:43Z","author":[{"first_name":"Ji","full_name":"Lee, Ji","last_name":"Lee"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231"}],"language":[{"iso":"eng"}],"year":"2016","scopus_import":1,"issue":"6","volume":26,"department":[{"_id":"LaEr"}],"title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","page":"3786 - 3839","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"publication_status":"published","_id":"1157","ec_funded":1,"publist_id":"6201","publisher":"Institute of Mathematical Statistics","acknowledgement":"We thank Horng-Tzer Yau for numerous discussions and remarks. We are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os, Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the anonymous referee for carefully reading our manuscript and suggesting several improvements.","quality_controlled":"1","month":"12","date_created":"2018-12-11T11:50:27Z","oa_version":"Preprint","citation":{"short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” <i>Annals of Applied Probability</i>, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839, 2016.","ista":"Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 26(6), 3786–3839.","chicago":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>.","ama":"Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. 2016;26(6):3786-3839. doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>","apa":"Lee, J., &#38; Schnelli, K. (2016). Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>","mla":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp. 3786–839, doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>."},"publication":"Annals of Applied Probability","type":"journal_article","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1409.4979","open_access":"1"}],"day":"15","status":"public","intvolume":"        26","date_published":"2016-12-15T00:00:00Z","doi":"10.1214/16-AAP1193"},{"acknowledgement":"We thank the anonymous referee for useful and constructive comments and suggestions which greatly improved the quality and clarity of our work. The authors acknowledge financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship. SS and DS acknowledge funding from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). SS also acknowledges support from FCT through the research grants UID/FIS/04434/2013 and PTDC/FIS-AST/2194/2012. JM acknowledges a Huygens PhD fellowship from Leiden University. Based on observations with the Subaru Telescope (Program IDs: S05B-027, S06A-025, S06B-010, S07A-013, S07B-008, S08B-008, S09A-017, S14A-086). Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 294.A-5018. Based on observations obtained with MegaPrime/Megacam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at TERAPIX available at the Canadian Astronomy Data Centre as part of the Canada–France–Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme ID 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. We are grateful to the CFHTLS, COSMOS-UltraVISTA, UKIDSS, SXDF and COSMOS survey teams. Without these legacy surveys, this research would have been impossible. The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Mauna Kea has always had within the indigenous Hawaiian community. We are most fortunate to have the opportunity to conduct and explore observations from this mountain. Finally, the authors acknowledge the unique value of the publicly available programming language PYTHON, including the NUMPY, PYFITS, MATPLOTLIB, SCIPY and ASTROPY (Astropy Collaboration et al.","quality_controlled":"1","month":"12","arxiv":1,"date_created":"2022-07-13T10:08:20Z","oa_version":"Preprint","citation":{"ieee":"S. Santos, D. Sobral, and J. J. Matthee, “The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 463, no. 2. Oxford University Press, pp. 1678–1691, 2016.","short":"S. Santos, D. Sobral, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 463 (2016) 1678–1691.","chicago":"Santos, Sérgio, David Sobral, and Jorryt J Matthee. “The Lyα Luminosity Function at Z= 5.7–6.6 and the Steep Drop of the Faint End: Implications for Reionization.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/mnras/stw2076\">https://doi.org/10.1093/mnras/stw2076</a>.","ista":"Santos S, Sobral D, Matthee JJ. 2016. The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization. Monthly Notices of the Royal Astronomical Society. 463(2), 1678–1691.","ama":"Santos S, Sobral D, Matthee JJ. The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization. <i>Monthly Notices of the Royal Astronomical Society</i>. 2016;463(2):1678-1691. doi:<a href=\"https://doi.org/10.1093/mnras/stw2076\">10.1093/mnras/stw2076</a>","apa":"Santos, S., Sobral, D., &#38; Matthee, J. J. (2016). The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stw2076\">https://doi.org/10.1093/mnras/stw2076</a>","mla":"Santos, Sérgio, et al. “The Lyα Luminosity Function at Z= 5.7–6.6 and the Steep Drop of the Faint End: Implications for Reionization.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 463, no. 2, Oxford University Press, 2016, pp. 1678–91, doi:<a href=\"https://doi.org/10.1093/mnras/stw2076\">10.1093/mnras/stw2076</a>."},"publication":"Monthly Notices of the Royal Astronomical Society","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift","galaxies: luminosity function","mass function","cosmology: observations","dark ages","reionization","first stars"],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07435"}],"day":"01","extern":"1","external_id":{"arxiv":["1606.07435"]},"status":"public","intvolume":"       463","date_published":"2016-12-01T00:00:00Z","doi":"10.1093/mnras/stw2076","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present new results from the widest narrow-band survey search for Lyα emitters at z = 5.7, just after reionization. We survey a total of 7 deg2 spread over the COSMOS, UDS and SA22 fields. We find over 11 000 line emitters, out of which 514 are robust Lyα candidates at z = 5.7 within a volume of 6.3 × 106 Mpc3. Our Lyα emitters span a wide range in Lyα luminosities, from faint to bright (LLyα ∼ 1042.5–44 erg s−1) and rest-frame equivalent widths (EW0 ∼ 25–1000 Å) in a single, homogeneous data set. By combining all our fields, we find that the faint end slope of the z = 5.7 Lyα luminosity function is very steep, with α=−2.3+0.4−0.3⁠. We also present an updated z = 6.6 Lyα luminosity function, based on comparable volumes and obtained with the same methods, which we directly compare with that at z = 5.7. We find a significant decline of the number density of faint Lyα emitters from z = 5.7 to 6.6 (by 0.5 ± 0.1 dex), but no evolution at the bright end/no evolution in L*. Faint Lyα emitters at z = 6.6 show much more extended haloes than those at z = 5.7, suggesting that neutral Hydrogen plays an important role, increasing the scattering and leading to observations missing faint Lyα emission within the epoch of reionization. Altogether, our results suggest that we are observing patchy reionization which happens first around the brightest Lyα emitters, allowing the number densities of those sources to remain unaffected by the increase of neutral Hydrogen fraction from z ∼ 5 to 7.","lang":"eng"}],"date_updated":"2022-08-19T08:09:54Z","article_processing_charge":"No","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"author":[{"first_name":"Sérgio","full_name":"Santos, Sérgio","last_name":"Santos"},{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"orcid":"0000-0003-2871-127X","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"}],"language":[{"iso":"eng"}],"year":"2016","issue":"2","scopus_import":"1","volume":463,"title":"The Lyα luminosity function at z= 5.7–6.6 and the steep drop of the faint end: Implications for reionization","page":"1678-1691","publication_status":"published","_id":"11574","article_type":"original","publisher":"Oxford University Press"},{"doi":"10.1093/mnras/stw717","date_published":"2016-07-01T00:00:00Z","intvolume":"       459","status":"public","oa":1,"extern":"1","external_id":{"arxiv":["1510.08067"]},"day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1510.08067","open_access":"1"}],"keyword":["Space and Planetary Science","Astronomy and Astrophysics  stars: formation","ISM: evolution","galaxies: evolution","galaxies: formation","galaxies: ISM"],"type":"journal_article","citation":{"short":"C. del P. Lagos, T. Theuns, J. Schaye, M. Furlong, R.G. Bower, M. Schaller, R.A. Crain, J.W. Trayford, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 459 (2016) 2632–2650.","ieee":"C. del P. Lagos <i>et al.</i>, “The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 459, no. 3. Oxford University Press, pp. 2632–2650, 2016.","chicago":"Lagos, Claudia del P., Tom Theuns, Joop Schaye, Michelle Furlong, Richard G. Bower, Matthieu Schaller, Robert A. Crain, James W. Trayford, and Jorryt J Matthee. “The Fundamental Plane of Star Formation in Galaxies Revealed by the EAGLE Hydrodynamical Simulations.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/mnras/stw717\">https://doi.org/10.1093/mnras/stw717</a>.","ista":"Lagos C del P, Theuns T, Schaye J, Furlong M, Bower RG, Schaller M, Crain RA, Trayford JW, Matthee JJ. 2016. The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations. Monthly Notices of the Royal Astronomical Society. 459(3), 2632–2650.","ama":"Lagos C del P, Theuns T, Schaye J, et al. The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations. <i>Monthly Notices of the Royal Astronomical Society</i>. 2016;459(3):2632-2650. doi:<a href=\"https://doi.org/10.1093/mnras/stw717\">10.1093/mnras/stw717</a>","apa":"Lagos, C. del P., Theuns, T., Schaye, J., Furlong, M., Bower, R. G., Schaller, M., … Matthee, J. J. (2016). The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stw717\">https://doi.org/10.1093/mnras/stw717</a>","mla":"Lagos, Claudia del P., et al. “The Fundamental Plane of Star Formation in Galaxies Revealed by the EAGLE Hydrodynamical Simulations.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 459, no. 3, Oxford University Press, 2016, pp. 2632–50, doi:<a href=\"https://doi.org/10.1093/mnras/stw717\">10.1093/mnras/stw717</a>."},"oa_version":"Preprint","date_created":"2022-07-13T10:21:24Z","publication":"Monthly Notices of the Royal Astronomical Society","month":"07","arxiv":1,"acknowledgement":"We thank Luca Cortese, Matt Bothwell, Paola Santini and Tim Davis for providing observational data sets, and Aaron Robotham, Luca Cortese and Barbara Catinella for useful discussions. CdPL is funded by a Discovery Early Career Researcher Award (DE150100618). CdPL also thanks the MERAC Foundation for a Postdoctoral Research Award. This work used the DiRAC Data Centric system at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/H008519/1, and STFC DiRAC Operations grant ST/K003267/1 and Durham University. DiRAC is part of the National E-Infrastructure. Support was also received via the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office ([AP P7/08 CHARM]), the National Science Foundation under grant no. NSF PHY11-25915, and the UK Science and Technology Facilities Council (grant numbers ST/F001166/1 and ST/I000976/1) via rolling and consolidating grants awarded to the ICC. The research was supported in part by the European Research Council under the European Union‘s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement 278594-GasAroundGalaxies.","quality_controlled":"1","_id":"11575","publisher":"Oxford University Press","article_type":"original","publication_status":"published","page":"2632-2650","title":"The Fundamental Plane of star formation in galaxies revealed by the EAGLE hydrodynamical simulations","volume":459,"issue":"3","scopus_import":"1","year":"2016","author":[{"first_name":"Claudia del P.","full_name":"Lagos, Claudia del P.","last_name":"Lagos"},{"last_name":"Theuns","full_name":"Theuns, Tom","first_name":"Tom"},{"first_name":"Joop","full_name":"Schaye, Joop","last_name":"Schaye"},{"full_name":"Furlong, Michelle","last_name":"Furlong","first_name":"Michelle"},{"first_name":"Richard G.","full_name":"Bower, Richard G.","last_name":"Bower"},{"last_name":"Schaller","full_name":"Schaller, Matthieu","first_name":"Matthieu"},{"full_name":"Crain, Robert A.","last_name":"Crain","first_name":"Robert A."},{"first_name":"James W.","full_name":"Trayford, James W.","last_name":"Trayford"},{"orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J"}],"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"language":[{"iso":"eng"}],"abstract":[{"text":"We investigate correlations between different physical properties of star-forming galaxies in the ‘Evolution and Assembly of GaLaxies and their Environments’ (EAGLE) cosmological hydrodynamical simulation suite over the redshift range 0 ≤ z ≤ 4.5. A principal component analysis reveals that neutral gas fraction (fgas,neutral), stellar mass (Mstellar) and star formation rate (SFR) account for most of the variance seen in the population, with galaxies tracing a two-dimensional, nearly flat, surface in the three-dimensional space of fgas, neutral–Mstellar–SFR with little scatter. The location of this plane varies little with redshift, whereas galaxies themselves move along the plane as their fgas, neutral and SFR drop with redshift. The positions of galaxies along the plane are highly correlated with gas metallicity. The metallicity can therefore be robustly predicted from fgas, neutral, or from the Mstellar and SFR. We argue that the appearance of this ‘Fundamental Plane of star formation’ is a consequence of self-regulation, with the plane's curvature set by the dependence of the SFR on gas density and metallicity. We analyse a large compilation of observations spanning the redshift range 0 ≲ z ≲ 3, and find that such a plane is also present in the data. The properties of the observed Fundamental Plane of star formation are in good agreement with EAGLE's predictions.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2022-08-19T08:12:07Z"},{"doi":"10.1093/mnras/stw022","date_published":"2016-04-01T00:00:00Z","intvolume":"       457","status":"public","external_id":{"arxiv":["1601.02266"]},"extern":"1","day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1601.02266","open_access":"1"}],"oa":1,"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","cosmology: observations"],"type":"journal_article","publication":"Monthly Notices of the Royal Astronomical Society","oa_version":"Preprint","citation":{"ieee":"D. Sobral <i>et al.</i>, “The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 457, no. 2. Oxford University Press, pp. 1739–1752, 2016.","short":"D. Sobral, S.A. Kohn, P.N. Best, I. Smail, C.M. Harrison, J. Stott, J. Calhau, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 457 (2016) 1739–1752.","chicago":"Sobral, David, Saul A. Kohn, Philip N. Best, Ian Smail, Chris M. Harrison, John Stott, João Calhau, and Jorryt J Matthee. “The Most Luminous H α Emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and Star-Forming Galaxies.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/mnras/stw022\">https://doi.org/10.1093/mnras/stw022</a>.","ista":"Sobral D, Kohn SA, Best PN, Smail I, Harrison CM, Stott J, Calhau J, Matthee JJ. 2016. The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies. Monthly Notices of the Royal Astronomical Society. 457(2), 1739–1752.","ama":"Sobral D, Kohn SA, Best PN, et al. The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies. <i>Monthly Notices of the Royal Astronomical Society</i>. 2016;457(2):1739-1752. doi:<a href=\"https://doi.org/10.1093/mnras/stw022\">10.1093/mnras/stw022</a>","mla":"Sobral, David, et al. “The Most Luminous H α Emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and Star-Forming Galaxies.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 457, no. 2, Oxford University Press, 2016, pp. 1739–52, doi:<a href=\"https://doi.org/10.1093/mnras/stw022\">10.1093/mnras/stw022</a>.","apa":"Sobral, D., Kohn, S. A., Best, P. N., Smail, I., Harrison, C. M., Stott, J., … Matthee, J. J. (2016). The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stw022\">https://doi.org/10.1093/mnras/stw022</a>"},"date_created":"2022-07-13T12:50:36Z","arxiv":1,"month":"04","quality_controlled":"1","acknowledgement":"The authors would like to thank the anonymous reviewer for the many helpful comments and suggestions which greatly improved the clarity and quality of this work. DS and SAK acknowledge financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship. DS also acknowledges funding from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010) and from FCT grant PEst-OE/FIS/UI2751/2014. Part of this project was undertaken during the inaugural Leiden/ESA Astrophysics Program for Summer Students (LEAPS). IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson merit award. CH acknowledges support from STFC. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 087.A-0337 and ID 089.A-0965. Also based on data from the Telescopio Nazionale Galileo, with time awarded through OPTICON programmes 2011A/026 and 2012A020 and the William Herschel Telescope under programme W12BN007. The William Herschel Telescope is operated on the island of La Palma by the Isaac Newton Group in the Spanish\r\nObservatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. The authors wish to thank all the help given by the telescope staff from all the observatories used in this study: ESO staff in La Silla, and the TNG and WHT staff in La Palma. This publication makes use of data products from the Two Micron All-Sky Survey, which is a joint project of the University of Massachusetts and the Infrared Processing and Analysis Center/California Institute of Technology, funded by the National Aeronautics and Space Administration and the National Science Foundation.","publisher":"Oxford University Press","article_type":"original","_id":"11576","publication_status":"published","title":"The most luminous H α emitters at z ∼ 0.8–2.23 from HiZELS: Evolution of AGN and star-forming galaxies","page":"1739-1752","volume":457,"issue":"2","scopus_import":"1","year":"2016","language":[{"iso":"eng"}],"author":[{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"full_name":"Kohn, Saul A.","last_name":"Kohn","first_name":"Saul A."},{"first_name":"Philip N.","last_name":"Best","full_name":"Best, Philip N."},{"full_name":"Smail, Ian","last_name":"Smail","first_name":"Ian"},{"first_name":"Chris M.","last_name":"Harrison","full_name":"Harrison, Chris M."},{"first_name":"John","full_name":"Stott, John","last_name":"Stott"},{"first_name":"João","full_name":"Calhau, João","last_name":"Calhau"},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X"}],"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"article_processing_charge":"No","date_updated":"2022-08-19T08:15:21Z","abstract":[{"lang":"eng","text":"We use new near-infrared spectroscopic observations to investigate the nature and evolution of the most luminous Hα emitters at z ∼ 0.8–2.23, which evolve strongly in number density over this period, and compare them to more typical Hα emitters. We study 59 luminous Hα emitters with LHα > L∗Hα⁠, roughly equally split per redshift slice at z ∼ 0.8, 1.47 and 2.23 from the HiZELS and CF-HiZELS surveys. We find that, overall, 30 ± 8 per cent are active galactic nuclei [AGNs; 80 ± 30 per cent of these AGNs are broad-line AGNs, BL-AGNs], and we find little to no evolution in the AGN fraction with redshift, within the errors. However, the AGN fraction increases strongly with Hα luminosity and correlates best with LHα/L∗Hα(z)⁠. While LHα ≤ L∗Hα(z) Hα emitters are largely dominated by star-forming galaxies (>80 per cent), the most luminous Hα emitters (⁠LHα>10L∗Hα(z)⁠) at any cosmic time are essentially all BL-AGN. Using our AGN-decontaminated sample of luminous star-forming galaxies, and integrating down to a fixed Hα luminosity, we find a factor of ∼1300 evolution in the star formation rate density from z = 0 to 2.23. This is much stronger than the evolution from typical Hα star-forming galaxies and in line with the evolution seen for constant luminosity cuts used to select ‘ultraluminous’ infrared galaxies and/or sub-millimetre galaxies. By taking into account the evolution in the typical Hα luminosity, we show that the most strongly star-forming Hα-selected galaxies at any epoch (⁠LHα>L∗Hα(z)⁠) contribute the same fractional amount of ≈15 per cent to the total star formation rate density, at least up to z = 2.23."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]