[{"type":"journal_article","abstract":[{"lang":"eng","text":"This special issue of the Journal on Formal Methods in System Design is dedicated to Prof. Helmut Veith, who unexpectedly passed away in March 2016. Helmut Veith was a brilliant researcher, inspiring collaborator, passionate mentor, generous friend, and valued member of the formal methods community. Helmut was not only known for his numerous and influential contributions in the field of automated verification (most prominently his work on Counterexample-Guided Abstraction Refinement [1,2]), but also for his untiring and passionate efforts for the logic community: he co-organized the Vienna Summer of Logic (an event comprising twelve conferences and numerous workshops which attracted thousands of researchers from all over the world), he initiated the Vienna Center for Logic and Algorithms (which promotes international collaboration on logic and algorithms and organizes outreach events such as the LogicLounge), and he coordinated the Doctoral Program on Logical Methods in Computer Science at TU Wien (currently educating more than 40 doctoral students) and a National Research Network on Rigorous Systems Engineering (uniting fifteen researchers in Austria to address the challenge of building reliable and safe computer\r\nsystems). With his enthusiasm and commitment, Helmut completely reshaped the Austrian research landscape in the field of logic and verification in his few years as a full professor at TU Wien."}],"publist_id":"6924","issue":"2","_id":"743","year":"2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Preface of the special issue in memoriam Helmut Veith","status":"public","publication_status":"published","publisher":"Springer","intvolume":" 51","department":[{"_id":"ToHe"}],"author":[{"last_name":"Gottlob","first_name":"Georg","full_name":"Gottlob, Georg"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Georg","last_name":"Weißenbacher","full_name":"Weißenbacher, Georg"}],"date_created":"2018-12-11T11:48:16Z","date_updated":"2023-09-27T12:29:29Z","volume":51,"oa_version":"None","day":"14","month":"11","article_processing_charge":"No","publication":"Formal Methods in System Design","citation":{"ista":"Gottlob G, Henzinger TA, Weißenbacher G. 2017. Preface of the special issue in memoriam Helmut Veith. Formal Methods in System Design. 51(2), 267–269.","ieee":"G. Gottlob, T. A. Henzinger, and G. Weißenbacher, “Preface of the special issue in memoriam Helmut Veith,” Formal Methods in System Design, vol. 51, no. 2. Springer, pp. 267–269, 2017.","apa":"Gottlob, G., Henzinger, T. A., & Weißenbacher, G. (2017). Preface of the special issue in memoriam Helmut Veith. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-017-0307-6","ama":"Gottlob G, Henzinger TA, Weißenbacher G. Preface of the special issue in memoriam Helmut Veith. Formal Methods in System Design. 2017;51(2):267-269. doi:10.1007/s10703-017-0307-6","chicago":"Gottlob, Georg, Thomas A Henzinger, and Georg Weißenbacher. “Preface of the Special Issue in Memoriam Helmut Veith.” Formal Methods in System Design. Springer, 2017. https://doi.org/10.1007/s10703-017-0307-6.","mla":"Gottlob, Georg, et al. “Preface of the Special Issue in Memoriam Helmut Veith.” Formal Methods in System Design, vol. 51, no. 2, Springer, 2017, pp. 267–69, doi:10.1007/s10703-017-0307-6.","short":"G. Gottlob, T.A. Henzinger, G. Weißenbacher, Formal Methods in System Design 51 (2017) 267–269."},"external_id":{"isi":["000415615600001"]},"isi":1,"quality_controlled":"1","page":"267 - 269","date_published":"2017-11-14T00:00:00Z","doi":"10.1007/s10703-017-0307-6","language":[{"iso":"eng"}]},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Cell-cell contact formation constitutes the first step in the emergence of multicellularity in evolution, thereby allowing the differentiation of specialized cell types. In metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell fate specification has been implicated in cell-cell contact formation. However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and mesendoderm cell fate specification during zebrafish gastrulation. We show that long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an effective positive feedback loop between ppl cell-cell contact duration and cell fate specification. Finally, by using a combination of theoretical modeling and experimentation, we show that this feedback loop determines whether anterior axial mesendoderm cells become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal that the gene regulatory networks leading to cell fate diversification within the developing embryo are controlled by the interdependent activities of cell-cell signaling and contact formation."}],"_id":"961","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["570","590"],"title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","pubrep_id":"825","file":[{"file_name":"2017_Barone_thesis_final.docx","access_level":"closed","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":14497822,"file_id":"6205","relation":"source_file","date_created":"2019-04-05T08:36:52Z","date_updated":"2020-07-14T12:48:16Z","checksum":"242f88c87f2cf267bf05049fa26a687b"},{"file_id":"6206","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","date_created":"2019-04-05T08:36:52Z","checksum":"ba5b0613ed8bade73a409acdd880fb8a","file_name":"2017_Barone_thesis_.pdf","access_level":"open_access","creator":"dernst","file_size":14995941,"content_type":"application/pdf"}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"chicago":"Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_825.","mla":"Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_825.","short":"V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.","apa":"Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_825","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.","ama":"Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:10.15479/AT:ISTA:th_825"},"page":"109","date_published":"2017-03-01T00:00:00Z","publist_id":"6444","file_date_updated":"2020-07-14T12:48:16Z","acknowledgement":"Many people accompanied me during this trip: I would not have reached my destination nor \r\nenjoyed the travelling without them. First of all, thanks to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting and incredibly competent people and thanks for \r\nall the good science I witnessed and participated in. It has been a \r\nblast, an incredibly \r\nexciting one! Thanks to JLo, for teaching me how to master my pipettes and showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching me basically everything \r\nabout zebrafish and being always there to advice, sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing kicker matches, and Keisuke, for showing me the light, and to the three of them \r\ntogether for all the good laughs we\r\nhad. My start in Vienna would have been a lot more \r\ndifficult without you guys. Also it would not have been possible without Elena and Inês: \r\nthanks for helping setting up this lab and for the dinners in Gugging. Thanks to Martin, for \r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp, for the interest and \r\nadvice, and to Michael, for the Viennise take on things. Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel for the enthusiasm and the neverending energy and for all your \r\nhelp over the years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat. To Shayan, for being such a motivated student. To Matt, for helping out\r\nwith coding \r\nand for finding punk solutions to data analysis problems. Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla, Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments would have been much more difficult without your help. Special thanks to Katjia \r\nfor setting up an amazing imaging facility and for building the best team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith all the late sortings and for helping with all \r\nthe technical problems. Thanks to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald Janovjak for being a present and helpful committee member over the years \r\nand to Patrick Lemaire f\r\nor the helpful insight and extremely interesting discussion we had \r\nabout the project. Also, this journey would not have been the same without all the friends \r\nthat I met in Dresden and then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne, Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph, \r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled my days with \r\nfun and support. A special thank to my family, always close even if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William, e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe crazy life of a scientist, the living apart for\r\nso long, never knowing when things are going \r\nto happen. Thanks for being a great partner and my number one fan!","year":"2017","department":[{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1100"},{"relation":"part_of_dissertation","status":"public","id":"1537"},{"id":"1912","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"2926"},{"id":"3246","status":"public","relation":"part_of_dissertation"},{"id":"676","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"735"}]},"author":[{"first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa"}],"date_created":"2018-12-11T11:49:25Z","date_updated":"2023-09-27T14:16:45Z","publication_identifier":{"issn":["2663-337X"]},"month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/AT:ISTA:th_825","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"degree_awarded":"PhD"},{"file_date_updated":"2020-07-14T12:47:56Z","publist_id":"6933","year":"2017","publication_status":"published","publisher":"Cell Press","department":[{"_id":"SyCr"}],"author":[{"full_name":"Kennedy, Patrick","first_name":"Patrick","last_name":"Kennedy"},{"first_name":"Gemma","last_name":"Baron","full_name":"Baron, Gemma"},{"full_name":"Qiu, Bitao","last_name":"Qiu","first_name":"Bitao"},{"last_name":"Freitak","first_name":"Dalial","full_name":"Freitak, Dalial"},{"last_name":"Helantera","first_name":"Heikki","full_name":"Helantera, Heikki"},{"full_name":"Hunt, Edmund","last_name":"Hunt","first_name":"Edmund"},{"full_name":"Manfredini, Fabio","last_name":"Manfredini","first_name":"Fabio"},{"last_name":"O'Shea Wheller","first_name":"Thomas","full_name":"O'Shea Wheller, Thomas"},{"last_name":"Patalano","first_name":"Solenn","full_name":"Patalano, Solenn"},{"full_name":"Pull, Christopher","last_name":"Pull","first_name":"Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sasaki, Takao","last_name":"Sasaki","first_name":"Takao"},{"full_name":"Taylor, Daisy","first_name":"Daisy","last_name":"Taylor"},{"full_name":"Wyatt, Christopher","first_name":"Christopher","last_name":"Wyatt"},{"first_name":"Seirian","last_name":"Sumner","full_name":"Sumner, Seirian"}],"related_material":{"record":[{"id":"819","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:48:13Z","date_updated":"2023-09-27T14:15:15Z","volume":32,"month":"11","publication_identifier":{"issn":["01695347"]},"oa":1,"external_id":{"isi":["000413231900011"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.tree.2017.08.004","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Social insect societies are long-standing models for understanding social behaviour and evolution. Unlike other advanced biological societies (such as the multicellular body), the component parts of social insect societies can be easily deconstructed and manipulated. Recent methodological and theoretical innovations have exploited this trait to address an expanded range of biological questions. We illustrate the broadening range of biological insight coming from social insect biology with four examples. These new frontiers promote open-minded, interdisciplinary exploration of one of the richest and most complex of biological phenomena: sociality.","lang":"eng"}],"issue":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"734","status":"public","ddc":["570"],"title":"Deconstructing superorganisms and societies to address big questions in biology","intvolume":" 32","file":[{"checksum":"c8f49309ed9436201814fa7153d66a99","date_created":"2020-05-14T16:22:27Z","date_updated":"2020-07-14T12:47:56Z","file_id":"7842","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":15018382,"access_level":"open_access","file_name":"2017_TrendsEcology_Kennedy.pdf"}],"oa_version":"Submitted Version","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Trends in Ecology and Evolution","citation":{"short":"P. Kennedy, G. Baron, B. Qiu, D. Freitak, H. Helantera, E. Hunt, F. Manfredini, T. O’Shea Wheller, S. Patalano, C. Pull, T. Sasaki, D. Taylor, C. Wyatt, S. Sumner, Trends in Ecology and Evolution 32 (2017) 861–872.","mla":"Kennedy, Patrick, et al. “Deconstructing Superorganisms and Societies to Address Big Questions in Biology.” Trends in Ecology and Evolution, vol. 32, no. 11, Cell Press, 2017, pp. 861–72, doi:10.1016/j.tree.2017.08.004.","chicago":"Kennedy, Patrick, Gemma Baron, Bitao Qiu, Dalial Freitak, Heikki Helantera, Edmund Hunt, Fabio Manfredini, et al. “Deconstructing Superorganisms and Societies to Address Big Questions in Biology.” Trends in Ecology and Evolution. Cell Press, 2017. https://doi.org/10.1016/j.tree.2017.08.004.","ama":"Kennedy P, Baron G, Qiu B, et al. Deconstructing superorganisms and societies to address big questions in biology. Trends in Ecology and Evolution. 2017;32(11):861-872. doi:10.1016/j.tree.2017.08.004","apa":"Kennedy, P., Baron, G., Qiu, B., Freitak, D., Helantera, H., Hunt, E., … Sumner, S. (2017). Deconstructing superorganisms and societies to address big questions in biology. Trends in Ecology and Evolution. Cell Press. https://doi.org/10.1016/j.tree.2017.08.004","ieee":"P. Kennedy et al., “Deconstructing superorganisms and societies to address big questions in biology,” Trends in Ecology and Evolution, vol. 32, no. 11. Cell Press, pp. 861–872, 2017.","ista":"Kennedy P, Baron G, Qiu B, Freitak D, Helantera H, Hunt E, Manfredini F, O’Shea Wheller T, Patalano S, Pull C, Sasaki T, Taylor D, Wyatt C, Sumner S. 2017. Deconstructing superorganisms and societies to address big questions in biology. Trends in Ecology and Evolution. 32(11), 861–872."},"article_type":"original","page":"861 - 872","date_published":"2017-11-01T00:00:00Z"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. ","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"819","ddc":["576","577","578","579","590","592"],"status":"public","title":"Disease defence in garden ants","pubrep_id":"861","oa_version":"Published Version","file":[{"checksum":"4993cdd5382295758ecc3ecbd2a9aaff","date_updated":"2020-07-14T12:48:09Z","date_created":"2019-04-05T07:53:04Z","file_id":"6199","relation":"source_file","creator":"dernst","file_size":18580400,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"2017_Thesis_Pull.docx"},{"creator":"dernst","file_size":14400681,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_Thesis_Pull.pdf","checksum":"ee2e3ebb5b53c154c866f5b052b25153","date_updated":"2020-07-14T12:48:09Z","date_created":"2019-04-05T07:53:04Z","file_id":"6200","relation":"main_file"}],"day":"26","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Pull C. Disease defence in garden ants. 2017. doi:10.15479/AT:ISTA:th_861","ista":"Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria.","apa":"Pull, C. (2017). Disease defence in garden ants. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_861","ieee":"C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017.","mla":"Pull, Christopher. Disease Defence in Garden Ants. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_861.","short":"C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology Austria, 2017.","chicago":"Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_861."},"page":"122","date_published":"2017-09-26T00:00:00Z","file_date_updated":"2020-07-14T12:48:09Z","publist_id":"6830","acknowledgement":"ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely spoilt to work in a lab with such good resources and I must thank the wonderful Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help and keeping the lab up and running. You guys will probably be the most missed once I realise just how much work you have been saving me! For the same reason, I must say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you will be sorely missed now that I will have to take this task on myself. Of course, I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing and being a constant source of guidance and inspiration. You have given me the perfect balance of independence and supervision. I cannot thank you enough for creating such a great working environment and allowing me the freedom to follow my own research questions. I have had so many exceptional opportunities – attending and presenting at conferences all over the world, inviting me to write the ARE with you, going to workshops in Panama and Switzerland, and even organising our own PhD course – that I often think I must have had the best PhD in the world. You have taught me so much and made me a scientist. I sincerely hope we get the chance to work together again in the future. Thank you for everything. I must also thank my PhD Committee, Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout the duration of my PhD. ","year":"2017","publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Pull, Christopher","first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"616"},{"status":"public","relation":"part_of_dissertation","id":"806"},{"status":"public","relation":"part_of_dissertation","id":"734"},{"id":"732","status":"public","relation":"part_of_dissertation"}]},"date_created":"2018-12-11T11:48:40Z","date_updated":"2023-09-28T11:31:32Z","month":"09","publication_identifier":{"issn":["2663-337X"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:th_861","degree_awarded":"PhD","supervisor":[{"last_name":"Cremer","first_name":"Sylvia M","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia M"}],"language":[{"iso":"eng"}]},{"issue":"1","abstract":[{"lang":"eng","text":"Background: Social insects form densely crowded societies in environments with high pathogen loads, but have evolved collective defences that mitigate the impact of disease. However, colony-founding queens lack this protection and suffer high rates of mortality. The impact of pathogens may be exacerbated in species where queens found colonies together, as healthy individuals may contract pathogens from infectious co-founders. Therefore, we tested whether ant queens avoid founding colonies with pathogen-exposed conspecifics and how they might limit disease transmission from infectious individuals. Results: Using Lasius Niger queens and a naturally infecting fungal pathogen Metarhizium brunneum, we observed that queens were equally likely to found colonies with another pathogen-exposed or sham-treated queen. However, when one queen died, the surviving individual performed biting, burial and removal of the corpse. These undertaking behaviours were performed prophylactically, i.e. targeted equally towards non-infected and infected corpses, as well as carried out before infected corpses became infectious. Biting and burial reduced the risk of the queens contracting and dying from disease from an infectious corpse of a dead co-foundress. Conclusions: We show that co-founding ant queens express undertaking behaviours that, in mature colonies, are performed exclusively by workers. Such infection avoidance behaviours act before the queens can contract the disease and will therefore improve the overall chance of colony founding success in ant queens."}],"type":"journal_article","pubrep_id":"882","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5271","checksum":"3e24a2cfd48f49f7b3643d08d30fb480","date_updated":"2020-07-14T12:47:55Z","date_created":"2018-12-12T10:17:18Z","access_level":"open_access","file_name":"IST-2017-882-v1+1_12862_2017_Article_1062.pdf","content_type":"application/pdf","file_size":949857,"creator":"system"}],"_id":"732","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 17","status":"public","title":"Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour","ddc":["576","592"],"has_accepted_license":"1","article_processing_charge":"Yes","day":"13","scopus_import":"1","date_published":"2017-10-13T00:00:00Z","citation":{"ista":"Pull C, Cremer S. 2017. Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. BMC Evolutionary Biology. 17(1), 219.","ieee":"C. Pull and S. Cremer, “Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour,” BMC Evolutionary Biology, vol. 17, no. 1. BioMed Central, 2017.","apa":"Pull, C., & Cremer, S. (2017). Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/s12862-017-1062-4","ama":"Pull C, Cremer S. Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. BMC Evolutionary Biology. 2017;17(1). doi:10.1186/s12862-017-1062-4","chicago":"Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease by Performing Prophylactic Undertaking Behaviour.” BMC Evolutionary Biology. BioMed Central, 2017. https://doi.org/10.1186/s12862-017-1062-4.","mla":"Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease by Performing Prophylactic Undertaking Behaviour.” BMC Evolutionary Biology, vol. 17, no. 1, 219, BioMed Central, 2017, doi:10.1186/s12862-017-1062-4.","short":"C. Pull, S. Cremer, BMC Evolutionary Biology 17 (2017)."},"publication":"BMC Evolutionary Biology","article_type":"original","ec_funded":1,"publist_id":"6937","file_date_updated":"2020-07-14T12:47:55Z","article_number":"219","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"819"}]},"author":[{"full_name":"Pull, Christopher","first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"volume":17,"date_updated":"2023-09-28T11:31:32Z","date_created":"2018-12-11T11:48:12Z","year":"2017","department":[{"_id":"SyCr"}],"publisher":"BioMed Central","publication_status":"published","publication_identifier":{"issn":["14712148"]},"month":"10","doi":"10.1186/s12862-017-1062-4","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000412816800001"]},"oa":1,"project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"month":"09","publication_identifier":{"issn":["00928674"]},"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000411331800024"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2017.08.026","file_date_updated":"2020-07-14T12:47:55Z","publist_id":"6952","publication_status":"published","publisher":"Cell Press","department":[{"_id":"EdHa"}],"year":"2017","date_updated":"2023-09-28T11:34:17Z","date_created":"2018-12-11T11:48:10Z","volume":171,"author":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"first_name":"Colinda","last_name":"Scheele","full_name":"Scheele, Colinda"},{"last_name":"Moad","first_name":"Mohammad","full_name":"Moad, Mohammad"},{"full_name":"Drogo, Nicholas","first_name":"Nicholas","last_name":"Drogo"},{"first_name":"Rakesh","last_name":"Heer","full_name":"Heer, Rakesh"},{"full_name":"Sampogna, Rosemary","first_name":"Rosemary","last_name":"Sampogna"},{"full_name":"Van Rheenen, Jacco","first_name":"Jacco","last_name":"Van Rheenen"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"}],"scopus_import":"1","day":"21","has_accepted_license":"1","article_processing_charge":"No","page":"242 - 255","publication":"Cell","citation":{"ama":"Hannezo EB, Scheele C, Moad M, et al. A unifying theory of branching morphogenesis. Cell. 2017;171(1):242-255. doi:10.1016/j.cell.2017.08.026","ista":"Hannezo EB, Scheele C, Moad M, Drogo N, Heer R, Sampogna R, Van Rheenen J, Simons B. 2017. A unifying theory of branching morphogenesis. Cell. 171(1), 242–255.","ieee":"E. B. Hannezo et al., “A unifying theory of branching morphogenesis,” Cell, vol. 171, no. 1. Cell Press, pp. 242–255, 2017.","apa":"Hannezo, E. B., Scheele, C., Moad, M., Drogo, N., Heer, R., Sampogna, R., … Simons, B. (2017). A unifying theory of branching morphogenesis. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.08.026","mla":"Hannezo, Edouard B., et al. “A Unifying Theory of Branching Morphogenesis.” Cell, vol. 171, no. 1, Cell Press, 2017, pp. 242–55, doi:10.1016/j.cell.2017.08.026.","short":"E.B. Hannezo, C. Scheele, M. Moad, N. Drogo, R. Heer, R. Sampogna, J. Van Rheenen, B. Simons, Cell 171 (2017) 242–255.","chicago":"Hannezo, Edouard B, Colinda Scheele, Mohammad Moad, Nicholas Drogo, Rakesh Heer, Rosemary Sampogna, Jacco Van Rheenen, and Benjamin Simons. “A Unifying Theory of Branching Morphogenesis.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.08.026."},"date_published":"2017-09-21T00:00:00Z","type":"journal_article","abstract":[{"text":"The morphogenesis of branched organs remains a subject of abiding interest. Although much is known about the underlying signaling pathways, it remains unclear how macroscopic features of branched organs, including their size, network topology, and spatial patterning, are encoded. Here, we show that, in mouse mammary gland, kidney, and human prostate, these features can be explained quantitatively within a single unifying framework of branching and annihilating random walks. Based on quantitative analyses of large-scale organ reconstructions and proliferation kinetics measurements, we propose that morphogenesis follows from the proliferative activity of equipotent tips that stochastically branch and randomly explore their environment but compete neutrally for space, becoming proliferatively inactive when in proximity with neighboring ducts. These results show that complex branched epithelial structures develop as a self-organized process, reliant upon a strikingly simple but generic rule, without recourse to a rigid and deterministic sequence of genetically programmed events.","lang":"eng"}],"issue":"1","ddc":["539"],"status":"public","title":"A unifying theory of branching morphogenesis","intvolume":" 171","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"726","file":[{"content_type":"application/pdf","file_size":12670204,"creator":"system","file_name":"IST-2017-883-v1+1_PIIS0092867417309510.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:55Z","date_created":"2018-12-12T10:11:17Z","checksum":"7a036d93a9e2e597af9bb504d6133aca","relation":"main_file","file_id":"4870"}],"oa_version":"Published Version","pubrep_id":"883"},{"scopus_import":"1","day":"21","article_processing_charge":"No","publication":"Cell","citation":{"short":"J. Mueller, G. Szep, M. Nemethova, I. de Vries, A. Lieber, C. Winkler, K. Kruse, J. Small, C. Schmeiser, K. Keren, R. Hauschild, M.K. Sixt, Cell 171 (2017) 188–200.","mla":"Mueller, Jan, et al. “Load Adaptation of Lamellipodial Actin Networks.” Cell, vol. 171, no. 1, Cell Press, 2017, pp. 188–200, doi:10.1016/j.cell.2017.07.051.","chicago":"Mueller, Jan, Gregory Szep, Maria Nemethova, Ingrid de Vries, Arnon Lieber, Christoph Winkler, Karsten Kruse, et al. “Load Adaptation of Lamellipodial Actin Networks.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.07.051.","ama":"Mueller J, Szep G, Nemethova M, et al. Load adaptation of lamellipodial actin networks. Cell. 2017;171(1):188-200. doi:10.1016/j.cell.2017.07.051","apa":"Mueller, J., Szep, G., Nemethova, M., de Vries, I., Lieber, A., Winkler, C., … Sixt, M. K. (2017). Load adaptation of lamellipodial actin networks. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.07.051","ieee":"J. Mueller et al., “Load adaptation of lamellipodial actin networks,” Cell, vol. 171, no. 1. Cell Press, pp. 188–200, 2017.","ista":"Mueller J, Szep G, Nemethova M, de Vries I, Lieber A, Winkler C, Kruse K, Small J, Schmeiser C, Keren K, Hauschild R, Sixt MK. 2017. Load adaptation of lamellipodial actin networks. Cell. 171(1), 188–200."},"page":"188 - 200","date_published":"2017-09-21T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Actin filaments polymerizing against membranes power endocytosis, vesicular traffic, and cell motility. In vitro reconstitution studies suggest that the structure and the dynamics of actin networks respond to mechanical forces. We demonstrate that lamellipodial actin of migrating cells responds to mechanical load when membrane tension is modulated. In a steady state, migrating cell filaments assume the canonical dendritic geometry, defined by Arp2/3-generated 70° branch points. Increased tension triggers a dense network with a broadened range of angles, whereas decreased tension causes a shift to a sparse configuration dominated by filaments growing perpendicularly to the plasma membrane. We show that these responses emerge from the geometry of branched actin: when load per filament decreases, elongation speed increases and perpendicular filaments gradually outcompete others because they polymerize the shortest distance to the membrane, where they are protected from capping. This network-intrinsic geometrical adaptation mechanism tunes protrusive force in response to mechanical load."}],"issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"727","status":"public","title":"Load adaptation of lamellipodial actin networks","intvolume":" 171","oa_version":"None","month":"09","publication_identifier":{"issn":["00928674"]},"external_id":{"isi":["000411331800020"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"LS13-029","_id":"25AD6156-B435-11E9-9278-68D0E5697425","name":"Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments"},{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"doi":"10.1016/j.cell.2017.07.051","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"publist_id":"6951","ec_funded":1,"year":"2017","publication_status":"published","department":[{"_id":"MiSi"},{"_id":"Bio"}],"publisher":"Cell Press","author":[{"full_name":"Mueller, Jan","last_name":"Mueller","first_name":"Jan"},{"last_name":"Szep","first_name":"Gregory","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Gregory"},{"last_name":"Nemethova","first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","first_name":"Ingrid","full_name":"De Vries, Ingrid"},{"first_name":"Arnon","last_name":"Lieber","full_name":"Lieber, Arnon"},{"last_name":"Winkler","first_name":"Christoph","full_name":"Winkler, Christoph"},{"first_name":"Karsten","last_name":"Kruse","full_name":"Kruse, Karsten"},{"full_name":"Small, John","last_name":"Small","first_name":"John"},{"full_name":"Schmeiser, Christian","first_name":"Christian","last_name":"Schmeiser"},{"full_name":"Keren, Kinneret","first_name":"Kinneret","last_name":"Keren"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"date_updated":"2023-09-28T11:33:49Z","date_created":"2018-12-11T11:48:10Z","volume":171},{"month":"10","publication_identifier":{"issn":["09594388"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.conb.2017.08.001","quality_controlled":"1","isi":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"external_id":{"isi":["000416196400016"]},"publist_id":"6943","ec_funded":1,"date_created":"2018-12-11T11:48:11Z","date_updated":"2023-09-28T11:32:22Z","volume":46,"author":[{"full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaTk"}],"year":"2017","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2017-10-01T00:00:00Z","page":"120 - 126","publication":"Current Opinion in Neurobiology","citation":{"ieee":"C. Savin and G. Tkačik, “Maximum entropy models as a tool for building precise neural controls,” Current Opinion in Neurobiology, vol. 46. Elsevier, pp. 120–126, 2017.","apa":"Savin, C., & Tkačik, G. (2017). Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.08.001","ista":"Savin C, Tkačik G. 2017. Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology. 46, 120–126.","ama":"Savin C, Tkačik G. Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology. 2017;46:120-126. doi:10.1016/j.conb.2017.08.001","chicago":"Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” Current Opinion in Neurobiology. Elsevier, 2017. https://doi.org/10.1016/j.conb.2017.08.001.","short":"C. Savin, G. Tkačik, Current Opinion in Neurobiology 46 (2017) 120–126.","mla":"Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” Current Opinion in Neurobiology, vol. 46, Elsevier, 2017, pp. 120–26, doi:10.1016/j.conb.2017.08.001."},"abstract":[{"lang":"eng","text":"Neural responses are highly structured, with population activity restricted to a small subset of the astronomical range of possible activity patterns. Characterizing these statistical regularities is important for understanding circuit computation, but challenging in practice. Here we review recent approaches based on the maximum entropy principle used for quantifying collective behavior in neural activity. We highlight recent models that capture population-level statistics of neural data, yielding insights into the organization of the neural code and its biological substrate. Furthermore, the MaxEnt framework provides a general recipe for constructing surrogate ensembles that preserve aspects of the data, but are otherwise maximally unstructured. This idea can be used to generate a hierarchy of controls against which rigorous statistical tests are possible."}],"type":"journal_article","oa_version":"None","title":"Maximum entropy models as a tool for building precise neural controls","status":"public","intvolume":" 46","_id":"730","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"external_id":{"isi":["000411581800019"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.cub.2017.07.010","language":[{"iso":"eng"}],"publication_identifier":{"issn":["09609822"]},"month":"09","year":"2017","department":[{"_id":"CaHe"}],"publisher":"Cell Press","publication_status":"published","author":[{"first_name":"Chii","last_name":"Chan","full_name":"Chan, Chii"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Hiiragi, Takashi","first_name":"Takashi","last_name":"Hiiragi"}],"volume":27,"date_created":"2018-12-11T11:48:11Z","date_updated":"2023-09-28T11:33:21Z","publist_id":"6949","citation":{"chicago":"Chan, Chii, Carl-Philipp J Heisenberg, and Takashi Hiiragi. “Coordination of Morphogenesis and Cell Fate Specification in Development.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.07.010.","mla":"Chan, Chii, et al. “Coordination of Morphogenesis and Cell Fate Specification in Development.” Current Biology, vol. 27, no. 18, Cell Press, 2017, pp. R1024–35, doi:10.1016/j.cub.2017.07.010.","short":"C. Chan, C.-P.J. Heisenberg, T. Hiiragi, Current Biology 27 (2017) R1024–R1035.","ista":"Chan C, Heisenberg C-PJ, Hiiragi T. 2017. Coordination of morphogenesis and cell fate specification in development. Current Biology. 27(18), R1024–R1035.","apa":"Chan, C., Heisenberg, C.-P. J., & Hiiragi, T. (2017). Coordination of morphogenesis and cell fate specification in development. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.07.010","ieee":"C. Chan, C.-P. J. Heisenberg, and T. Hiiragi, “Coordination of morphogenesis and cell fate specification in development,” Current Biology, vol. 27, no. 18. Cell Press, pp. R1024–R1035, 2017.","ama":"Chan C, Heisenberg C-PJ, Hiiragi T. Coordination of morphogenesis and cell fate specification in development. Current Biology. 2017;27(18):R1024-R1035. doi:10.1016/j.cub.2017.07.010"},"publication":"Current Biology","page":"R1024 - R1035","date_published":"2017-09-18T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"18","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"728","intvolume":" 27","title":"Coordination of morphogenesis and cell fate specification in development","status":"public","oa_version":"None","type":"journal_article","issue":"18","abstract":[{"lang":"eng","text":"During animal development, cell-fate-specific changes in gene expression can modify the material properties of a tissue and drive tissue morphogenesis. While mechanistic insights into the genetic control of tissue-shaping events are beginning to emerge, how tissue morphogenesis and mechanics can reciprocally impact cell-fate specification remains relatively unexplored. Here we review recent findings reporting how multicellular morphogenetic events and their underlying mechanical forces can feed back into gene regulatory pathways to specify cell fate. We further discuss emerging techniques that allow for the direct measurement and manipulation of mechanical signals in vivo, offering unprecedented access to study mechanotransduction during development. Examination of the mechanical control of cell fate during tissue morphogenesis will pave the way to an integrated understanding of the design principles that underlie robust tissue patterning in embryonic development."}]},{"scopus_import":"1","day":"01","article_processing_charge":"No","page":"559 - 560","publication":"Developmental Cell","citation":{"ista":"Spiro ZP, Heisenberg C-PJ. 2017. Regeneration tensed up polyploidy takes the lead. Developmental Cell. 42(6), 559–560.","ieee":"Z. P. Spiro and C.-P. J. Heisenberg, “Regeneration tensed up polyploidy takes the lead,” Developmental Cell, vol. 42, no. 6. Cell Press, pp. 559–560, 2017.","apa":"Spiro, Z. P., & Heisenberg, C.-P. J. (2017). Regeneration tensed up polyploidy takes the lead. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.09.008","ama":"Spiro ZP, Heisenberg C-PJ. Regeneration tensed up polyploidy takes the lead. Developmental Cell. 2017;42(6):559-560. doi:10.1016/j.devcel.2017.09.008","chicago":"Spiro, Zoltan P, and Carl-Philipp J Heisenberg. “Regeneration Tensed up Polyploidy Takes the Lead.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.008.","mla":"Spiro, Zoltan P., and Carl-Philipp J. Heisenberg. “Regeneration Tensed up Polyploidy Takes the Lead.” Developmental Cell, vol. 42, no. 6, Cell Press, 2017, pp. 559–60, doi:10.1016/j.devcel.2017.09.008.","short":"Z.P. Spiro, C.-P.J. Heisenberg, Developmental Cell 42 (2017) 559–560."},"date_published":"2017-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"The cellular mechanisms allowing tissues to efficiently regenerate are not fully understood. In this issue of Developmental Cell, Cao et al. (2017)) discover that during zebrafish heart regeneration, epicardial cells at the leading edge of regenerating tissue undergo endoreplication, possibly due to increased tissue tension, thereby boosting their regenerative capacity.","lang":"eng"}],"issue":"6","status":"public","title":"Regeneration tensed up polyploidy takes the lead","intvolume":" 42","_id":"729","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","month":"01","publication_identifier":{"issn":["15345807"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000411582800003"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2017.09.008","publist_id":"6948","publication_status":"published","publisher":"Cell Press","department":[{"_id":"CaHe"}],"year":"2017","date_created":"2018-12-11T11:48:11Z","date_updated":"2023-09-28T11:32:49Z","volume":42,"author":[{"id":"426AD026-F248-11E8-B48F-1D18A9856A87","last_name":"Spiro","first_name":"Zoltan P","full_name":"Spiro, Zoltan P"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}]},{"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"American Physical Society","year":"2017","date_created":"2018-12-11T11:47:06Z","date_updated":"2023-10-10T13:29:38Z","volume":96,"author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele"}],"article_number":"060401","publist_id":"7266","ec_funded":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1707.00320","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.96.060401","month":"12","publication_identifier":{"issn":["2470-0045"]},"title":"Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes","status":"public","intvolume":" 96","_id":"548","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","alternative_title":["Rapid Communications"],"type":"journal_article","abstract":[{"text":"In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region.","lang":"eng"}],"issue":"6","publication":"Physical Review E","citation":{"mla":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E, vol. 96, no. 6, 060401, American Physical Society, 2017, doi:10.1103/PhysRevE.96.060401.","short":"D. De Martino, Physical Review E 96 (2017).","chicago":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.96.060401.","ama":"De Martino D. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 2017;96(6). doi:10.1103/PhysRevE.96.060401","ista":"De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401.","ieee":"D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” Physical Review E, vol. 96, no. 6. American Physical Society, 2017.","apa":"De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.96.060401"},"date_published":"2017-12-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No"},{"oa_version":"Submitted Version","intvolume":" 95","title":"Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"673","issue":"5","abstract":[{"text":"We present a numerical study of wavy supercritical cylindrical Couette flow between counter-rotating cylinders in which the wavy pattern propagates either prograde with the inner cylinder or retrograde opposite the rotation of the inner cylinder. The wave propagation reversals from prograde to retrograde and vice versa occur at distinct values of the inner cylinder Reynolds number when the associated frequency of the wavy instability vanishes. The reversal occurs for both twofold and threefold symmetric wavy vortices. Moreover, the wave propagation reversal only occurs for sufficiently strong counter-rotation. The flow pattern reversal appears to be intrinsic in the system as either periodic boundary conditions or fixed end wall boundary conditions for different system sizes always result in the wave propagation reversal. We present a detailed bifurcation sequence and parameter space diagram with respect to retrograde behavior of wavy flows. The retrograde propagation of the instability occurs when the inner Reynolds number is about two times the outer Reynolds number. The mechanism for the retrograde propagation is associated with the inviscidly unstable region near the inner cylinder and the direction of the global average azimuthal velocity. Flow dynamics, spatio-temporal behavior, global mean angular velocity, and torque of the flow with the wavy pattern are explored.","lang":"eng"}],"type":"journal_article","date_published":"2017-05-10T00:00:00Z","citation":{"ieee":"S. Altmeyer and R. Lueptow, “Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow,” Physical Review E, vol. 95, no. 5. American Physical Society, 2017.","apa":"Altmeyer, S., & Lueptow, R. (2017). Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.95.053103","ista":"Altmeyer S, Lueptow R. 2017. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. 95(5), 053103.","ama":"Altmeyer S, Lueptow R. Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow. Physical Review E. 2017;95(5). doi:10.1103/PhysRevE.95.053103","chicago":"Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” Physical Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.95.053103.","short":"S. Altmeyer, R. Lueptow, Physical Review E 95 (2017).","mla":"Altmeyer, Sebastian, and Richard Lueptow. “Wave Propagation Reversal for Wavy Vortices in Wide Gap Counter Rotating Cylindrical Couette Flow.” Physical Review E, vol. 95, no. 5, 053103, American Physical Society, 2017, doi:10.1103/PhysRevE.95.053103."},"publication":"Physical Review E","article_processing_charge":"No","day":"10","scopus_import":"1","volume":95,"date_created":"2018-12-11T11:47:50Z","date_updated":"2023-10-10T13:30:03Z","author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","first_name":"Sebastian","last_name":"Altmeyer","full_name":"Altmeyer, Sebastian"},{"full_name":"Lueptow, Richard","first_name":"Richard","last_name":"Lueptow"}],"department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","year":"2017","publist_id":"7049","article_number":"053103","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.95.053103","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/physics/0505164.pdf"}],"publication_identifier":{"issn":["2470-0045"]},"month":"05"},{"language":[{"iso":"eng"}],"doi":"10.30757/ALEA.v14-17","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://alea.impa.br/articles/v14/14-17.pdf"}],"oa":1,"month":"03","volume":9,"date_updated":"2023-10-10T13:10:32Z","date_created":"2018-12-11T11:46:31Z","author":[{"last_name":"Ferrari","first_name":"Patrik","full_name":"Ferrari, Patrik"},{"full_name":"Nejjar, Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","last_name":"Nejjar","first_name":"Peter"}],"publisher":"Instituto Nacional de Matematica Pura e Aplicada","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"publication_status":"published","year":"2017","ec_funded":1,"publist_id":"7376","date_published":"2017-03-23T00:00:00Z","page":"299 - 325","article_type":"original","citation":{"chicago":"Ferrari, Patrik, and Peter Nejjar. “Fluctuations of the Competition Interface in Presence of Shocks.” Revista Latino-Americana de Probabilidade e Estatística. Instituto Nacional de Matematica Pura e Aplicada, 2017. https://doi.org/10.30757/ALEA.v14-17.","short":"P. Ferrari, P. Nejjar, Revista Latino-Americana de Probabilidade e Estatística 9 (2017) 299–325.","mla":"Ferrari, Patrik, and Peter Nejjar. “Fluctuations of the Competition Interface in Presence of Shocks.” Revista Latino-Americana de Probabilidade e Estatística, vol. 9, Instituto Nacional de Matematica Pura e Aplicada, 2017, pp. 299–325, doi:10.30757/ALEA.v14-17.","apa":"Ferrari, P., & Nejjar, P. (2017). Fluctuations of the competition interface in presence of shocks. Revista Latino-Americana de Probabilidade e Estatística. Instituto Nacional de Matematica Pura e Aplicada. https://doi.org/10.30757/ALEA.v14-17","ieee":"P. Ferrari and P. Nejjar, “Fluctuations of the competition interface in presence of shocks,” Revista Latino-Americana de Probabilidade e Estatística, vol. 9. Instituto Nacional de Matematica Pura e Aplicada, pp. 299–325, 2017.","ista":"Ferrari P, Nejjar P. 2017. Fluctuations of the competition interface in presence of shocks. Revista Latino-Americana de Probabilidade e Estatística. 9, 299–325.","ama":"Ferrari P, Nejjar P. Fluctuations of the competition interface in presence of shocks. Revista Latino-Americana de Probabilidade e Estatística. 2017;9:299-325. doi:10.30757/ALEA.v14-17"},"publication":"Revista Latino-Americana de Probabilidade e Estatística","article_processing_charge":"No","day":"23","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 9","title":"Fluctuations of the competition interface in presence of shocks","status":"public","_id":"447","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We consider last passage percolation (LPP) models with exponentially distributed random variables, which are linked to the totally asymmetric simple exclusion process (TASEP). The competition interface for LPP was introduced and studied in Ferrari and Pimentel (2005a) for cases where the corresponding exclusion process had a rarefaction fan. Here we consider situations with a shock and determine the law of the fluctuations of the competition interface around its deter- ministic law of large number position. We also study the multipoint distribution of the LPP around the shock, extending our one-point result of Ferrari and Nejjar (2015).","lang":"eng"}],"type":"journal_article"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:47:04Z","publist_id":"7254","date_updated":"2023-10-10T14:06:18Z","date_created":"2018-12-11T11:47:10Z","volume":58,"author":[{"last_name":"Nickells","first_name":"Robert","full_name":"Nickells, Robert"},{"last_name":"Schmitt","first_name":"Heather","full_name":"Schmitt, Heather"},{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","first_name":"Margaret E","last_name":"Maes","full_name":"Maes, Margaret E"},{"full_name":"Schlamp, Cassandra","last_name":"Schlamp","first_name":"Cassandra"}],"publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Association for Research in Vision and Ophthalmology","year":"2017","month":"12","publication_identifier":{"issn":["01460404"]},"language":[{"iso":"eng"}],"doi":"10.1167/iovs.17-22634","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"abstract":[{"text":"PURPOSE. Gene therapy of retinal ganglion cells (RGCs) has promise as a powerful therapeutic for the rescue and regeneration of these cells after optic nerve damage. However, early after damage, RGCs undergo atrophic changes, including gene silencing. It is not known if these changes will deleteriously affect transduction and transgene expression, or if the therapeutic protein can influence reactivation of the endogenous genome. METHODS. Double-transgenic mice carrying a Rosa26-(LoxP)-tdTomato reporter, and a mutant allele for the proapoptotic Bax gene were reared. The Bax mutant blocks apoptosis, but RGCs still exhibit nuclear atrophy and gene silencing. At times ranging from 1 hour to 4 weeks after optic nerve crush (ONC), eyes received an intravitreal injection of AAV2 virus carrying the Cre recombinase. Successful transduction was monitored by expression of the tdTomato reporter. Immunostaining was used to localize tdTomato expression in select cell types. RESULTS. Successful transduction of RGCs was achieved at all time points after ONC using AAV2 expressing Cre from the phosphoglycerate kinase (Pgk) promoter, but not the CMV promoter. ONC promoted an increase in the transduction of cell types in the inner nuclear layer, including Müller cells and rod bipolar neurons. There was minimal evidence of transduction of amacrine cells and astrocytes in the inner retina or optic nerve. CONCLUSIONS. Damaged RGCs can be transduced and at least some endogenous genes can be subsequently activated. Optic nerve damage may change retinal architecture to allow greater penetration of an AAV2 virus to transduce several additional cell types in the inner nuclear layer.","lang":"eng"}],"issue":"14","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5311","checksum":"d7a7b6f1fa9211a04e5e65634a0265d9","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T10:17:53Z","access_level":"open_access","file_name":"IST-2018-920-v1+1_i1552-5783-58-14-6091.pdf","content_type":"application/pdf","file_size":2955559,"creator":"system"}],"pubrep_id":"920","status":"public","title":"AAV2 mediated transduction of the mouse retina after optic nerve injury","ddc":["576"],"intvolume":" 58","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"557","day":"14","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2017-12-14T00:00:00Z","page":"6091 - 6104","publication":"Investigative Ophthalmology and Visual Science","citation":{"short":"R. Nickells, H. Schmitt, M.E. Maes, C. Schlamp, Investigative Ophthalmology and Visual Science 58 (2017) 6091–6104.","mla":"Nickells, Robert, et al. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” Investigative Ophthalmology and Visual Science, vol. 58, no. 14, Association for Research in Vision and Ophthalmology, 2017, pp. 6091–104, doi:10.1167/iovs.17-22634.","chicago":"Nickells, Robert, Heather Schmitt, Margaret E Maes, and Cassandra Schlamp. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology, 2017. https://doi.org/10.1167/iovs.17-22634.","ama":"Nickells R, Schmitt H, Maes ME, Schlamp C. AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. 2017;58(14):6091-6104. doi:10.1167/iovs.17-22634","ieee":"R. Nickells, H. Schmitt, M. E. Maes, and C. Schlamp, “AAV2 mediated transduction of the mouse retina after optic nerve injury,” Investigative Ophthalmology and Visual Science, vol. 58, no. 14. Association for Research in Vision and Ophthalmology, pp. 6091–6104, 2017.","apa":"Nickells, R., Schmitt, H., Maes, M. E., & Schlamp, C. (2017). AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. Association for Research in Vision and Ophthalmology. https://doi.org/10.1167/iovs.17-22634","ista":"Nickells R, Schmitt H, Maes ME, Schlamp C. 2017. AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. 58(14), 6091–6104."}},{"ec_funded":1,"publist_id":"6401","article_number":"235301","author":[{"first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"full_name":"Deuchert, Andreas","first_name":"Andreas","last_name":"Deuchert","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"}],"volume":119,"date_updated":"2023-10-10T13:31:54Z","date_created":"2018-12-11T11:49:36Z","year":"2017","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"publisher":"American Physical Society","publication_status":"published","publication_identifier":{"issn":["0031-9007"]},"month":"12","doi":"10.1103/PhysRevLett.119.235301","language":[{"iso":"eng"}],"external_id":{"isi":["000417132100007"],"arxiv":["1705.05162"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05162"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"issue":"23","abstract":[{"text":"Recently it was shown that molecules rotating in superfluid helium can be described in terms of the angulon quasiparticles (Phys. Rev. Lett. 118, 095301 (2017)). Here we demonstrate that in the experimentally realized regime the angulon can be seen as a point charge on a 2-sphere interacting with a gauge field of a non-abelian magnetic monopole. Unlike in several other settings, the gauge fields of the angulon problem emerge in the real coordinate space, as opposed to the momentum space or some effective parameter space. Furthermore, we find a topological transition associated with making the monopole abelian, which takes place in the vicinity of the previously reported angulon instabilities. These results pave the way for studying topological phenomena in experiments on molecules trapped in superfluid helium nanodroplets, as well as on other realizations of orbital impurity problems.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"997","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 119","status":"public","title":"Emergence of non-abelian magnetic monopoles in a quantum impurity problem","article_processing_charge":"No","day":"06","scopus_import":"1","date_published":"2017-12-06T00:00:00Z","citation":{"chicago":"Yakaboylu, Enderalp, Andreas Deuchert, and Mikhail Lemeshko. “Emergence of Non-Abelian Magnetic Monopoles in a Quantum Impurity Problem.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.235301.","mla":"Yakaboylu, Enderalp, et al. “Emergence of Non-Abelian Magnetic Monopoles in a Quantum Impurity Problem.” Physical Review Letters, vol. 119, no. 23, 235301, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.235301.","short":"E. Yakaboylu, A. Deuchert, M. Lemeshko, Physical Review Letters 119 (2017).","ista":"Yakaboylu E, Deuchert A, Lemeshko M. 2017. Emergence of non-abelian magnetic monopoles in a quantum impurity problem. Physical Review Letters. 119(23), 235301.","ieee":"E. Yakaboylu, A. Deuchert, and M. Lemeshko, “Emergence of non-abelian magnetic monopoles in a quantum impurity problem,” Physical Review Letters, vol. 119, no. 23. American Physical Society, 2017.","apa":"Yakaboylu, E., Deuchert, A., & Lemeshko, M. (2017). Emergence of non-abelian magnetic monopoles in a quantum impurity problem. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.235301","ama":"Yakaboylu E, Deuchert A, Lemeshko M. Emergence of non-abelian magnetic monopoles in a quantum impurity problem. Physical Review Letters. 2017;119(23). doi:10.1103/PhysRevLett.119.235301"},"publication":"Physical Review Letters","article_type":"original"},{"quality_controlled":"1","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"external_id":{"arxiv":["1705.04258"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"London, United Kingdom","start_date":"2017-09-04","end_date":"2017-09-07","name":"BMVC: British Machine Vision Conference"},"doi":"10.5244/c.31.85","month":"09","publication_identifier":{"eisbn":["190172560X"]},"publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"BMVA Press","year":"2017","date_updated":"2023-10-16T10:04:02Z","date_created":"2018-12-11T11:49:09Z","author":[{"full_name":"Royer, Amélie","last_name":"Royer","first_name":"Amélie","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8390"}]},"file_date_updated":"2020-08-10T07:14:33Z","ec_funded":1,"publist_id":"6532","page":"85.1-85.12","citation":{"ista":"Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization. BMVC: British Machine Vision Conference, 85.1-85.12.","ieee":"A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,” presented at the BMVC: British Machine Vision Conference, London, United Kingdom, 2017, p. 85.1-85.12.","apa":"Royer, A., Kolesnikov, A., & Lampert, C. (2017). Probabilistic image colorization (p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London, United Kingdom: BMVA Press. https://doi.org/10.5244/c.31.85","ama":"Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA Press; 2017:85.1-85.12. doi:10.5244/c.31.85","chicago":"Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic Image Colorization,” 85.1-85.12. BMVA Press, 2017. https://doi.org/10.5244/c.31.85.","mla":"Royer, Amélie, et al. Probabilistic Image Colorization. BMVA Press, 2017, p. 85.1-85.12, doi:10.5244/c.31.85.","short":"A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12."},"date_published":"2017-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","status":"public","title":"Probabilistic image colorization","ddc":["000"],"_id":"911","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"success":1,"date_created":"2020-08-10T07:14:33Z","date_updated":"2020-08-10T07:14:33Z","relation":"main_file","file_id":"8224","content_type":"application/pdf","file_size":1625363,"creator":"dernst","access_level":"open_access","file_name":"2017_BMVC_Royer.pdf"}],"type":"conference","abstract":[{"text":"We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset.","lang":"eng"}]},{"date_published":"2017-08-01T00:00:00Z","publication":"Clinical Nutrition","citation":{"short":"W. Sun, M.-Z. Zhai, D. Li, Y. Zhou, N. Chen, M. Guo, S. Zhou, Clinical Nutrition 36 (2017) 1136–1142.","mla":"Sun, Wuping, et al. “Comparison of the Effects of Nicotinic Acid and Nicotinamide Degradation on Plasma Betaine and Choline Levels.” Clinical Nutrition, vol. 36, no. 4, Elsevier, 2017, pp. 1136–42, doi:10.1016/j.clnu.2016.07.016.","chicago":"Sun, Wuping, Ming-Zhu Zhai, Da Li, Yiming Zhou, Nana Chen, Ming Guo, and Shisheng Zhou. “Comparison of the Effects of Nicotinic Acid and Nicotinamide Degradation on Plasma Betaine and Choline Levels.” Clinical Nutrition. Elsevier, 2017. https://doi.org/10.1016/j.clnu.2016.07.016.","ama":"Sun W, Zhai M-Z, Li D, et al. Comparison of the effects of nicotinic acid and nicotinamide degradation on plasma betaine and choline levels. Clinical Nutrition. 2017;36(4):1136-1142. doi:10.1016/j.clnu.2016.07.016","ieee":"W. Sun et al., “Comparison of the effects of nicotinic acid and nicotinamide degradation on plasma betaine and choline levels,” Clinical Nutrition, vol. 36, no. 4. Elsevier, pp. 1136–1142, 2017.","apa":"Sun, W., Zhai, M.-Z., Li, D., Zhou, Y., Chen, N., Guo, M., & Zhou, S. (2017). Comparison of the effects of nicotinic acid and nicotinamide degradation on plasma betaine and choline levels. Clinical Nutrition. Elsevier. https://doi.org/10.1016/j.clnu.2016.07.016","ista":"Sun W, Zhai M-Z, Li D, Zhou Y, Chen N, Guo M, Zhou S. 2017. Comparison of the effects of nicotinic acid and nicotinamide degradation on plasma betaine and choline levels. Clinical Nutrition. 36(4), 1136–1142."},"page":"1136-1142","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"None","_id":"1146","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Comparison of the effects of nicotinic acid and nicotinamide degradation on plasma betaine and choline levels","status":"public","intvolume":" 36","abstract":[{"lang":"eng","text":"Aim: The present study was to compare the effects of nicotinic acid and nicotinamide on the plasma methyl donors, choline and betaine. Methods: Thirty adult subjects were randomly divided into three groups of equal size, and orally received purified water (C group), nicotinic acid (300 mg, NA group) or nicotinamide (300 mg, NM group). Plasma nicotinamide, N 1-methylnicotinamide, homocysteine, betaine and choline levels before and 1.5-h and 3-h post-dosing, plasma normetanephrine and metanephrine concentrations at 3-h post-dosing, and the urinary excretion of N 1-methyl-2-pyridone-5-carboxamide during the test period were examined. Results: The level of 3-h plasma nicotinamide, N 1-methylnicotinamide, homocysteine, the urinary excretion of N 1-methyl-2-pyridone-5-carboxamide and pulse pressure (PP) in the NM group was 221%, 3972%, 61%, 1728% and 21.2% higher than that of the control group (P < 0.01, except homocysteine and PP P < 0.05), while the 3-h plasma betaine, normetanephrine and metanephrine level in the NM group was 24.4%, 9.4% and 11.7% lower (P < 0.05, except betaine P < 0.01), without significant difference in choline levels. Similar but less pronounced changes were observed in the NA group, with a lower level of 3-h plasma N 1-methylnicotinamide (1.90 ± 0.20 μmol/l vs. 3.62 ± 0.27 μmol/l, P < 0.01) and homocysteine (12.85 ± 1.39 μmol/l vs. 18.08 ± 1.02 μmol/l, P < 0.05) but a higher level of betaine (27.44 ± 0.71 μmol/l vs. 23.52 ± 0.61 μmol/l, P < 0.05) than that of the NM group. Conclusion: The degradation of nicotinamide consumes more betaine than that of nicotinic acid at identical doses. This difference should be taken into consideration in niacin fortification. © 2016 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism."}],"issue":"4","type":"journal_article","doi":"10.1016/j.clnu.2016.07.016","language":[{"iso":"eng"}],"quality_controlled":"1","month":"08","publication_identifier":{"issn":["0261-5614"]},"author":[{"full_name":"Sun, Wuping","last_name":"Sun","first_name":"Wuping"},{"full_name":"Zhai, Ming-Zhu","id":"34009CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Zhai","first_name":"Ming-Zhu"},{"last_name":"Li","first_name":"Da","full_name":"Li, Da"},{"last_name":"Zhou","first_name":"Yiming","full_name":"Zhou, Yiming"},{"full_name":"Chen, Nana","first_name":"Nana","last_name":"Chen"},{"full_name":"Guo, Ming","first_name":"Ming","last_name":"Guo"},{"last_name":"Zhou","first_name":"Shisheng","full_name":"Zhou, Shisheng"}],"date_updated":"2023-10-16T11:09:39Z","date_created":"2018-12-11T11:50:24Z","volume":36,"year":"2017","acknowledgement":"We thank all the participants for their contribution to this study and volunteers from the Nursing School of Dalian University for their supporting to collect blood and urine samples of the participants. We also thank Dr. Yasunori Takayama from National Institute for Physiological Sciences of Japan for his kind help.","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Elsevier","publist_id":"6212"},{"type":"book_chapter","abstract":[{"text":"The advent of high-throughput technologies and the concurrent advances in information sciences have led to a data revolution in biology. This revolution is most significant in molecular biology, with an increase in the number and scale of the “omics” projects over the last decade. Genomics projects, for example, have produced impressive advances in our knowledge of the information concealed into genomes, from the many genes that encode for the proteins that are responsible for most if not all cellular functions, to the noncoding regions that are now known to provide regulatory functions. Proteomics initiatives help to decipher the role of post-translation modifications on the protein structures and provide maps of protein-protein interactions, while functional genomics is the field that attempts to make use of the data produced by these projects to understand protein functions. The biggest challenge today is to assimilate the wealth of information provided by these initiatives into a conceptual framework that will help us decipher life. For example, the current views of the relationship between protein structure and function remain fragmented. We know of their sequences, more and more about their structures, we have information on their biological activities, but we have difficulties connecting this dotted line into an informed whole. We lack the experimental and computational tools for directly studying protein structure, function, and dynamics at the molecular and supra-molecular levels. In this chapter, we review some of the current developments in building the computational tools that are needed, focusing on the role that geometry and topology play in these efforts. One of our goals is to raise the general awareness about the importance of geometric methods in elucidating the mysterious foundations of our very existence. Another goal is the broadening of what we consider a geometric algorithm. There is plenty of valuable no-man’s-land between combinatorial and numerical algorithms, and it seems opportune to explore this land with a computational-geometric frame of mind.","lang":"eng"}],"publist_id":"7970","status":"public","title":"Computational topology for structural molecular biology","publication_status":"published","department":[{"_id":"HeEd"}],"editor":[{"last_name":"Toth","first_name":"Csaba","full_name":"Toth, Csaba"},{"full_name":"O'Rourke, Joseph","first_name":"Joseph","last_name":"O'Rourke"},{"last_name":"Goodman","first_name":"Jacob","full_name":"Goodman, Jacob"}],"publisher":"Taylor & Francis","_id":"84","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-16T11:15:22Z","date_created":"2018-12-11T11:44:32Z","oa_version":"None","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"first_name":"Patrice","last_name":"Koehl","full_name":"Koehl, Patrice"}],"series_title":"Handbook of Discrete and Computational Geometry","scopus_import":"1","day":"09","month":"11","article_processing_charge":"No","publication_identifier":{"eisbn":["9781498711425"]},"quality_controlled":"1","page":"1709 - 1735","publication":"Handbook of Discrete and Computational Geometry, Third Edition","citation":{"mla":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” Handbook of Discrete and Computational Geometry, Third Edition, edited by Csaba Toth et al., Taylor & Francis, 2017, pp. 1709–35, doi:10.1201/9781315119601.","short":"H. Edelsbrunner, P. Koehl, in:, C. Toth, J. O’Rourke, J. Goodman (Eds.), Handbook of Discrete and Computational Geometry, Third Edition, Taylor & Francis, 2017, pp. 1709–1735.","chicago":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” In Handbook of Discrete and Computational Geometry, Third Edition, edited by Csaba Toth, Joseph O’Rourke, and Jacob Goodman, 1709–35. Handbook of Discrete and Computational Geometry. Taylor & Francis, 2017. https://doi.org/10.1201/9781315119601.","ama":"Edelsbrunner H, Koehl P. Computational topology for structural molecular biology. In: Toth C, O’Rourke J, Goodman J, eds. Handbook of Discrete and Computational Geometry, Third Edition. Handbook of Discrete and Computational Geometry. Taylor & Francis; 2017:1709-1735. doi:10.1201/9781315119601","ista":"Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular biology. In: Handbook of Discrete and Computational Geometry, Third Edition. , 1709–1735.","ieee":"H. Edelsbrunner and P. Koehl, “Computational topology for structural molecular biology,” in Handbook of Discrete and Computational Geometry, Third Edition, C. Toth, J. O’Rourke, and J. Goodman, Eds. Taylor & Francis, 2017, pp. 1709–1735.","apa":"Edelsbrunner, H., & Koehl, P. (2017). Computational topology for structural molecular biology. In C. Toth, J. O’Rourke, & J. Goodman (Eds.), Handbook of Discrete and Computational Geometry, Third Edition (pp. 1709–1735). Taylor & Francis. https://doi.org/10.1201/9781315119601"},"language":[{"iso":"eng"}],"doi":"10.1201/9781315119601","date_published":"2017-11-09T00:00:00Z"},{"issue":"43","abstract":[{"text":"Beige adipocytes are a new type of recruitable brownish adipocytes, with highly mitochondrial membrane uncoupling protein 1 expression and thermogenesis. Beige adipocytes were found among white adipocytes, especially in subcutaneous white adipose tissue (sWAT). Therefore, beige adipocytes may be involved in the regulation of energy metabolism and fat deposition. Transient receptor potential melastatin 8 (TRPM8), a Ca2+-permeable non-selective cation channel, plays vital roles in the regulation of various cellular functions. It has been reported that TRPM8 activation enhanced the thermogenic function of brown adiposytes. However, the involvement of TRPM8 in the thermogenic function of WAT remains unexplored. Our data revealed that TRPM8 was expressed in mouse white adipocytes at mRNA, protein and functional levels. The mRNA expression of Trpm8 was significantly increased in the differentiated white adipocytes than pre-adipocytes. Moreover, activation of TRPM8 by menthol enhanced the expression of thermogenic genes in cultured white aidpocytes. And menthol-induced increases of the thermogenic genes in white adipocytes was inhibited by either KT5720 (a protein kinase A inhibitor) or BAPTA-AM. In addition, high fat diet (HFD)-induced obesity in mice was significantly recovered by co-treatment with menthol. Dietary menthol enhanced WAT "browning" and improved glucose metabolism in HFD-induced obesity mice as well. Therefore, we concluded that TRPM8 might be involved in WAT "browning" by increasing the expression levels of genes related to thermogenesis and energy metabolism. And dietary menthol could be a novel approach for combating human obesity and related metabolic diseases.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"IST-2017-907-v1+1_20540-294640-4-PB.pdf","access_level":"open_access","file_size":6101606,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5201","date_created":"2018-12-12T10:16:15Z","date_updated":"2020-07-14T12:47:26Z","checksum":"2219e5348bbfe1aac2725aa620c33280"}],"oa_version":"Published Version","pubrep_id":"907","intvolume":" 8","ddc":["571"],"status":"public","title":"Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates diet-induced obesity","_id":"627","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"No","day":"24","scopus_import":"1","date_published":"2017-08-24T00:00:00Z","page":"75114 - 75126","citation":{"mla":"Jiang, Changyu, et al. “Dietary Menthol-Induced TRPM8 Activation Enhances WAT ‘Browning’ and Ameliorates Diet-Induced Obesity.” Oncotarget, vol. 8, no. 43, Impact Journals, 2017, pp. 75114–26, doi:10.18632/oncotarget.20540.","short":"C. Jiang, M.-Z. Zhai, D. Yan, D. Li, C. Li, Y. Zhang, L. Xiao, D. Xiong, Q. Deng, W. Sun, Oncotarget 8 (2017) 75114–75126.","chicago":"Jiang, Changyu, Ming-Zhu Zhai, Dong Yan, Da Li, Chen Li, Yonghong Zhang, Lizu Xiao, Donglin Xiong, Qiwen Deng, and Wuping Sun. “Dietary Menthol-Induced TRPM8 Activation Enhances WAT ‘Browning’ and Ameliorates Diet-Induced Obesity.” Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.20540.","ama":"Jiang C, Zhai M-Z, Yan D, et al. Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates diet-induced obesity. Oncotarget. 2017;8(43):75114-75126. doi:10.18632/oncotarget.20540","ista":"Jiang C, Zhai M-Z, Yan D, Li D, Li C, Zhang Y, Xiao L, Xiong D, Deng Q, Sun W. 2017. Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates diet-induced obesity. Oncotarget. 8(43), 75114–75126.","apa":"Jiang, C., Zhai, M.-Z., Yan, D., Li, D., Li, C., Zhang, Y., … Sun, W. (2017). Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates diet-induced obesity. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.20540","ieee":"C. Jiang et al., “Dietary menthol-induced TRPM8 activation enhances WAT ‘browning’ and ameliorates diet-induced obesity,” Oncotarget, vol. 8, no. 43. Impact Journals, pp. 75114–75126, 2017."},"publication":"Oncotarget","publist_id":"7167","file_date_updated":"2020-07-14T12:47:26Z","volume":8,"date_updated":"2023-10-17T08:56:37Z","date_created":"2018-12-11T11:47:34Z","author":[{"full_name":"Jiang, Changyu","last_name":"Jiang","first_name":"Changyu"},{"last_name":"Zhai","first_name":"Ming-Zhu","id":"34009CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Zhai, Ming-Zhu"},{"full_name":"Yan, Dong","first_name":"Dong","last_name":"Yan"},{"first_name":"Da","last_name":"Li","full_name":"Li, Da"},{"first_name":"Chen","last_name":"Li","full_name":"Li, Chen"},{"first_name":"Yonghong","last_name":"Zhang","full_name":"Zhang, Yonghong"},{"last_name":"Xiao","first_name":"Lizu","full_name":"Xiao, Lizu"},{"last_name":"Xiong","first_name":"Donglin","full_name":"Xiong, Donglin"},{"full_name":"Deng, Qiwen","last_name":"Deng","first_name":"Qiwen"},{"full_name":"Sun, Wuping","last_name":"Sun","first_name":"Wuping"}],"department":[{"_id":"RySh"}],"publisher":"Impact Journals","publication_status":"published","year":"2017","publication_identifier":{"issn":["1949-2553"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.18632/oncotarget.20540","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"publication_identifier":{"issn":["0005-1098"]},"month":"06","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000403513900006"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.automatica.2017.03.030","ec_funded":1,"publist_id":"6391","file_date_updated":"2018-12-12T10:11:29Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"International Federation of Automatic Control","publication_status":"published","year":"2017","volume":"81C","date_updated":"2023-10-17T08:51:18Z","date_created":"2018-12-11T11:49:39Z","author":[{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","last_name":"Lang"},{"last_name":"Sontag","first_name":"Eduardo","full_name":"Sontag, Eduardo"}],"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","page":"46 - 55","citation":{"ama":"Lang M, Sontag E. Zeros of nonlinear systems with input invariances. Automatica. 2017;81C:46-55. doi:10.1016/j.automatica.2017.03.030","ista":"Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances. Automatica. 81C, 46–55.","apa":"Lang, M., & Sontag, E. (2017). Zeros of nonlinear systems with input invariances. Automatica. International Federation of Automatic Control. https://doi.org/10.1016/j.automatica.2017.03.030","ieee":"M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,” Automatica, vol. 81C. International Federation of Automatic Control, pp. 46–55, 2017.","mla":"Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” Automatica, vol. 81C, International Federation of Automatic Control, 2017, pp. 46–55, doi:10.1016/j.automatica.2017.03.030.","short":"M. Lang, E. Sontag, Automatica 81C (2017) 46–55.","chicago":"Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” Automatica. International Federation of Automatic Control, 2017. https://doi.org/10.1016/j.automatica.2017.03.030."},"publication":"Automatica","date_published":"2017-06-01T00:00:00Z","type":"journal_article","abstract":[{"text":"A nonlinear system possesses an invariance with respect to a set of transformations if its output dynamics remain invariant when transforming the input, and adjusting the initial condition accordingly. Most research has focused on invariances with respect to time-independent pointwise transformations like translational-invariance (u(t) -> u(t) + p, p in R) or scale-invariance (u(t) -> pu(t), p in R>0). In this article, we introduce the concept of s0-invariances with respect to continuous input transformations exponentially growing/decaying over time. We show that s0-invariant systems not only encompass linear time-invariant (LTI) systems with transfer functions having an irreducible zero at s0 in R, but also that the input/output relationship of nonlinear s0-invariant systems possesses properties well known from their linear counterparts. Furthermore, we extend the concept of s0-invariances to second- and higher-order s0-invariances, corresponding to invariances with respect to transformations of the time-derivatives of the input, and encompassing LTI systems with zeros of multiplicity two or higher. Finally, we show that nth-order 0-invariant systems realize – under mild conditions – nth-order nonlinear differential operators: when excited by an input of a characteristic functional form, the system’s output converges to a constant value only depending on the nth (nonlinear) derivative of the input.","lang":"eng"}],"status":"public","ddc":["000"],"title":"Zeros of nonlinear systems with input invariances","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1007","oa_version":"Published Version","file":[{"creator":"system","file_size":1401954,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-813-v1+1_ZerosOfNonlinearSystems.pdf","date_updated":"2018-12-12T10:11:29Z","date_created":"2018-12-12T10:11:29Z","file_id":"4884","relation":"main_file"}],"pubrep_id":"813"},{"page":"213 - 222","citation":{"ama":"Zimin A, Lampert C. Learning theory for conditional risk minimization. In: Vol 54. ML Research Press; 2017:213-222.","ista":"Zimin A, Lampert C. 2017. Learning theory for conditional risk minimization. AISTATS: Artificial Intelligence and Statistics, PMLR, vol. 54, 213–222.","apa":"Zimin, A., & Lampert, C. (2017). Learning theory for conditional risk minimization (Vol. 54, pp. 213–222). Presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States: ML Research Press.","ieee":"A. Zimin and C. Lampert, “Learning theory for conditional risk minimization,” presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 213–222.","mla":"Zimin, Alexander, and Christoph Lampert. Learning Theory for Conditional Risk Minimization. Vol. 54, ML Research Press, 2017, pp. 213–22.","short":"A. Zimin, C. Lampert, in:, ML Research Press, 2017, pp. 213–222.","chicago":"Zimin, Alexander, and Christoph Lampert. “Learning Theory for Conditional Risk Minimization,” 54:213–22. ML Research Press, 2017."},"date_published":"2017-04-01T00:00:00Z","day":"01","article_processing_charge":"No","title":"Learning theory for conditional risk minimization","status":"public","intvolume":" 54","_id":"1108","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","alternative_title":["PMLR"],"type":"conference","abstract":[{"text":"In this work we study the learnability of stochastic processes with respect to the conditional risk, i.e. the existence of a learning algorithm that improves its next-step performance with the amount of observed data. We introduce a notion of pairwise discrepancy between conditional distributions at different times steps and show how certain properties of these discrepancies can be used to construct a successful learning algorithm. Our main results are two theorems that establish criteria for learnability for many classes of stochastic processes, including all special cases studied previously in the literature.","lang":"eng"}],"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"http://proceedings.mlr.press/v54/zimin17a/zimin17a.pdf"}],"external_id":{"isi":["000509368500024"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"AISTATS: Artificial Intelligence and Statistics","start_date":"2017-04-20","location":"Fort Lauderdale, FL, United States","end_date":"2017-04-22"},"month":"04","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"ML Research Press","year":"2017","date_updated":"2023-10-17T10:01:12Z","date_created":"2018-12-11T11:50:11Z","volume":54,"author":[{"id":"37099E9C-F248-11E8-B48F-1D18A9856A87","last_name":"Zimin","first_name":"Alexander","full_name":"Zimin, Alexander"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"ec_funded":1,"publist_id":"6261"},{"_id":"909","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 124","status":"public","title":"On the lengths of curves passing through boundary points of a planar convex shape","oa_version":"Submitted Version","type":"journal_article","issue":"7","abstract":[{"text":"We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor ½ cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape.","lang":"eng"}],"citation":{"chicago":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” The American Mathematical Monthly. Mathematical Association of America, 2017. https://doi.org/10.4169/amer.math.monthly.124.7.588.","mla":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” The American Mathematical Monthly, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96, doi:10.4169/amer.math.monthly.124.7.588.","short":"A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.","ista":"Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596.","ieee":"A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary points of a planar convex shape,” The American Mathematical Monthly, vol. 124, no. 7. Mathematical Association of America, pp. 588–596, 2017.","apa":"Akopyan, A., & Vysotsky, V. (2017). On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. Mathematical Association of America. https://doi.org/10.4169/amer.math.monthly.124.7.588","ama":"Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 2017;124(7):588-596. doi:10.4169/amer.math.monthly.124.7.588"},"publication":"The American Mathematical Monthly","page":"588 - 596","article_type":"original","date_published":"2017-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","year":"2017","department":[{"_id":"HeEd"}],"publisher":"Mathematical Association of America","publication_status":"published","author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"first_name":"Vladislav","last_name":"Vysotsky","full_name":"Vysotsky, Vladislav"}],"volume":124,"date_updated":"2023-10-17T11:24:57Z","date_created":"2018-12-11T11:49:09Z","publist_id":"6534","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07997"}],"oa":1,"external_id":{"arxiv":["1605.07997"],"isi":["000413947300002"]},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","isi":1,"doi":"10.4169/amer.math.monthly.124.7.588","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00029890"]},"month":"01"},{"year":"2017","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Neural Information Processing Systems Foundation","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"last_name":"Grubic","first_name":"Demjan","full_name":"Grubic, Demjan"},{"full_name":"Li, Jerry","last_name":"Li","first_name":"Jerry"},{"full_name":"Tomioka, Ryota","first_name":"Ryota","last_name":"Tomioka"},{"first_name":"Milan","last_name":"Vojnović","full_name":"Vojnović, Milan"}],"date_updated":"2023-10-17T11:48:03Z","date_created":"2018-12-11T11:46:26Z","volume":2017,"publist_id":"7392","main_file_link":[{"url":"https://arxiv.org/abs/1610.02132","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1610.02132"]},"quality_controlled":"1","conference":{"end_date":"2017-12-09","location":"Long Beach, CA, United States","start_date":"2017-12-04","name":"NIPS: Neural Information Processing System"},"language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["10495258"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"431","title":"QSGD: Communication-efficient SGD via gradient quantization and encoding","status":"public","intvolume":" 2017","oa_version":"Submitted Version","type":"conference","alternative_title":["Advances in Neural Information Processing Systems"],"abstract":[{"text":"Parallel implementations of stochastic gradient descent (SGD) have received significant research attention, thanks to its excellent scalability properties. A fundamental barrier when parallelizing SGD is the high bandwidth cost of communicating gradient updates between nodes; consequently, several lossy compresion heuristics have been proposed, by which nodes only communicate quantized gradients. Although effective in practice, these heuristics do not always converge. In this paper, we propose Quantized SGD (QSGD), a family of compression schemes with convergence guarantees and good practical performance. QSGD allows the user to smoothly trade off communication bandwidth and convergence time: nodes can adjust the number of bits sent per iteration, at the cost of possibly higher variance. We show that this trade-off is inherent, in the sense that improving it past some threshold would violate information-theoretic lower bounds. QSGD guarantees convergence for convex and non-convex objectives, under asynchrony, and can be extended to stochastic variance-reduced techniques. When applied to training deep neural networks for image classification and automated speech recognition, QSGD leads to significant reductions in end-to-end training time. For instance, on 16GPUs, we can train the ResNet-152 network to full accuracy on ImageNet 1.8 × faster than the full-precision variant. ","lang":"eng"}],"citation":{"apa":"Alistarh, D.-A., Grubic, D., Li, J., Tomioka, R., & Vojnović, M. (2017). QSGD: Communication-efficient SGD via gradient quantization and encoding (Vol. 2017, pp. 1710–1721). Presented at the NIPS: Neural Information Processing System, Long Beach, CA, United States: Neural Information Processing Systems Foundation.","ieee":"D.-A. Alistarh, D. Grubic, J. Li, R. Tomioka, and M. Vojnović, “QSGD: Communication-efficient SGD via gradient quantization and encoding,” presented at the NIPS: Neural Information Processing System, Long Beach, CA, United States, 2017, vol. 2017, pp. 1710–1721.","ista":"Alistarh D-A, Grubic D, Li J, Tomioka R, Vojnović M. 2017. QSGD: Communication-efficient SGD via gradient quantization and encoding. NIPS: Neural Information Processing System, Advances in Neural Information Processing Systems, vol. 2017, 1710–1721.","ama":"Alistarh D-A, Grubic D, Li J, Tomioka R, Vojnović M. QSGD: Communication-efficient SGD via gradient quantization and encoding. In: Vol 2017. Neural Information Processing Systems Foundation; 2017:1710-1721.","chicago":"Alistarh, Dan-Adrian, Demjan Grubic, Jerry Li, Ryota Tomioka, and Milan Vojnović. “QSGD: Communication-Efficient SGD via Gradient Quantization and Encoding,” 2017:1710–21. Neural Information Processing Systems Foundation, 2017.","short":"D.-A. Alistarh, D. Grubic, J. Li, R. Tomioka, M. Vojnović, in:, Neural Information Processing Systems Foundation, 2017, pp. 1710–1721.","mla":"Alistarh, Dan-Adrian, et al. QSGD: Communication-Efficient SGD via Gradient Quantization and Encoding. Vol. 2017, Neural Information Processing Systems Foundation, 2017, pp. 1710–21."},"page":"1710-1721","date_published":"2017-01-01T00:00:00Z","day":"01","article_processing_charge":"No"},{"file":[{"file_name":"IST-2018-925-v1+1_1710.03391v1.pdf","access_level":"open_access","file_size":209294,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4939","date_created":"2018-12-12T10:12:21Z","date_updated":"2020-07-14T12:47:00Z","checksum":"6274f6c0da3376a7b079180d81568518"}],"oa_version":"Submitted Version","pubrep_id":"925","intvolume":" 259","title":"Causality-based model checking","status":"public","ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"549","abstract":[{"text":"Model checking is usually based on a comprehensive traversal of the state space. Causality-based model checking is a radically different approach that instead analyzes the cause-effect relationships in a program. We give an overview on a new class of model checking algorithms that capture the causal relationships in a special data structure called concurrent traces. Concurrent traces identify key events in an execution history and link them through their cause-effect relationships. The model checker builds a tableau of concurrent traces, where the case splits represent different causal explanations of a hypothetical error. Causality-based model checking has been implemented in the ARCTOR tool, and applied to previously intractable multi-threaded benchmarks.","lang":"eng"}],"alternative_title":["EPTCS"],"type":"conference","date_published":"2017-10-10T00:00:00Z","page":"31 - 38","citation":{"mla":"Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.” Electronic Proceedings in Theoretical Computer Science, vol. 259, Open Publishing Association, 2017, pp. 31–38, doi:10.4204/EPTCS.259.3.","short":"B. Finkbeiner, A. Kupriyanov, in:, Electronic Proceedings in Theoretical Computer Science, Open Publishing Association, 2017, pp. 31–38.","chicago":"Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.” In Electronic Proceedings in Theoretical Computer Science, 259:31–38. Open Publishing Association, 2017. https://doi.org/10.4204/EPTCS.259.3.","ama":"Finkbeiner B, Kupriyanov A. Causality-based model checking. In: Electronic Proceedings in Theoretical Computer Science. Vol 259. Open Publishing Association; 2017:31-38. doi:10.4204/EPTCS.259.3","ista":"Finkbeiner B, Kupriyanov A. 2017. Causality-based model checking. Electronic Proceedings in Theoretical Computer Science. CREST: Causal Reasoning for Embedded and Safety-Critical Systems Technologies, EPTCS, vol. 259, 31–38.","apa":"Finkbeiner, B., & Kupriyanov, A. (2017). Causality-based model checking. In Electronic Proceedings in Theoretical Computer Science (Vol. 259, pp. 31–38). Uppsala, Sweden: Open Publishing Association. https://doi.org/10.4204/EPTCS.259.3","ieee":"B. Finkbeiner and A. Kupriyanov, “Causality-based model checking,” in Electronic Proceedings in Theoretical Computer Science, Uppsala, Sweden, 2017, vol. 259, pp. 31–38."},"publication":"Electronic Proceedings in Theoretical Computer Science","article_processing_charge":"No","has_accepted_license":"1","day":"10","scopus_import":"1","volume":259,"date_created":"2018-12-11T11:47:07Z","date_updated":"2023-10-17T12:02:46Z","author":[{"last_name":"Finkbeiner","first_name":"Bernd","full_name":"Finkbeiner, Bernd"},{"id":"2C311BF8-F248-11E8-B48F-1D18A9856A87","first_name":"Andrey","last_name":"Kupriyanov","full_name":"Kupriyanov, Andrey"}],"publisher":"Open Publishing Association","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2017","publist_id":"7264","file_date_updated":"2020-07-14T12:47:00Z","language":[{"iso":"eng"}],"doi":"10.4204/EPTCS.259.3","conference":{"name":"CREST: Causal Reasoning for Embedded and Safety-Critical Systems Technologies","start_date":"2017-04-29","location":"Uppsala, Sweden","end_date":"2017-04-29"},"project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.03391v1"}],"oa":1,"publication_identifier":{"issn":["2075-2180"]},"month":"10"},{"year":"2017","publisher":"ML Research Press","department":[{"_id":"ChLa"}],"publication_status":"published","author":[{"first_name":"Anastasia","last_name":"Pentina","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","full_name":"Pentina, Anastasia"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"volume":70,"date_created":"2018-12-11T11:49:37Z","date_updated":"2023-10-17T11:53:32Z","ec_funded":1,"publist_id":"6399","oa":1,"external_id":{"isi":["000683309502093"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.06518"}],"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2017-08-11","location":"Sydney, Australia","start_date":"2017-08-06"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781510855144"]},"month":"06","_id":"999","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 70","title":"Multi-task learning with labeled and unlabeled tasks","status":"public","oa_version":"Submitted Version","type":"conference","alternative_title":["PMLR"],"abstract":[{"text":"In multi-task learning, a learner is given a collection of prediction tasks and needs to solve all of them. In contrast to previous work, which required that annotated training data must be available for all tasks, we consider a new setting, in which for some tasks, potentially most of them, only unlabeled training data is provided. Consequently, to solve all tasks, information must be transferred between tasks with labels and tasks without labels. Focusing on an instance-based transfer method we analyze two variants of this setting: when the set of labeled tasks is fixed, and when it can be actively selected by the learner. We state and prove a generalization bound that covers both scenarios and derive from it an algorithm for making the choice of labeled tasks (in the active case) and for transferring information between the tasks in a principled way. We also illustrate the effectiveness of the algorithm on synthetic and real data. ","lang":"eng"}],"citation":{"short":"A. Pentina, C. Lampert, in:, ML Research Press, 2017, pp. 2807–2816.","mla":"Pentina, Anastasia, and Christoph Lampert. Multi-Task Learning with Labeled and Unlabeled Tasks. Vol. 70, ML Research Press, 2017, pp. 2807–16.","chicago":"Pentina, Anastasia, and Christoph Lampert. “Multi-Task Learning with Labeled and Unlabeled Tasks,” 70:2807–16. ML Research Press, 2017.","ama":"Pentina A, Lampert C. Multi-task learning with labeled and unlabeled tasks. In: Vol 70. ML Research Press; 2017:2807-2816.","ieee":"A. Pentina and C. Lampert, “Multi-task learning with labeled and unlabeled tasks,” presented at the ICML: International Conference on Machine Learning, Sydney, Australia, 2017, vol. 70, pp. 2807–2816.","apa":"Pentina, A., & Lampert, C. (2017). Multi-task learning with labeled and unlabeled tasks (Vol. 70, pp. 2807–2816). Presented at the ICML: International Conference on Machine Learning, Sydney, Australia: ML Research Press.","ista":"Pentina A, Lampert C. 2017. Multi-task learning with labeled and unlabeled tasks. ICML: International Conference on Machine Learning, PMLR, vol. 70, 2807–2816."},"page":"2807 - 2816","date_published":"2017-06-08T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"08"},{"scopus_import":"1","day":"01","month":"07","article_processing_charge":"No","publication_identifier":{"isbn":["978-155752820-9"]},"publication":"Optics InfoBase Conference Papers","citation":{"chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Single Sideband Microwave to Optical Photon Conversion-an-Electro-Optic-Realization.” In Optics InfoBase Conference Papers, Vol. F54. Optica Publishing Group, 2017. https://doi.org/10.1364/NLO.2017.NM3A.1.","mla":"Rueda Sanchez, Alfredo R., et al. “Single Sideband Microwave to Optical Photon Conversion-an-Electro-Optic-Realization.” Optics InfoBase Conference Papers, vol. F54, NM3A.1, Optica Publishing Group, 2017, doi:10.1364/NLO.2017.NM3A.1.","short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, Optics InfoBase Conference Papers, Optica Publishing Group, 2017.","ista":"Rueda Sanchez AR, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2017. Single sideband microwave to optical photon conversion-an-electro-optic-realization. Optics InfoBase Conference Papers. NLO: Nonlinear Optics vol. F54, NM3A.1.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2017). Single sideband microwave to optical photon conversion-an-electro-optic-realization. In Optics InfoBase Conference Papers (Vol. F54). Waikoloa, HI, United States: Optica Publishing Group. https://doi.org/10.1364/NLO.2017.NM3A.1","ieee":"A. R. Rueda Sanchez et al., “Single sideband microwave to optical photon conversion-an-electro-optic-realization,” in Optics InfoBase Conference Papers, Waikoloa, HI, United States, 2017, vol. F54.","ama":"Rueda Sanchez AR, Sedlmeir F, Collodo M, et al. Single sideband microwave to optical photon conversion-an-electro-optic-realization. In: Optics InfoBase Conference Papers. Vol F54. Optica Publishing Group; 2017. doi:10.1364/NLO.2017.NM3A.1"},"quality_controlled":"1","conference":{"end_date":"2017-07-21","start_date":"2017-07-17","location":"Waikoloa, HI, United States","name":"NLO: Nonlinear Optics"},"doi":"10.1364/NLO.2017.NM3A.1","date_published":"2017-07-01T00:00:00Z","language":[{"iso":"eng"}],"article_number":"NM3A.1","type":"conference","abstract":[{"text":"We present results on nonlinear electro-optical conversion of microwave radiation into the optical telecommunication band with more than 0.1% photon number conversion efficiency with MHz bandwidth, in a crystalline whispering gallery mode resonator","lang":"eng"}],"publist_id":"7335","_id":"485","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Single sideband microwave to optical photon conversion-an-electro-optic-realization","publication_status":"published","status":"public","publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"author":[{"orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R"},{"last_name":"Sedlmeir","first_name":"Florian","full_name":"Sedlmeir, Florian"},{"first_name":"Michele","last_name":"Collodo","full_name":"Collodo, Michele"},{"last_name":"Vogl","first_name":"Ulrich","full_name":"Vogl, Ulrich"},{"first_name":"Birgit","last_name":"Stiller","full_name":"Stiller, Birgit"},{"full_name":"Schunk, Gerhard","first_name":"Gerhard","last_name":"Schunk"},{"full_name":"Strekalov, Dmitry","last_name":"Strekalov","first_name":"Dmitry"},{"first_name":"Christoph","last_name":"Marquardt","full_name":"Marquardt, Christoph"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"full_name":"Schwefel, Harald","first_name":"Harald","last_name":"Schwefel"}],"date_updated":"2023-10-17T12:15:38Z","date_created":"2018-12-11T11:46:44Z","volume":"F54","oa_version":"None"},{"status":"public","title":"Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas","ddc":["530"],"intvolume":" 42","_id":"675","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"We report the enhancement of infrared absorption of chemisorbed carbon monoxide on platinum in the gap of plasmonic nanoantennas. Our method is based on the self-assembled formation of platinum nanoislands on nanoscopic dipole antenna arrays manufactured via electron beam lithography. We employ systematic variations of the plasmonic antenna resonance to precisely couple to the molecular stretch vibration of carbon monoxide adsorbed on the platinum nanoislands. Ultimately, we reach more than 1500-fold infrared absorption enhancements, allowing for an ultrasensitive detection of a monolayer of chemisorbed carbon monoxide. The developed procedure can be adapted to other metal adsorbents and molecular species and could be utilized for coverage sensing in surface catalytic reactions. "}],"issue":"10","article_type":"original","page":"1931 - 1934","publication":"Optics Letters","citation":{"chicago":"Haase, Johannes, Salvatore Bagiante, Hans Sigg, and Jeroen Van Bokhoven. “Surface Enhanced Infrared Absorption of Chemisorbed Carbon Monoxide Using Plasmonic Nanoantennas.” Optics Letters. Optica Publishing Group, 2017. https://doi.org/10.1364/OL.42.001931.","mla":"Haase, Johannes, et al. “Surface Enhanced Infrared Absorption of Chemisorbed Carbon Monoxide Using Plasmonic Nanoantennas.” Optics Letters, vol. 42, no. 10, Optica Publishing Group, 2017, pp. 1931–34, doi:10.1364/OL.42.001931.","short":"J. Haase, S. Bagiante, H. Sigg, J. Van Bokhoven, Optics Letters 42 (2017) 1931–1934.","ista":"Haase J, Bagiante S, Sigg H, Van Bokhoven J. 2017. Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas. Optics Letters. 42(10), 1931–1934.","apa":"Haase, J., Bagiante, S., Sigg, H., & Van Bokhoven, J. (2017). Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.42.001931","ieee":"J. Haase, S. Bagiante, H. Sigg, and J. Van Bokhoven, “Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas,” Optics Letters, vol. 42, no. 10. Optica Publishing Group, pp. 1931–1934, 2017.","ama":"Haase J, Bagiante S, Sigg H, Van Bokhoven J. Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas. Optics Letters. 2017;42(10):1931-1934. doi:10.1364/OL.42.001931"},"date_published":"2017-05-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","publication_status":"published","department":[{"_id":"NanoFab"}],"publisher":"Optica Publishing Group","year":"2017","date_created":"2018-12-11T11:47:51Z","date_updated":"2023-10-17T12:16:02Z","volume":42,"author":[{"first_name":"Johannes","last_name":"Haase","full_name":"Haase, Johannes"},{"full_name":"Bagiante, Salvatore","first_name":"Salvatore","last_name":"Bagiante","id":"38ED402E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0122-9603"},{"full_name":"Sigg, Hans","first_name":"Hans","last_name":"Sigg"},{"first_name":"Jeroen","last_name":"Van Bokhoven","full_name":"Van Bokhoven, Jeroen"}],"publist_id":"7048","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1364/OL.42.001931","month":"05"},{"has_accepted_license":"1","article_processing_charge":"No","day":"04","citation":{"ista":"Cremer S. 2017. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. 46, 105–116.","apa":"Cremer, S. (2017). Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. Verlag Dr. Friedrich Pfeil.","ieee":"S. Cremer, “Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern,” Rundgespräche Forum Ökologie, vol. 46. Verlag Dr. Friedrich Pfeil, pp. 105–116, 2017.","ama":"Cremer S. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. 2017;46:105-116.","chicago":"Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und Die Heimische Fauna Verändern.” Rundgespräche Forum Ökologie. Verlag Dr. Friedrich Pfeil, 2017.","mla":"Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und Die Heimische Fauna Verändern.” Rundgespräche Forum Ökologie, vol. 46, Verlag Dr. Friedrich Pfeil, 2017, pp. 105–16.","short":"S. Cremer, Rundgespräche Forum Ökologie 46 (2017) 105–116."},"publication":"Rundgespräche Forum Ökologie","page":"105 - 116","date_published":"2017-04-04T00:00:00Z","type":"journal_article","abstract":[{"text":"The social insects bees, wasps, ants, and termites are species-rich, occur in many habitats, and often constitute a large part of the biomass. Many are also invasive, including species of termites, the red imported fire ant, and the Argentine ant. While invasive social insects have been a problem in Southern Europe for some time, Central Europa was free of invasive ant species until recently because most ants are adapted to warmer climates. Only in the 1990s, did Lasius neglectus, a close relative of the common black garden ant, arrive in Germany. First described in 1990 based on individuals collected in Budapest, the species has since been detected for example in France, Germany, Spain, England, and Kyrgyzstan. The species is spread with soil during construction work or plantings, and L. neglectus therefore is often found in parks and botanical gardens. Another invasive ant now spreading in southern Germany is Formica fuscocinerea, which occurs along rivers, including in the sandy floodplains of the river Isar. As is typical of pioneer species, F. fuscocinerea quickly becomes extremely abundant and therefore causes problems for example on playgrounds in Munich. All invasive ant species are characterized by cooperation across nests, leading to strongly interconnected, very large super-colonies. The resulting dominance results in the extinction of native ant species as well as other arthropod species and thus in the reduction of biodiversity.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"459","intvolume":" 46","title":"Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern","status":"public","ddc":["592"],"pubrep_id":"962","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-962-v1+1_044676698_07_Cremer__Invasive_Ameisen_in_Europa_...__BY-ND_.pdf","file_size":1711131,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5175","checksum":"4919baf9050415ca151fe22497379f78","date_updated":"2020-07-14T12:46:32Z","date_created":"2018-12-12T10:15:52Z"}],"publication_identifier":{"issn":["2366-2875"]},"month":"04","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publist_id":"7362","file_date_updated":"2020-07-14T12:46:32Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","year":"2017","publisher":"Verlag Dr. Friedrich Pfeil","department":[{"_id":"SyCr"}],"publication_status":"published","author":[{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"volume":46,"date_updated":"2023-10-17T12:28:13Z","date_created":"2018-12-11T11:46:35Z"},{"file":[{"date_updated":"2020-07-14T12:46:26Z","date_created":"2019-01-22T08:23:58Z","checksum":"86156ba7f4318e47cef3eb9092593c10","relation":"main_file","file_id":"5869","file_size":849345,"content_type":"application/pdf","creator":"dernst","file_name":"2017_ICML_Zhang.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"432","ddc":["000"],"status":"public","title":"ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning","abstract":[{"text":"Recently there has been significant interest in training machine-learning models at low precision: by reducing precision, one can reduce computation and communication by one order of magnitude. We examine training at reduced precision, both from a theoretical and practical perspective, and ask: is it possible to train models at end-to-end low precision with provable guarantees? Can this lead to consistent order-of-magnitude speedups? We mainly focus on linear models, and the answer is yes for linear models. We develop a simple framework called ZipML based on one simple but novel strategy called double sampling. Our ZipML framework is able to execute training at low precision with no bias, guaranteeing convergence, whereas naive quanti- zation would introduce significant bias. We val- idate our framework across a range of applica- tions, and show that it enables an FPGA proto- type that is up to 6.5 × faster than an implemen- tation using full 32-bit precision. We further de- velop a variance-optimal stochastic quantization strategy and show that it can make a significant difference in a variety of settings. When applied to linear models together with double sampling, we save up to another 1.7 × in data movement compared with uniform quantization. When training deep networks with quantized models, we achieve higher accuracy than the state-of-the- art XNOR-Net. ","lang":"eng"}],"type":"conference","alternative_title":["PMLR Press"],"date_published":"2017-01-01T00:00:00Z","publication":"Proceedings of Machine Learning Research","citation":{"apa":"Zhang, H., Li, J., Kara, K., Alistarh, D.-A., Liu, J., & Zhang, C. (2017). ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning. In Proceedings of Machine Learning Research (Vol. 70, pp. 4035–4043). Sydney, Australia: ML Research Press.","ieee":"H. Zhang, J. Li, K. Kara, D.-A. Alistarh, J. Liu, and C. Zhang, “ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning,” in Proceedings of Machine Learning Research, Sydney, Australia, 2017, vol. 70, pp. 4035–4043.","ista":"Zhang H, Li J, Kara K, Alistarh D-A, Liu J, Zhang C. 2017. ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning. Proceedings of Machine Learning Research. ICML: International Conference on Machine Learning, PMLR Press, vol. 70, 4035–4043.","ama":"Zhang H, Li J, Kara K, Alistarh D-A, Liu J, Zhang C. ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning. In: Proceedings of Machine Learning Research. Vol 70. ML Research Press; 2017:4035-4043.","chicago":"Zhang, Hantian, Jerry Li, Kaan Kara, Dan-Adrian Alistarh, Ji Liu, and Ce Zhang. “ZipML: Training Linear Models with End-to-End Low Precision, and a Little Bit of Deep Learning.” In Proceedings of Machine Learning Research, 70:4035–43. ML Research Press, 2017.","short":"H. Zhang, J. Li, K. Kara, D.-A. Alistarh, J. Liu, C. Zhang, in:, Proceedings of Machine Learning Research, ML Research Press, 2017, pp. 4035–4043.","mla":"Zhang, Hantian, et al. “ZipML: Training Linear Models with End-to-End Low Precision, and a Little Bit of Deep Learning.” Proceedings of Machine Learning Research, vol. 70, ML Research Press, 2017, pp. 4035–43."},"page":"4035 - 4043","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Zhang, Hantian","last_name":"Zhang","first_name":"Hantian"},{"full_name":"Li, Jerry","last_name":"Li","first_name":"Jerry"},{"full_name":"Kara, Kaan","last_name":"Kara","first_name":"Kaan"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Liu","first_name":"Ji","full_name":"Liu, Ji"},{"last_name":"Zhang","first_name":"Ce","full_name":"Zhang, Ce"}],"date_created":"2018-12-11T11:46:26Z","date_updated":"2023-10-17T12:31:15Z","volume":" 70","year":"2017","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ML Research Press","file_date_updated":"2020-07-14T12:46:26Z","publist_id":"7391","conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2017-08-11","location":"Sydney, Australia","start_date":"2017-08-06"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"01","publication_identifier":{"isbn":["978-151085514-4"]}},{"year":"2017","publisher":"ML Research Press","department":[{"_id":"VlKo"}],"publication_status":"published","author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"volume":75,"date_updated":"2023-10-17T12:32:13Z","date_created":"2018-12-11T11:45:33Z","publist_id":"7628","ec_funded":1,"file_date_updated":"2020-07-14T12:45:45Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1608.04223"]},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"quality_controlled":"1","conference":{"name":"COLT: Annual Conference on Learning Theory ","end_date":"2018-07-09","start_date":"2018-07-06"},"language":[{"iso":"eng"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"274","intvolume":" 75","status":"public","title":"A faster approximation algorithm for the Gibbs partition function","ddc":["510"],"oa_version":"Published Version","file":[{"file_name":"2018_PMLR_Kolmogorov.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":408974,"file_id":"7820","relation":"main_file","date_created":"2020-05-12T09:23:27Z","date_updated":"2020-07-14T12:45:45Z","checksum":"89db06a0e8083524449cb59b56bf4e5b"}],"type":"conference","abstract":[{"text":"We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x)) of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in [0,β]. The current best known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in {0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within O(ε2qlnn) variation distance from exact oracles. Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model of computation.","lang":"eng"}],"citation":{"mla":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” Proceedings of the 31st Conference On Learning Theory, vol. 75, ML Research Press, 2017, pp. 228–49.","short":"V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory, ML Research Press, 2017, pp. 228–249.","chicago":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” In Proceedings of the 31st Conference On Learning Theory, 75:228–49. ML Research Press, 2017.","ama":"Kolmogorov V. A faster approximation algorithm for the Gibbs partition function. In: Proceedings of the 31st Conference On Learning Theory. Vol 75. ML Research Press; 2017:228-249.","ista":"Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual Conference on Learning Theory vol. 75, 228–249.","apa":"Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition function. In Proceedings of the 31st Conference On Learning Theory (Vol. 75, pp. 228–249). ML Research Press.","ieee":"V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,” in Proceedings of the 31st Conference On Learning Theory, 2017, vol. 75, pp. 228–249."},"publication":"Proceedings of the 31st Conference On Learning Theory","page":"228-249","date_published":"2017-12-27T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"27"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2017-12-01T00:00:00Z","publication":"Biology Letters","citation":{"ama":"Futo M, Sell M, Kutzer M, Kurtz J. Specificity of oral immune priming in the red flour beetle Tribolium castaneum. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0632","ista":"Futo M, Sell M, Kutzer M, Kurtz J. 2017. Specificity of oral immune priming in the red flour beetle Tribolium castaneum. Biology Letters. 13(12), 0632.","ieee":"M. Futo, M. Sell, M. Kutzer, and J. Kurtz, “Specificity of oral immune priming in the red flour beetle Tribolium castaneum,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017.","apa":"Futo, M., Sell, M., Kutzer, M., & Kurtz, J. (2017). Specificity of oral immune priming in the red flour beetle Tribolium castaneum. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0632","mla":"Futo, Momir, et al. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” Biology Letters, vol. 13, no. 12, 0632, The Royal Society, 2017, doi:10.1098/rsbl.2017.0632.","short":"M. Futo, M. Sell, M. Kutzer, J. Kurtz, Biology Letters 13 (2017).","chicago":"Futo, Momir, Marie Sell, Megan Kutzer, and Joachim Kurtz. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0632."},"article_type":"original","abstract":[{"text":"Immune specificity is the degree to which a host’s immune system discriminates among various pathogens or antigenic variants. Vertebrate immune memory is highly specific due to antibody responses. On the other hand, some invertebrates show immune priming, i.e. improved survival after secondary exposure to a previously encountered pathogen. Until now, specificity of priming has only been demonstrated via the septic infection route or when live pathogens were used for priming. Therefore, we tested for specificity in the oral priming route in the red flour beetle, Tribolium castaneum. For priming, we used pathogen-free supernatants derived from three different strains of the entomopathogen, Bacillus thuringiensis, which express different Cry toxin variants known for their toxicity against this beetle. Subsequent exposure to the infective spores showed that oral priming was specific for two naturally occurring strains, while a third engineered strain did not induce any priming effect. Our data demonstrate that oral immune priming with a non-infectious bacterial agent can be specific, but the priming effect is not universal across all bacterial strains.","lang":"eng"}],"issue":"12","type":"journal_article","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"558","title":"Specificity of oral immune priming in the red flour beetle Tribolium castaneum","status":"public","intvolume":" 13","month":"12","publication_identifier":{"issn":["1744-9561"]},"doi":"10.1098/rsbl.2017.0632","language":[{"iso":"eng"}],"external_id":{"pmid":["29237813"]},"quality_controlled":"1","publist_id":"7255","article_number":"0632","author":[{"first_name":"Momir","last_name":"Futo","full_name":"Futo, Momir"},{"first_name":"Marie","last_name":"Sell","full_name":"Sell, Marie"},{"full_name":"Kutzer, Megan","first_name":"Megan","last_name":"Kutzer","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"}],"date_updated":"2023-10-18T06:42:25Z","date_created":"2018-12-11T11:47:10Z","volume":13,"year":"2017","pmid":1,"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"SyCr"}]},{"author":[{"last_name":"Villányi","first_name":"Márton","orcid":"0000-0001-8126-0426","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","full_name":"Villányi, Márton"}],"volume":3,"date_updated":"2023-10-18T07:49:29Z","date_created":"2018-12-11T11:49:46Z","year":"2017","department":[{"_id":"E-Lib"}],"publisher":"Verein Informationspraxis ","publication_status":"published","publist_id":"6360","file_date_updated":"2018-12-12T10:08:20Z","doi":"10.11588/ip.2017.1.35227","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2297-3249"]},"month":"01","pubrep_id":"799","popular_science":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":201163,"creator":"system","file_name":"IST-2017-799-v1+1_35227-112025-1-PB.pdf","access_level":"open_access","date_updated":"2018-12-12T10:08:20Z","date_created":"2018-12-12T10:08:20Z","relation":"main_file","file_id":"4680"}],"_id":"1030","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 3","ddc":["020"],"status":"public","title":"Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library","issue":"1","abstract":[{"lang":"ger","text":"Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die Bibliothek auf eine erfolgreiche Implementierung zurückblicken."},{"text":"IST Austria was looking for a new library system until 2014 when the research institute decided\r\nto implement Koha. The library first activated basic functions of the open-source product and\r\nthen brought additional tools into operation. The high flexibility of the system allows customized\r\nsolutions for different institutions. Although the library faced some challenges, it can now look\r\nback on a successful implementation.","lang":"eng"}],"type":"journal_article","date_published":"2017-01-01T00:00:00Z","citation":{"mla":"Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” Informationspraxis, vol. 3, no. 1, Verein Informationspraxis , 2017, doi:10.11588/ip.2017.1.35227.","short":"M. Villányi, Informationspraxis 3 (2017).","chicago":"Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” Informationspraxis. Verein Informationspraxis , 2017. https://doi.org/10.11588/ip.2017.1.35227.","ama":"Villányi M. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. 2017;3(1). doi:10.11588/ip.2017.1.35227","ista":"Villányi M. 2017. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. 3(1).","apa":"Villányi, M. (2017). Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. Verein Informationspraxis . https://doi.org/10.11588/ip.2017.1.35227","ieee":"M. Villányi, “Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library,” Informationspraxis, vol. 3, no. 1. Verein Informationspraxis , 2017."},"publication":"Informationspraxis","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"volume":50,"date_updated":"2023-10-18T07:21:53Z","date_created":"2023-01-16T09:18:05Z","author":[{"full_name":"Walker, James","first_name":"James","last_name":"Walker"},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"full_name":"Zhang, Jingyi","first_name":"Jingyi","last_name":"Zhang"},{"first_name":"Billy","last_name":"Aldridge","full_name":"Aldridge, Billy"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"last_name":"Higgins","first_name":"James D.","full_name":"Higgins, James D."},{"full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234"}],"publisher":"Nature Research","department":[{"_id":"XiFe"}],"publication_status":"published","pmid":1,"year":"2017","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","language":[{"iso":"eng"}],"doi":"10.1038/s41588-017-0008-5","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/"}],"external_id":{"pmid":["29255257"]},"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"month":"12","oa_version":"None","intvolume":" 50","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12193","issue":"1","abstract":[{"lang":"eng","text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants."}],"type":"journal_article","date_published":"2017-12-18T00:00:00Z","page":"130-137","article_type":"original","citation":{"chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” Nature Genetics. Nature Research, 2017. https://doi.org/10.1038/s41588-017-0008-5.","short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” Nature Genetics, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:10.1038/s41588-017-0008-5.","ieee":"J. Walker et al., “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” Nature Genetics, vol. 50, no. 1. Nature Research, pp. 130–137, 2017.","apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., & Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. Nature Research. https://doi.org/10.1038/s41588-017-0008-5","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137.","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 2017;50(1):130-137. doi:10.1038/s41588-017-0008-5"},"publication":"Nature Genetics","article_processing_charge":"No","day":"18","keyword":["Genetics"],"scopus_import":"1"},{"publication_status":"published","publisher":"Elsevier","year":"2017","date_updated":"2023-11-07T11:28:58Z","date_created":"2023-09-06T13:19:10Z","volume":112,"author":[{"first_name":"Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M"},{"full_name":"Dietz, Hendrik","last_name":"Dietz","first_name":"Hendrik"}],"article_number":"25a","extern":"1","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2016.11.171","month":"02","publication_identifier":{"issn":["0006-3495"]},"title":"Genetically encoded DNA-protein hybrid origami","status":"public","intvolume":" 112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14308","oa_version":"None","type":"journal_article","abstract":[{"text":"Here we describe an approach to bottom-up fabrication with nanometer-precision that allows integrating the functional diversity of proteins in designed three-dimensional structural frameworks. We reimagined the successful DNA origami design principle using a set of custom staple proteins to fold a double-stranded DNA template into a user-defined shape. Each staple protein recognizes two distinct double-helical DNA sequences and can carry additional functionalities. The staple proteins we present here are based on the transcription activator-like (TAL) effector proteins. Due to their repetitive structure these proteins offer a unique programmability that enables us to construct numerous staple proteins targeting any desired DNA sequence. Our approach is general, meaning that many different objects may be created using the same set of rules, and it is modular, because components can be modified or exchanged individually. We present rules for constructing megadalton-scale DNA-protein hybrid nanostructures; introduce important structural motifs, such as curvature, corners, and vertices; describe principles for creating multi-layer DNA-protein objects with enhanced rigidity; and demonstrate the possibility to combine our DNA-protein hybrid origami with conventional DNA nanotechnology. Since all components can be encoded genetically, our structures should be amenable to biotechnological mass-production. Moreover, since the target objects can self-assemble at room temperature in near-physiological buffer, our hybrid origami may also provide an attractive method to realize positioning and scaffolding tasks in vivo. We expect our method to find application both in scaffolding protein functionalities and in manipulating the spatial arrangement of genomic DNA.","lang":"eng"}],"issue":"3","article_type":"original","publication":"Biophysical Journal","citation":{"chicago":"Praetorius, Florian M, and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” Biophysical Journal. Elsevier, 2017. https://doi.org/10.1016/j.bpj.2016.11.171.","short":"F.M. Praetorius, H. Dietz, Biophysical Journal 112 (2017).","mla":"Praetorius, Florian M., and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” Biophysical Journal, vol. 112, no. 3, 25a, Elsevier, 2017, doi:10.1016/j.bpj.2016.11.171.","ieee":"F. M. Praetorius and H. Dietz, “Genetically encoded DNA-protein hybrid origami,” Biophysical Journal, vol. 112, no. 3. Elsevier, 2017.","apa":"Praetorius, F. M., & Dietz, H. (2017). Genetically encoded DNA-protein hybrid origami. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2016.11.171","ista":"Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami. Biophysical Journal. 112(3), 25a.","ama":"Praetorius FM, Dietz H. Genetically encoded DNA-protein hybrid origami. Biophysical Journal. 2017;112(3). doi:10.1016/j.bpj.2016.11.171"},"date_published":"2017-02-03T00:00:00Z","keyword":["Biophysics"],"scopus_import":"1","day":"03","article_processing_charge":"No"},{"extern":"1","author":[{"first_name":"M","last_name":"Siavashpouri","full_name":"Siavashpouri, M"},{"full_name":"Wachauf, CH","last_name":"Wachauf","first_name":"CH"},{"first_name":"MJ","last_name":"Zakhary","full_name":"Zakhary, MJ"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M","full_name":"Praetorius, Florian M"},{"first_name":"H","last_name":"Dietz","full_name":"Dietz, H"},{"full_name":"Dogic, Z","first_name":"Z","last_name":"Dogic"}],"volume":16,"date_updated":"2023-11-07T11:40:00Z","date_created":"2023-09-06T13:37:27Z","pmid":1,"year":"2017","publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"month":"05","doi":"10.1038/nmat4909","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["28530665"],"arxiv":["1705.08944"]},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1705.08944"}],"quality_controlled":"1","issue":"8","abstract":[{"text":"Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of one-dimensional twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14309","intvolume":" 16","status":"public","title":"Molecular engineering of chiral colloidal liquid crystals using DNA origami","article_processing_charge":"No","day":"22","scopus_import":"1","date_published":"2017-05-22T00:00:00Z","citation":{"ama":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials. 2017;16(8):849-856. doi:10.1038/nmat4909","ieee":"M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z. Dogic, “Molecular engineering of chiral colloidal liquid crystals using DNA origami,” Nature Materials, vol. 16, no. 8. Springer Nature, pp. 849–856, 2017.","apa":"Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., & Dogic, Z. (2017). Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat4909","ista":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017. Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials. 16(8), 849–856.","short":"M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic, Nature Materials 16 (2017) 849–856.","mla":"Siavashpouri, M., et al. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” Nature Materials, vol. 16, no. 8, Springer Nature, 2017, pp. 849–56, doi:10.1038/nmat4909.","chicago":"Siavashpouri, M, CH Wachauf, MJ Zakhary, Florian M Praetorius, H Dietz, and Z Dogic. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” Nature Materials. Springer Nature, 2017. https://doi.org/10.1038/nmat4909."},"publication":"Nature Materials","page":"849-856","article_type":"original"},{"date_created":"2023-09-06T13:40:20Z","date_updated":"2023-11-07T11:36:15Z","oa_version":"None","author":[{"full_name":"Siavashpouri, Mahsa","last_name":"Siavashpouri","first_name":"Mahsa"},{"full_name":"Wachauf, Christian","last_name":"Wachauf","first_name":"Christian"},{"full_name":"Zakhary, Mark","last_name":"Zakhary","first_name":"Mark"},{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M"},{"full_name":"Dietz, Hendrik","first_name":"Hendrik","last_name":"Dietz"},{"full_name":"Dogic, Zvonimir","first_name":"Zvonimir","last_name":"Dogic"}],"publication_status":"published","status":"public","title":"Molecular engineering of colloidal liquid crystals using DNA origami","publisher":"APS","_id":"14310","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","extern":"1","type":"conference_abstract","language":[{"iso":"eng"}],"date_published":"2017-03-01T00:00:00Z","quality_controlled":"1","publication":"APS March Meeting 2017","citation":{"apa":"Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., & Dogic, Z. (2017). Molecular engineering of colloidal liquid crystals using DNA origami. In APS March Meeting 2017. APS.","ieee":"M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z. Dogic, “Molecular engineering of colloidal liquid crystals using DNA origami,” in APS March Meeting 2017, 2017.","ista":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017. Molecular engineering of colloidal liquid crystals using DNA origami. APS March Meeting 2017. .","ama":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular engineering of colloidal liquid crystals using DNA origami. In: APS March Meeting 2017. APS; 2017.","chicago":"Siavashpouri, Mahsa, Christian Wachauf, Mark Zakhary, Florian M Praetorius, Hendrik Dietz, and Zvonimir Dogic. “Molecular Engineering of Colloidal Liquid Crystals Using DNA Origami.” In APS March Meeting 2017. APS, 2017.","short":"M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic, in:, APS March Meeting 2017, APS, 2017.","mla":"Siavashpouri, Mahsa, et al. “Molecular Engineering of Colloidal Liquid Crystals Using DNA Origami.” APS March Meeting 2017, APS, 2017."},"month":"03","day":"01","article_processing_charge":"No"},{"type":"journal_article","issue":"7683","abstract":[{"lang":"eng","text":"DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features1,2,3,4,5,6,7,8,9,10,11,12. These structures are customizable in that they can be site-specifically functionalized13 or constructed to exhibit machine-like14,15 or logic-gating behaviour16. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials3,16,17,18,19,20,21,22, could be realized if more material could be used. In DNA origami, a nanostructure is assembled from a very long single-stranded scaffold molecule held in place by many short single-stranded staple oligonucleotides. Only the bacteriophage-derived scaffold molecules are amenable to scalable and efficient mass production23; the shorter staple strands are obtained through costly solid-phase synthesis24 or enzymatic processes25. Here we show that single strands of DNA of virtually arbitrary length and with virtually arbitrary sequences can be produced in a scalable and cost-efficient manner by using bacteriophages to generate single-stranded precursor DNA that contains target strand sequences interleaved with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA for several DNA origami using shaker-flask cultures, and demonstrate end-to-end production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank bioreactor. Our method is compatible with existing DNA origami design frameworks and retains the modularity and addressability of DNA origami objects that are necessary for implementing custom modifications using functional groups. With all of the production and purification steps amenable to scaling, we expect that our method will expand the scope of DNA nanotechnology in many areas of science and technology."}],"intvolume":" 552","title":"Biotechnological mass production of DNA origami","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14290","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"07","page":"84-87","article_type":"original","citation":{"ista":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. 2017. Biotechnological mass production of DNA origami. Nature. 552(7683), 84–87.","ieee":"F. M. Praetorius, B. Kick, K. L. Behler, M. N. Honemann, D. Weuster-Botz, and H. Dietz, “Biotechnological mass production of DNA origami,” Nature, vol. 552, no. 7683. Springer Nature, pp. 84–87, 2017.","apa":"Praetorius, F. M., Kick, B., Behler, K. L., Honemann, M. N., Weuster-Botz, D., & Dietz, H. (2017). Biotechnological mass production of DNA origami. Nature. Springer Nature. https://doi.org/10.1038/nature24650","ama":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. Biotechnological mass production of DNA origami. Nature. 2017;552(7683):84-87. doi:10.1038/nature24650","chicago":"Praetorius, Florian M, Benjamin Kick, Karl L. Behler, Maximilian N. Honemann, Dirk Weuster-Botz, and Hendrik Dietz. “Biotechnological Mass Production of DNA Origami.” Nature. Springer Nature, 2017. https://doi.org/10.1038/nature24650.","mla":"Praetorius, Florian M., et al. “Biotechnological Mass Production of DNA Origami.” Nature, vol. 552, no. 7683, Springer Nature, 2017, pp. 84–87, doi:10.1038/nature24650.","short":"F.M. Praetorius, B. Kick, K.L. Behler, M.N. Honemann, D. Weuster-Botz, H. Dietz, Nature 552 (2017) 84–87."},"publication":"Nature","date_published":"2017-12-07T00:00:00Z","extern":"1","publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2017","volume":552,"date_created":"2023-09-06T12:14:20Z","date_updated":"2023-11-07T12:24:49Z","author":[{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius"},{"last_name":"Kick","first_name":"Benjamin","full_name":"Kick, Benjamin"},{"last_name":"Behler","first_name":"Karl L.","full_name":"Behler, Karl L."},{"full_name":"Honemann, Maximilian N.","first_name":"Maximilian N.","last_name":"Honemann"},{"first_name":"Dirk","last_name":"Weuster-Botz","full_name":"Weuster-Botz, Dirk"},{"full_name":"Dietz, Hendrik","first_name":"Hendrik","last_name":"Dietz"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"12","quality_controlled":"1","external_id":{"pmid":["29219963"]},"language":[{"iso":"eng"}],"doi":"10.1038/nature24650"},{"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface and its ability to self-assemble into colloidal membranes. Additionally, its single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods for phage and scaffold ssDNA are underexamined with respect to future industrial usage. Here, the high-cell-density phage production with Escherichia coli as host organism was studied in respect of medium composition, infection time, multiplicity of infection, and specific growth rate. The specific growth rate and the multiplicity of infection were identified as the crucial state variables that influence phage amplification rate on one hand and the concentration of produced ssDNA on the other hand. Using a growth rate of 0.15 h−1 and a multiplicity of infection of 0.05 pfu cfu−1 in the fed-batch production process, the concentration of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced by 54% to 590 mg L−1. Thus, our results help enabling M13 production for industrial uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777–784."}],"_id":"14286","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 114","status":"public","title":"Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production","oa_version":"None","scopus_import":"1","keyword":["Applied Microbiology and Biotechnology","Bioengineering","Biotechnology"],"article_processing_charge":"No","day":"01","citation":{"apa":"Kick, B., Hensler, S., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2017). Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering. Wiley. https://doi.org/10.1002/bit.26200","ieee":"B. Kick, S. Hensler, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production,” Biotechnology and Bioengineering, vol. 114, no. 4. Wiley, pp. 777–784, 2017.","ista":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. 2017. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering. 114(4), 777–784.","ama":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering. 2017;114(4):777-784. doi:10.1002/bit.26200","chicago":"Kick, Benjamin, Samantha Hensler, Florian M Praetorius, Hendrik Dietz, and Dirk Weuster-Botz. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” Biotechnology and Bioengineering. Wiley, 2017. https://doi.org/10.1002/bit.26200.","short":"B. Kick, S. Hensler, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Biotechnology and Bioengineering 114 (2017) 777–784.","mla":"Kick, Benjamin, et al. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” Biotechnology and Bioengineering, vol. 114, no. 4, Wiley, 2017, pp. 777–84, doi:10.1002/bit.26200."},"publication":"Biotechnology and Bioengineering","page":"777-784","article_type":"original","date_published":"2017-04-01T00:00:00Z","extern":"1","pmid":1,"year":"2017","publisher":"Wiley","publication_status":"published","author":[{"first_name":"Benjamin","last_name":"Kick","full_name":"Kick, Benjamin"},{"full_name":"Hensler, Samantha","first_name":"Samantha","last_name":"Hensler"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius","full_name":"Praetorius, Florian M"},{"full_name":"Dietz, Hendrik","first_name":"Hendrik","last_name":"Dietz"},{"first_name":"Dirk","last_name":"Weuster-Botz","full_name":"Weuster-Botz, Dirk"}],"volume":114,"date_updated":"2023-11-07T12:36:20Z","date_created":"2023-09-06T12:08:29Z","publication_identifier":{"issn":["0006-3592"]},"month":"04","external_id":{"pmid":["27748519"]},"quality_controlled":"1","doi":"10.1002/bit.26200","language":[{"iso":"eng"}]},{"day":"24","article_processing_charge":"No","scopus_import":"1","date_published":"2017-03-24T00:00:00Z","article_type":"original","publication":"Science","citation":{"ista":"Praetorius FM, Dietz H. 2017. Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. Science. 355(6331), eaam5488.","apa":"Praetorius, F. M., & Dietz, H. (2017). Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam5488","ieee":"F. M. Praetorius and H. Dietz, “Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes,” Science, vol. 355, no. 6331. American Association for the Advancement of Science, 2017.","ama":"Praetorius FM, Dietz H. Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. Science. 2017;355(6331). doi:10.1126/science.aam5488","chicago":"Praetorius, Florian M, and Hendrik Dietz. “Self-Assembly of Genetically Encoded DNA-Protein Hybrid Nanoscale Shapes.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5488.","mla":"Praetorius, Florian M., and Hendrik Dietz. “Self-Assembly of Genetically Encoded DNA-Protein Hybrid Nanoscale Shapes.” Science, vol. 355, no. 6331, eaam5488, American Association for the Advancement of Science, 2017, doi:10.1126/science.aam5488.","short":"F.M. Praetorius, H. Dietz, Science 355 (2017)."},"abstract":[{"text":"We describe an approach to bottom-up fabrication that allows integration of the functional diversity of proteins into designed three-dimensional structural frameworks. A set of custom staple proteins based on transcription activator–like effector proteins folds a double-stranded DNA template into a user-defined shape. Each staple protein is designed to recognize and closely link two distinct double-helical DNA sequences at separate positions on the template. We present design rules for constructing megadalton-scale DNA-protein hybrid shapes; introduce various structural motifs, such as custom curvature, corners, and vertices; and describe principles for creating multilayer DNA-protein objects with enhanced rigidity. We demonstrate self-assembly of our hybrid nanostructures in one-pot mixtures that include the genetic information for the designed proteins, the template DNA, RNA polymerase, ribosomes, and cofactors for transcription and translation.","lang":"eng"}],"issue":"6331","type":"journal_article","oa_version":"None","status":"public","title":"Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes","intvolume":" 355","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14287","month":"03","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.aam5488","quality_controlled":"1","external_id":{"pmid":["28336611"]},"extern":"1","article_number":"eaam5488","date_created":"2023-09-06T12:08:55Z","date_updated":"2023-11-07T12:33:05Z","volume":355,"author":[{"full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"first_name":"Hendrik","last_name":"Dietz","full_name":"Dietz, Hendrik"}],"publication_status":"published","publisher":"American Association for the Advancement of Science","year":"2017","pmid":1},{"ec_funded":1,"publist_id":"6157","volume":52,"date_updated":"2023-11-30T10:55:36Z","date_created":"2018-12-11T11:50:39Z","related_material":{"record":[{"id":"14539","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr"},{"last_name":"Zikelic","first_name":"Djordje","full_name":"Zikelic, Djordje"}],"department":[{"_id":"KrCh"}],"publisher":"ACM","publication_status":"published","year":"2017","publication_identifier":{"issn":["07308566"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1145/3009837.3009873","conference":{"name":"POPL: Principles of Programming Languages","end_date":"2017-01-21","start_date":"2017-01-15","location":"Paris, France"},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.01063"}],"oa":1,"external_id":{"isi":["000408311200013"]},"issue":"1","abstract":[{"text":"Termination is one of the basic liveness properties, and we study the termination problem for probabilistic programs with real-valued variables. Previous works focused on the qualitative problem that asks whether an input program terminates with probability~1 (almost-sure termination). A powerful approach for this qualitative problem is the notion of ranking supermartingales with respect to a given set of invariants. The quantitative problem (probabilistic termination) asks for bounds on the termination probability. A fundamental and conceptual drawback of the existing approaches to address probabilistic termination is that even though the supermartingales consider the probabilistic behavior of the programs, the invariants are obtained completely ignoring the probabilistic aspect. In this work we address the probabilistic termination problem for linear-arithmetic probabilistic programs with nondeterminism. We define the notion of {\\em stochastic invariants}, which are constraints along with a probability bound that the constraints hold. We introduce a concept of {\\em repulsing supermartingales}. First, we show that repulsing supermartingales can be used to obtain bounds on the probability of the stochastic invariants. Second, we show the effectiveness of repulsing supermartingales in the following three ways: (1)~With a combination of ranking and repulsing supermartingales we can compute lower bounds on the probability of termination; (2)~repulsing supermartingales provide witnesses for refutation of almost-sure termination; and (3)~with a combination of ranking and repulsing supermartingales we can establish persistence properties of probabilistic programs. We also present results on related computational problems and an experimental evaluation of our approach on academic examples. ","lang":"eng"}],"alternative_title":["ACM SIGPLAN Notices"],"type":"conference","oa_version":"Submitted Version","intvolume":" 52","status":"public","title":"Stochastic invariants for probabilistic termination","_id":"1194","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2017-01-01T00:00:00Z","page":"145 - 160","citation":{"chicago":"Chatterjee, Krishnendu, Petr Novotný, and Djordje Zikelic. “Stochastic Invariants for Probabilistic Termination,” 52:145–60. ACM, 2017. https://doi.org/10.1145/3009837.3009873.","short":"K. Chatterjee, P. Novotný, D. Zikelic, in:, ACM, 2017, pp. 145–160.","mla":"Chatterjee, Krishnendu, et al. Stochastic Invariants for Probabilistic Termination. Vol. 52, no. 1, ACM, 2017, pp. 145–60, doi:10.1145/3009837.3009873.","apa":"Chatterjee, K., Novotný, P., & Zikelic, D. (2017). Stochastic invariants for probabilistic termination (Vol. 52, pp. 145–160). Presented at the POPL: Principles of Programming Languages, Paris, France: ACM. https://doi.org/10.1145/3009837.3009873","ieee":"K. Chatterjee, P. Novotný, and D. Zikelic, “Stochastic invariants for probabilistic termination,” presented at the POPL: Principles of Programming Languages, Paris, France, 2017, vol. 52, no. 1, pp. 145–160.","ista":"Chatterjee K, Novotný P, Zikelic D. 2017. Stochastic invariants for probabilistic termination. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 52, 145–160.","ama":"Chatterjee K, Novotný P, Zikelic D. Stochastic invariants for probabilistic termination. In: Vol 52. ACM; 2017:145-160. doi:10.1145/3009837.3009873"}},{"status":"public","ddc":["581"],"title":"Vascular tissue development and regeneration in the model plant arabidopsis","_id":"545","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:12:49Z","date_updated":"2020-07-14T12:46:58Z","checksum":"e1f05e5850dfd9f9434d2d373ca61941","file_id":"4969","relation":"main_file","creator":"system","file_size":7443683,"content_type":"application/pdf","file_name":"IST-2018-929-v1+1_56106.pdf","access_level":"open_access"}],"pubrep_id":"929","alternative_title":["Agricultural and Biological Sciences"],"type":"book_chapter","abstract":[{"text":"Development of vascular tissue is a remarkable example of intercellular communication and coordinated development involving hormonal signaling and tissue polarity. Thus far, studies on vascular patterning and regeneration have been conducted mainly in trees—woody plants—with a well-developed layer of vascular cambium and secondary tissues. Trees are difficult to use as genetic models, i.e., due to long generation time, unstable environmental conditions, and lack of available mutants and transgenic lines. Therefore, the use of the main genetic model plant Arabidopsis thaliana (L.) Heynh., with a wealth of available marker and transgenic lines, provides a unique opportunity to address molecular mechanism of vascular tissue formation and regeneration. With specific treatments, the tiny weed Arabidopsis can serve as a model to understand the growth of mighty trees and interconnect a tree physiology with molecular genetics and cell biology of Arabidopsis.","lang":"eng"}],"page":"113 - 140","citation":{"chicago":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” In Plant Engineering, edited by Snježana Jurić, 113–40. Plant Engineering. InTech, 2017. https://doi.org/10.5772/intechopen.69712.","mla":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” Plant Engineering, edited by Snježana Jurić, InTech, 2017, pp. 113–40, doi:10.5772/intechopen.69712.","short":"E. Mazur, J. Friml, in:, S. Jurić (Ed.), Plant Engineering, InTech, 2017, pp. 113–140.","ista":"Mazur E, Friml J. 2017.Vascular tissue development and regeneration in the model plant arabidopsis. In: Plant Engineering. Agricultural and Biological Sciences, , 113–140.","ieee":"E. Mazur and J. Friml, “Vascular tissue development and regeneration in the model plant arabidopsis,” in Plant Engineering, S. Jurić, Ed. InTech, 2017, pp. 113–140.","apa":"Mazur, E., & Friml, J. (2017). Vascular tissue development and regeneration in the model plant arabidopsis. In S. Jurić (Ed.), Plant Engineering (pp. 113–140). InTech. https://doi.org/10.5772/intechopen.69712","ama":"Mazur E, Friml J. Vascular tissue development and regeneration in the model plant arabidopsis. In: Jurić S, ed. Plant Engineering. Plant Engineering. InTech; 2017:113-140. doi:10.5772/intechopen.69712"},"publication":"Plant Engineering","date_published":"2017-11-17T00:00:00Z","series_title":"Plant Engineering","has_accepted_license":"1","day":"17","department":[{"_id":"JiFr"}],"editor":[{"full_name":"Jurić, Snježana","last_name":"Jurić","first_name":"Snježana"}],"publisher":"InTech","publication_status":"published","year":"2017","date_created":"2018-12-11T11:47:05Z","date_updated":"2024-02-12T12:03:42Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1274"}]},"author":[{"full_name":"Mazur, Ewa","last_name":"Mazur","first_name":"Ewa"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"ec_funded":1,"publist_id":"7269","file_date_updated":"2020-07-14T12:46:58Z","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.5772/intechopen.69712","month":"11"},{"file_date_updated":"2020-07-14T12:47:24Z","publist_id":"7183","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"last_name":"Beattie","first_name":"Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","full_name":"Beattie, Robert J"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-14T12:02:08Z","date_created":"2018-12-11T11:47:32Z","volume":591,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Wiley-Blackwell","month":"12","publication_identifier":{"issn":["00145793"]},"doi":"10.1002/1873-3468.12906","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"pmid":["29121403"]},"quality_controlled":"1","project":[{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"The mammalian cerebral cortex is responsible for higher cognitive functions such as perception, consciousness, and acquiring and processing information. The neocortex is organized into six distinct laminae, each composed of a rich diversity of cell types which assemble into highly complex cortical circuits. Radial glia progenitors (RGPs) are responsible for producing all neocortical neurons and certain glia lineages. Here, we discuss recent discoveries emerging from clonal lineage analysis at the single RGP cell level that provide us with an inaugural quantitative framework of RGP lineage progression. We further discuss the importance of the relative contribution of intrinsic gene functions and non-cell-autonomous or community effects in regulating RGP proliferation behavior and lineage progression."}],"issue":"24","type":"journal_article","pubrep_id":"928","file":[{"checksum":"a46dadc84e0c28d389dd3e9e954464db","date_created":"2018-12-12T10:16:24Z","date_updated":"2020-07-14T12:47:24Z","file_id":"5211","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":644149,"access_level":"open_access","file_name":"IST-2018-928-v1+1_Beattie_et_al-2017-FEBS_Letters.pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"621","status":"public","ddc":["571","610"],"title":"Mechanisms of radial glia progenitor cell lineage progression","intvolume":" 591","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2017-12-01T00:00:00Z","publication":"FEBS letters","citation":{"chicago":"Beattie, Robert J, and Simon Hippenmeyer. “Mechanisms of Radial Glia Progenitor Cell Lineage Progression.” FEBS Letters. Wiley-Blackwell, 2017. https://doi.org/10.1002/1873-3468.12906.","mla":"Beattie, Robert J., and Simon Hippenmeyer. “Mechanisms of Radial Glia Progenitor Cell Lineage Progression.” FEBS Letters, vol. 591, no. 24, Wiley-Blackwell, 2017, pp. 3993–4008, doi:10.1002/1873-3468.12906.","short":"R.J. Beattie, S. Hippenmeyer, FEBS Letters 591 (2017) 3993–4008.","ista":"Beattie RJ, Hippenmeyer S. 2017. Mechanisms of radial glia progenitor cell lineage progression. FEBS letters. 591(24), 3993–4008.","ieee":"R. J. Beattie and S. Hippenmeyer, “Mechanisms of radial glia progenitor cell lineage progression,” FEBS letters, vol. 591, no. 24. Wiley-Blackwell, pp. 3993–4008, 2017.","apa":"Beattie, R. J., & Hippenmeyer, S. (2017). Mechanisms of radial glia progenitor cell lineage progression. FEBS Letters. Wiley-Blackwell. https://doi.org/10.1002/1873-3468.12906","ama":"Beattie RJ, Hippenmeyer S. Mechanisms of radial glia progenitor cell lineage progression. FEBS letters. 2017;591(24):3993-4008. doi:10.1002/1873-3468.12906"},"page":"3993 - 4008"},{"year":"2017","_id":"5562","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"ddc":["570"],"status":"public","title":"Multi-electrode array recording from salamander retinal ganglion cells","related_material":{"record":[{"relation":"research_paper","status":"public","id":"2257"}]},"author":[{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"full_name":"Amodei, Dario","first_name":"Dario","last_name":"Amodei"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"full_name":"Berry, Michael","first_name":"Michael","last_name":"Berry"}],"oa_version":"Published Version","file":[{"checksum":"e620eff260646f57b479a69492c8b765","date_created":"2018-12-12T13:03:04Z","date_updated":"2020-07-14T12:47:03Z","relation":"main_file","file_id":"5622","content_type":"application/octet-stream","file_size":1336936,"creator":"system","access_level":"open_access","file_name":"IST-2017-61-v1+1_bint_fishmovie32_100.mat"},{"creator":"system","content_type":"application/zip","file_size":1897543,"access_level":"open_access","file_name":"IST-2017-61-v1+2_bint_fishmovie32_100.zip","checksum":"de83f9b81ea0aae3cddfc3ed982e0759","date_created":"2018-12-12T13:03:05Z","date_updated":"2020-07-14T12:47:03Z","file_id":"5623","relation":"main_file"}],"date_created":"2018-12-12T12:31:33Z","date_updated":"2024-02-21T13:46:14Z","type":"research_data","datarep_id":"61","abstract":[{"lang":"eng","text":"This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408."}],"file_date_updated":"2020-07-14T12:47:03Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:61.","ieee":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017.","apa":"Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:61","ama":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61","chicago":"Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.","mla":"Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:61.","short":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017)."},"oa":1,"doi":"10.15479/AT:ISTA:61","date_published":"2017-02-27T00:00:00Z","keyword":["multi-electrode recording","retinal ganglion cells"],"article_processing_charge":"No","has_accepted_license":"1","day":"27","month":"02"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5561","year":"2017","acknowledgement":"We thank Vladimir Kolmogorov and Stephan Saalfeld forinspiring discussions.","ddc":["000"],"status":"public","title":"Graph matching problems for annotating C. Elegans","publisher":"Institute of Science and Technology Austria","department":[{"_id":"VlKo"}],"author":[{"last_name":"Kainmueller","first_name":"Dagmar","full_name":"Kainmueller, Dagmar"},{"full_name":"Jug, Florian","first_name":"Florian","last_name":"Jug"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"},{"full_name":"Meyers, Gene","first_name":"Gene","last_name":"Meyers"}],"date_updated":"2024-02-21T13:46:31Z","date_created":"2018-12-12T12:31:32Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5614","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:02:54Z","checksum":"3dc3e1306a66028a34181ebef2923139","file_name":"IST-2017-57-v1+1_wormMatchingProblems.zip","access_level":"open_access","file_size":327042819,"content_type":"application/zip","creator":"system"}],"datarep_id":"57","type":"research_data","abstract":[{"lang":"eng","text":"Graph matching problems as described in \"Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans.\" by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in \"Feature Correspondence via Graph Matching: Models and Global Optimization.\" by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. "}],"file_date_updated":"2020-07-14T12:47:03Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Kainmueller D, Jug F, Rother C, Meyers G. 2017. Graph matching problems for annotating C. Elegans, Institute of Science and Technology Austria, 10.15479/AT:ISTA:57.","apa":"Kainmueller, D., Jug, F., Rother, C., & Meyers, G. (2017). Graph matching problems for annotating C. Elegans. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:57","ieee":"D. Kainmueller, F. Jug, C. Rother, and G. Meyers, “Graph matching problems for annotating C. Elegans.” Institute of Science and Technology Austria, 2017.","ama":"Kainmueller D, Jug F, Rother C, Meyers G. Graph matching problems for annotating C. Elegans. 2017. doi:10.15479/AT:ISTA:57","chicago":"Kainmueller, Dagmar, Florian Jug, Carsten Rother, and Gene Meyers. “Graph Matching Problems for Annotating C. Elegans.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:57.","mla":"Kainmueller, Dagmar, et al. Graph Matching Problems for Annotating C. Elegans. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:57.","short":"D. Kainmueller, F. Jug, C. Rother, G. Meyers, (2017)."},"oa":1,"date_published":"2017-02-13T00:00:00Z","doi":"10.15479/AT:ISTA:57","keyword":["graph matching","feature matching","QAP","MAP-inference"],"day":"13","month":"02","article_processing_charge":"No","has_accepted_license":"1"},{"date_updated":"2024-02-21T13:46:47Z","date_created":"2018-12-12T12:31:33Z","file":[{"access_level":"open_access","file_name":"IST-2016-45-v1+1_PaperCode.zip","content_type":"application/zip","file_size":296722548,"creator":"system","relation":"main_file","file_id":"5602","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:02:37Z"}],"oa_version":"Published Version","author":[{"full_name":"Lukacisin, Martin","last_name":"Lukacisin","first_name":"Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"}],"status":"public","title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","ddc":["571"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToBo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5563","year":"2017","license":"https://creativecommons.org/licenses/by-sa/4.0/","file_date_updated":"2020-07-14T12:47:03Z","abstract":[{"text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions","lang":"eng"}],"datarep_id":"64","type":"research_data","date_published":"2017-03-20T00:00:00Z","doi":"10.15479/AT:ISTA:64","citation":{"chicago":"Lukacisin, Martin. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:64.","short":"M. Lukacisin, (2017).","mla":"Lukacisin, Martin. MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:64.","ieee":"M. Lukacisin, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017.","apa":"Lukacisin, M. (2017). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:64","ista":"Lukacisin M. 2017. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:64.","ama":"Lukacisin M. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2017. doi:10.15479/AT:ISTA:64"},"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"day":"20","month":"03","article_processing_charge":"No","has_accepted_license":"1"},{"citation":{"apa":"Hahn, D. (2017). Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_855","ieee":"D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017.","ista":"Hahn D. 2017. Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria.","ama":"Hahn D. Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:10.15479/AT:ISTA:th_855","chicago":"Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_855.","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017.","mla":"Hahn, David. Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_855."},"page":"124","date_published":"2017-08-14T00:00:00Z","day":"14","article_processing_charge":"No","has_accepted_license":"1","_id":"839","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["004","005","006","531","621"],"status":"public","title":"Brittle fracture simulation with boundary elements for computer graphics","pubrep_id":"855","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":14596191,"creator":"system","access_level":"open_access","file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","checksum":"6c1ae8c90bfaba5e089417fefbc4a272","date_updated":"2020-07-14T12:48:13Z","date_created":"2018-12-12T10:14:46Z","relation":"main_file","file_id":"5100"},{"checksum":"421672f68d563b029869c5cf1713f919","date_updated":"2020-07-14T12:48:13Z","date_created":"2019-04-05T08:40:30Z","relation":"source_file","file_id":"6207","file_size":15060566,"content_type":"application/zip","creator":"dernst","access_level":"closed","file_name":"2017_thesis_Hahn_source.zip"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material's toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. ","lang":"eng"}],"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:th_855","supervisor":[{"last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["2663-337X"]},"year":"2017","acknowledgement":"ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all, let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for supporting me throughout my PhD. Obviously, none of this work would\r\nhave been possible without you.\r\nFurthermore, Thank You to all the people who have contributed to this work in various\r\nways, in particular Martin Schanz and his group for providing and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel, and all the members – past and present – of his\r\nand Chris’ research groups at IST Austria for always providing honest and insightful\r\nfeedback throughout many joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs only virtual objects have been harmed in the process of creating this work, I would\r\nlike to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo” models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different ways.\r\n","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Hahn","full_name":"Hahn, David"}],"related_material":{"record":[{"id":"1362","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1633"},{"id":"5568","relation":"popular_science","status":"public"}]},"date_updated":"2024-02-21T13:48:02Z","date_created":"2018-12-11T11:48:47Z","file_date_updated":"2020-07-14T12:48:13Z","publist_id":"6809","ec_funded":1},{"month":"12","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-017-01663-5","quality_controlled":"1","project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"external_id":{"pmid":["29133797"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:47:20Z","publist_id":"7190","article_number":"1486","date_updated":"2024-02-21T13:47:47Z","date_created":"2018-12-11T11:47:30Z","volume":8,"author":[{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","first_name":"Marion A","last_name":"Picard","full_name":"Picard, Marion A"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"7163"}]},"publication_status":"published","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Nature Publishing Group","year":"2017","pmid":1,"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"date_published":"2017-12-01T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ista":"Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486.","ieee":"C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","apa":"Fraisse, C., Picard, M. A. L., & Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01663-5","ama":"Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01663-5","chicago":"Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01663-5.","mla":"Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01663-5.","short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017)."},"abstract":[{"text":"Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"file_size":1201520,"content_type":"application/pdf","creator":"dernst","file_name":"2017_NatureComm_Fraisse.pdf","access_level":"open_access","date_created":"2020-03-03T15:55:50Z","date_updated":"2020-07-14T12:47:20Z","checksum":"4da2651303c8afc2f7fc419be42a2433","relation":"main_file","file_id":"7562"}],"oa_version":"Published Version","pubrep_id":"910","ddc":["570","576"],"title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","status":"public","intvolume":" 8","_id":"614","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"status":"public","ddc":["576"],"title":"Fastq files for \"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection\"","_id":"5564","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"5627","checksum":"31a0c01d022721073241a23d192cc37e","date_created":"2018-12-12T13:03:18Z","date_updated":"2020-07-14T12:47:03Z","access_level":"open_access","file_name":"IST-2017-65-v1+1_D_anc_1.fastq.zip","file_size":1225959109,"content_type":"application/zip","creator":"system"},{"relation":"main_file","file_id":"5628","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:03:30Z","checksum":"d8f26f83ce7e7e45436121f9c6cd9b83","file_name":"IST-2017-65-v1+1_D_anc_2.fastq.zip","access_level":"open_access","file_size":1422656107,"content_type":"application/zip","creator":"system"},{"content_type":"application/zip","file_size":565014975,"creator":"system","access_level":"open_access","file_name":"IST-2017-65-v1+2_D_A11_1.fastq.zip","checksum":"e07b99bcfe55b5f132ca03b8b48c8cbc","date_created":"2018-12-12T13:03:33Z","date_updated":"2020-07-14T12:47:03Z","relation":"main_file","file_id":"5629"},{"relation":"main_file","file_id":"5630","date_created":"2018-12-12T13:03:42Z","date_updated":"2020-07-14T12:47:03Z","checksum":"eda86143d5f32d844b54f8530041e32b","file_name":"IST-2017-65-v1+3_D_A11_2.fastq.zip","access_level":"open_access","file_size":564490030,"content_type":"application/zip","creator":"system"},{"relation":"main_file","file_id":"5631","date_created":"2018-12-12T13:03:46Z","date_updated":"2020-07-14T12:47:03Z","checksum":"906d44f950c1626d9b99f34fbf89cb12","file_name":"IST-2017-65-v1+4_D_C10_1.fastq.zip","access_level":"open_access","file_size":875430169,"content_type":"application/zip","creator":"system"},{"date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:03:54Z","checksum":"6ca14a032a79e0c787106bdf635725c9","relation":"main_file","file_id":"5632","content_type":"application/zip","file_size":638298201,"creator":"system","file_name":"IST-2017-65-v1+6_D_C08_2.fastq.zip","access_level":"open_access"},{"file_id":"5633","relation":"main_file","checksum":"66ab16ddb5ba64b2e263ef746ebf2893","date_created":"2018-12-12T13:04:01Z","date_updated":"2020-07-14T12:47:03Z","access_level":"open_access","file_name":"IST-2017-65-v1+5_D_C10_2.fastq.zip","creator":"system","content_type":"application/zip","file_size":894702866},{"file_name":"IST-2017-65-v1+7_D_C08_1.fastq.zip","access_level":"open_access","creator":"system","file_size":623648989,"content_type":"application/zip","file_id":"5634","relation":"main_file","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:04:07Z","checksum":"82607970174f8d37773b7d3acc712195"},{"date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:04:11Z","checksum":"225c30b243268c7dda9d6f8327933252","file_id":"5635","relation":"main_file","creator":"system","file_size":259359583,"content_type":"application/zip","file_name":"IST-2017-65-v1+8_D_D08_1.fastq.zip","access_level":"open_access"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:33Z","date_updated":"2024-02-21T13:47:28Z","related_material":{"record":[{"id":"704","status":"public","relation":"research_paper"}]},"author":[{"orcid":"0000-0003-1229-9719","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","first_name":"Magdalena","full_name":"Steinrück, Magdalena"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"type":"research_data","datarep_id":"65","file_date_updated":"2020-07-14T12:47:03Z","abstract":[{"text":"Compressed Fastq files with whole-genome sequencing data of IS-wt strain D and clones from four evolved populations (A11, C08, C10, D08). Information on this data collection is available in the Methods Section of the primary publication.","lang":"eng"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ieee":"M. Steinrück and C. C. Guet, “Fastq files for ‘Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.’” Institute of Science and Technology Austria, 2017.","apa":"Steinrück, M., & Guet, C. C. (2017). Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:65","ista":"Steinrück M, Guet CC. 2017. Fastq files for ‘Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:65.","ama":"Steinrück M, Guet CC. Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” 2017. doi:10.15479/AT:ISTA:65","chicago":"Steinrück, Magdalena, and Calin C Guet. “Fastq Files for ‘Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:65.","short":"M. Steinrück, C.C. Guet, (2017).","mla":"Steinrück, Magdalena, and Calin C. Guet. Fastq Files for “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:65."},"date_published":"2017-04-11T00:00:00Z","doi":"10.15479/AT:ISTA:65","has_accepted_license":"1","article_processing_charge":"No","month":"04","day":"11"},{"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"oa":1,"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"citation":{"chicago":"Hahn, David. “Source Codes: Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:73.","short":"D. Hahn, (2017).","mla":"Hahn, David. Source Codes: Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:73.","apa":"Hahn, D. (2017). Source codes: Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:73","ieee":"D. Hahn, “Source codes: Brittle fracture simulation with boundary elements for computer graphics.” Institute of Science and Technology Austria, 2017.","ista":"Hahn D. 2017. Source codes: Brittle fracture simulation with boundary elements for computer graphics, Institute of Science and Technology Austria, 10.15479/AT:ISTA:73.","ama":"Hahn D. Source codes: Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:10.15479/AT:ISTA:73"},"date_published":"2017-08-16T00:00:00Z","doi":"10.15479/AT:ISTA:73","keyword":["Boundary elements","brittle fracture","computer graphics","fracture simulation"],"month":"08","day":"16","has_accepted_license":"1","article_processing_charge":"No","status":"public","title":"Source codes: Brittle fracture simulation with boundary elements for computer graphics","ddc":["004"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChWo"}],"year":"2017","_id":"5568","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T12:31:35Z","date_updated":"2024-02-21T13:48:02Z","file":[{"access_level":"open_access","file_name":"IST-2017-73-v1+1_FractureRB_v1.1_2017_07_20_final_public.zip","creator":"system","content_type":"application/zip","file_size":199353471,"file_id":"5615","relation":"main_file","checksum":"2323a755842a3399cbc47d76545fc9a0","date_created":"2018-12-12T13:02:57Z","date_updated":"2020-07-14T12:47:04Z"}],"oa_version":"Published Version","author":[{"full_name":"Hahn, David","last_name":"Hahn","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"839","relation":"research_paper","status":"public"}]},"datarep_id":"73","type":"research_data","file_date_updated":"2020-07-14T12:47:04Z","abstract":[{"text":"Includes source codes, test cases, and example data used in the thesis Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Also includes pre-built binaries of the HyENA library, but not sources - please contact the HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena)","lang":"eng"}],"ec_funded":1},{"doi":"10.15479/AT:ISTA:7163","date_published":"2017-12-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"chicago":"Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:7163.","mla":"Fraisse, Christelle. Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:7163.","short":"C. Fraisse, (2017).","ista":"Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7163.","apa":"Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7163","ieee":"C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.’” Institute of Science and Technology Austria, 2017.","ama":"Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:10.15479/AT:ISTA:7163"},"project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"article_processing_charge":"No","has_accepted_license":"1","month":"12","day":"01","related_material":{"record":[{"status":"public","relation":"research_paper","id":"614"}]},"contributor":[{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"first_name":"Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"author":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"}],"file":[{"date_created":"2019-12-10T08:46:46Z","date_updated":"2020-07-14T12:47:50Z","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","file_id":"7164","relation":"main_file","creator":"cfraisse","content_type":"application/zip","file_size":841375478,"file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","access_level":"open_access"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:47:47Z","date_created":"2019-12-09T23:03:03Z","year":"2017","_id":"7163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","ddc":["576"],"status":"public","file_date_updated":"2020-07-14T12:47:50Z","abstract":[{"text":"The de novo genome assemblies generated for this study, and the associated metadata.","lang":"eng"}],"type":"research_data"},{"day":"04","month":"10","article_processing_charge":"No","has_accepted_license":"1","keyword":["Cell migration","tracking","forward migration index","FMI"],"doi":"10.15479/AT:ISTA:75","date_published":"2017-10-04T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Hauschild, Robert. “Forward Migration Indexes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:75.","mla":"Hauschild, Robert. Forward Migration Indexes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:75.","short":"R. Hauschild, (2017).","ista":"Hauschild R. 2017. Forward migration indexes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:75.","ieee":"R. Hauschild, “Forward migration indexes.” Institute of Science and Technology Austria, 2017.","apa":"Hauschild, R. (2017). Forward migration indexes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:75","ama":"Hauschild R. Forward migration indexes. 2017. doi:10.15479/AT:ISTA:75"},"oa":1,"abstract":[{"lang":"eng","text":"Matlab script to calculate the forward migration indexes (/) from TrackMate spot-statistics files."}],"file_date_updated":"2020-07-14T12:47:04Z","datarep_id":"75","type":"research_data","date_created":"2018-12-12T12:31:35Z","date_updated":"2024-02-21T13:47:14Z","oa_version":"Published Version","file":[{"file_name":"IST-2017-75-v1+1_FMI.m","access_level":"open_access","content_type":"application/octet-stream","file_size":799,"creator":"system","relation":"main_file","file_id":"5596","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:02:29Z","checksum":"cb7a2fa622460eca6231d659ce590e32"}],"author":[{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"}],"title":"Forward migration indexes","status":"public","ddc":["570"],"department":[{"_id":"Bio"}],"publisher":"Institute of Science and Technology Austria","_id":"5570","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2017-08-09T00:00:00Z","doi":"10.15479/AT:ISTA:71","citation":{"ama":"Leithner AF. Immunological synapse DC-Tcells. 2017. doi:10.15479/AT:ISTA:71","ista":"Leithner AF. 2017. Immunological synapse DC-Tcells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:71.","apa":"Leithner, A. F. (2017). Immunological synapse DC-Tcells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:71","ieee":"A. F. Leithner, “Immunological synapse DC-Tcells.” Institute of Science and Technology Austria, 2017.","mla":"Leithner, Alexander F. Immunological Synapse DC-Tcells. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:71.","short":"A.F. Leithner, (2017).","chicago":"Leithner, Alexander F. “Immunological Synapse DC-Tcells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:71."},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"month":"08","day":"09","has_accepted_license":"1","article_processing_charge":"No","keyword":["Immunological synapse"],"author":[{"full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F"}],"date_updated":"2024-02-21T13:47:00Z","date_created":"2018-12-12T12:31:34Z","file":[{"access_level":"open_access","file_name":"IST-2017-71-v1+1_Synapse_1.avi","content_type":"video/x-msvideo","file_size":236204020,"creator":"system","relation":"main_file","file_id":"5612","checksum":"3d6942d47d0737d064706b5728c4d8c8","date_created":"2018-12-12T13:02:47Z","date_updated":"2020-07-14T12:47:04Z"},{"creator":"system","content_type":"video/x-msvideo","file_size":226232496,"file_name":"IST-2017-71-v1+2_Synapse_2.avi","access_level":"open_access","date_created":"2018-12-12T13:02:51Z","date_updated":"2020-07-14T12:47:04Z","checksum":"4850006c047b0147a9e85b3c2f6f0af4","file_id":"5613","relation":"main_file"}],"oa_version":"Published Version","_id":"5567","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","status":"public","ddc":["570"],"title":"Immunological synapse DC-Tcells","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:47:04Z","abstract":[{"lang":"eng","text":"Immunological synapse DC-Tcells"}],"datarep_id":"71","type":"research_data"},{"date_published":"2017-03-10T00:00:00Z","doi":"10.15479/AT:ISTA:53","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:53.","mla":"Bergmiller, Tobias, et al. Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:53.","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, (2017).","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:53.","ieee":"T. Bergmiller et al., “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:53","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:10.15479/AT:ISTA:53"},"day":"10","month":"03","article_processing_charge":"No","has_accepted_license":"1","keyword":["single cell microscopy","mother machine microfluidic device","AcrAB-TolC pump","multi-drug efflux","Escherichia coli"],"date_updated":"2024-02-21T13:49:00Z","date_created":"2018-12-12T12:31:32Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5603","checksum":"d77859af757ac8025c50c7b12b52eaf3","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:02:38Z","access_level":"open_access","file_name":"IST-2017-53-v1+1_Data_MDE.zip","file_size":6773204,"content_type":"application/zip","creator":"system"}],"author":[{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"orcid":"0000-0003-2912-6769","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","last_name":"Andersson","first_name":"Anna M","full_name":"Andersson, Anna M"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","first_name":"Kathrin","last_name":"Tomasek","full_name":"Tomasek, Kathrin"},{"last_name":"Balleza","first_name":"Enrique","full_name":"Balleza, Enrique"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"665"}]},"ddc":["571"],"status":"public","title":"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5560","year":"2017","abstract":[{"text":"This repository contains the data collected for the manuscript \"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity\".\r\nThe data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.\r\nData is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic \"mother machine\" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:03Z","datarep_id":"53","type":"research_data"},{"scopus_import":1,"day":"21","article_processing_charge":"No","article_type":"original","page":"311 - 315","publication":"Science","citation":{"ieee":"T. Bergmiller et al., “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science, vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315, 2017.","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf4762","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 2017;356(6335):311-315. doi:10.1126/science.aaf4762","chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.","mla":"Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:10.1126/science.aaf4762."},"date_published":"2017-04-21T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria."}],"issue":"6335","status":"public","title":"Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity","intvolume":" 356","_id":"665","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","month":"04","publication_identifier":{"issn":["00368075"]},"quality_controlled":"1","project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"doi":"10.1126/science.aaf4762","publist_id":"7064","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"year":"2017","date_updated":"2024-02-21T13:49:00Z","date_created":"2018-12-11T11:47:48Z","volume":356,"author":[{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"first_name":"Anna M","last_name":"Andersson","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2912-6769","full_name":"Andersson, Anna M"},{"full_name":"Tomasek, Kathrin","first_name":"Kathrin","last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X"},{"full_name":"Balleza, Enrique","last_name":"Balleza","first_name":"Enrique"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5560"}]}},{"month":"11","day":"06","article_processing_charge":"No","has_accepted_license":"1","doi":"10.15479/AT:ISTA:78","date_published":"2017-11-06T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"short":"B. Vicoso, (2017).","mla":"Vicoso, Beatriz. Data for “The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:78.","chicago":"Vicoso, Beatriz. “Data for ‘The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:78.","ama":"Vicoso B. Data for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” 2017. doi:10.15479/AT:ISTA:78","ieee":"B. Vicoso, “Data for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.’” Institute of Science and Technology Austria, 2017.","apa":"Vicoso, B. (2017). Data for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:78","ista":"Vicoso B. 2017. Data for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:78."},"oa":1,"abstract":[{"text":"This folder contains all the data used in each of the main figures of \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures. \r\n","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:04Z","datarep_id":"78","type":"research_data","author":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"contributor":[{"first_name":"Beatriz","last_name":"Vicoso","contributor_type":"contact_person","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"542","relation":"research_paper","status":"public"}]},"date_created":"2018-12-12T12:31:36Z","date_updated":"2024-02-21T13:48:16Z","file":[{"file_name":"IST-2017-78-v1+1_Data.zip","access_level":"open_access","creator":"system","file_size":143697895,"content_type":"application/zip","file_id":"5618","relation":"main_file","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:03:00Z","checksum":"4520eb2b8379417ee916995719158f16"}],"oa_version":"Submitted Version","year":"2017","_id":"5571","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["576"],"title":"Data for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"}]},{"doi":"10.15479/AT:ISTA:51","date_published":"2017-01-02T00:00:00Z","oa":1,"citation":{"mla":"Pavlogiannis, Andreas, et al. Strong Amplifiers of Natural Selection. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:51.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak , (2017).","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak . “Strong Amplifiers of Natural Selection.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:51.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Strong amplifiers of natural selection. 2017. doi:10.15479/AT:ISTA:51","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Strong amplifiers of natural selection, Institute of Science and Technology Austria, 10.15479/AT:ISTA:51.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak , M. (2017). Strong amplifiers of natural selection. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:51","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak , “Strong amplifiers of natural selection.” Institute of Science and Technology Austria, 2017."},"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"has_accepted_license":"1","article_processing_charge":"No","month":"01","day":"02","keyword":["natural selection"],"related_material":{"record":[{"id":"5452","relation":"research_paper","status":"public"},{"status":"public","relation":"research_paper","id":"5751"}]},"author":[{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"},{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Nowak , Martin","last_name":"Nowak ","first_name":"Martin"}],"file":[{"file_id":"5644","relation":"main_file","checksum":"b427dd46a30096a1911b245640c47af8","date_created":"2018-12-12T13:05:18Z","date_updated":"2020-07-14T12:47:02Z","access_level":"open_access","file_name":"IST-2017-51-v1+2_illustration.mp4","creator":"system","file_size":32987015,"content_type":"video/mp4"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:32Z","date_updated":"2024-02-21T13:48:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5559","year":"2017","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrCh"}],"title":"Strong amplifiers of natural selection","ddc":["519"],"status":"public","ec_funded":1,"abstract":[{"lang":"eng","text":"Strong amplifiers of natural selection"}],"file_date_updated":"2020-07-14T12:47:02Z","type":"research_data","datarep_id":"51"},{"oa_version":"Submitted Version","file":[{"file_size":49823,"content_type":"application/zip","creator":"system","access_level":"open_access","file_name":"IST-2017-79-v1+1_Code.zip","checksum":"3e70a7bcd6ff0c38b79e4c8a7d137034","date_created":"2018-12-12T13:05:15Z","date_updated":"2020-07-14T12:47:05Z","relation":"main_file","file_id":"5643"}],"date_created":"2018-12-12T12:31:36Z","date_updated":"2024-02-21T13:48:28Z","related_material":{"record":[{"id":"542","status":"public","relation":"research_paper"}]},"author":[{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"department":[{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","status":"public","title":"Code for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","ddc":["576"],"_id":"5572","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","file_date_updated":"2020-07-14T12:47:05Z","abstract":[{"lang":"eng","text":"Code described in the Supplementary Methods of \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\" (Kelemen, R., Vicoso, B.)"}],"type":"research_data","datarep_id":"79","date_published":"2017-11-06T00:00:00Z","doi":"10.15479/AT:ISTA:79 ","citation":{"apa":"Vicoso, B. (2017). Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:79 ","ieee":"B. Vicoso, “Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.’” Institute of Science and Technology Austria, 2017.","ista":"Vicoso B. 2017. Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:79 .","ama":"Vicoso B. Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” 2017. doi:10.15479/AT:ISTA:79 ","chicago":"Vicoso, Beatriz. “Code for ‘The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:79 .","short":"B. Vicoso, (2017).","mla":"Vicoso, Beatriz. Code for “The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:79 ."},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"has_accepted_license":"1","article_processing_charge":"No","day":"06","month":"11"},{"publisher":"eLife Sciences Publications","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"publication_status":"published","acknowledgement":"Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013 no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop at IST Austria for their contribution to the microscope setup and to Yvonne Kemper for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility","year":"2017","volume":6,"date_updated":"2024-02-21T13:49:34Z","date_created":"2018-12-11T11:49:21Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5566"}]},"author":[{"full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"full_name":"Barone, Vanessa","first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"article_number":"e26792","publist_id":"6471","ec_funded":1,"file_date_updated":"2020-07-14T12:48:15Z","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular basis of root growth inhibition by auxin","grant_number":"M02128","_id":"2572ED28-B435-11E9-9278-68D0E5697425"},{"grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"},{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000404728300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"doi":"10.7554/eLife.26792","month":"06","intvolume":" 6","title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","ddc":["570"],"status":"public","_id":"946","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","file_id":"5315","checksum":"9af3398cb0d81f99d79016a616df22e9","date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-12T10:17:57Z","access_level":"open_access","file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","content_type":"application/pdf","file_size":19581847,"creator":"system"}],"oa_version":"Published Version","pubrep_id":"847","type":"journal_article","abstract":[{"lang":"eng","text":"Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes."}],"citation":{"mla":"von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences Publications, 2017, doi:10.7554/eLife.26792.","short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","chicago":"Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.26792.","ama":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 2017;6. doi:10.7554/eLife.26792","ista":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792.","ieee":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., & Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.26792"},"publication":"eLife","date_published":"2017-06-19T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"19"},{"oa":1,"external_id":{"isi":["000397847200041"]},"isi":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"doi":"10.3791/55044","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"01","year":"2017","publication_status":"published","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publisher":"Journal of Visualized Experiments","author":[{"first_name":"Daniel","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5565"}]},"date_updated":"2024-02-21T13:49:12Z","date_created":"2018-12-11T11:50:01Z","volume":2017,"article_number":"e55044","file_date_updated":"2018-12-12T10:16:32Z","publist_id":"6302","ec_funded":1,"publication":"Journal of visualized experiments JoVE","citation":{"ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” Journal of visualized experiments JoVE, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of Visualized Experiments JoVE. Journal of Visualized Experiments. https://doi.org/10.3791/55044","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017;2017(119). doi:10.3791/55044","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE. Journal of Visualized Experiments, 2017. https://doi.org/10.3791/55044.","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:10.3791/55044.","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017)."},"date_published":"2017-01-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1078","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","ddc":["580"],"status":"public","intvolume":" 2017","pubrep_id":"808","file":[{"file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","access_level":"open_access","creator":"system","file_size":57678,"content_type":"application/pdf","file_id":"5219","relation":"main_file","date_created":"2018-12-12T10:16:31Z","date_updated":"2018-12-12T10:16:31Z"},{"file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1317820,"creator":"system","relation":"main_file","file_id":"5220","date_updated":"2018-12-12T10:16:32Z","date_created":"2018-12-12T10:16:32Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. "}],"issue":"119"},{"date_published":"2017-04-10T00:00:00Z","doi":"10.15479/AT:ISTA:66","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1,"citation":{"ama":"von Wangenheim D, Hauschild R, Friml J. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. 2017. doi:10.15479/AT:ISTA:66","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel.” Institute of Science and Technology Austria, 2017.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:66","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel, Institute of Science and Technology Austria, 10.15479/AT:ISTA:66.","short":"D. von Wangenheim, R. Hauschild, J. Friml, (2017).","mla":"von Wangenheim, Daniel, et al. Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:66.","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:66."},"article_processing_charge":"No","has_accepted_license":"1","month":"04","day":"10","file":[{"creator":"system","content_type":"video/mp4","file_size":101497758,"access_level":"open_access","file_name":"IST-2017-66-v1+1_WangenheimHighResolution55044-NEW_1.mp4","checksum":"b7552fc23540a85dc5a22fd4484eae71","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:02:33Z","file_id":"5599","relation":"main_file"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:34Z","date_updated":"2024-02-21T13:49:13Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1078"}]},"author":[{"full_name":"Von Wangenheim, Daniel","last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"},{"_id":"Bio"}],"title":"Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel","status":"public","ddc":["580"],"year":"2017","_id":"5565","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"fund: FP7-ERC 0101109","ec_funded":1,"publist_id":"6302","file_date_updated":"2020-07-14T12:47:03Z","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. \r\nThe Video is licensed under a CC BY NC ND license. "}],"type":"research_data","datarep_id":"66"},{"datarep_id":"69","type":"research_data","file_date_updated":"2020-07-14T12:47:04Z","abstract":[{"text":"Current minimal version of TipTracker","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5566","year":"2017","status":"public","title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","ddc":["570"],"department":[{"_id":"Bio"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"}],"related_material":{"record":[{"id":"946","status":"public","relation":"research_paper"}]},"date_updated":"2024-02-21T13:49:34Z","date_created":"2018-12-12T12:31:34Z","oa_version":"Published Version","file":[{"file_id":"5636","relation":"main_file","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:12Z","checksum":"a976000e6715106724a271cc9422be4a","file_name":"IST-2017-69-v1+2_TipTrackerZeissLSM700.zip","access_level":"open_access","creator":"system","file_size":1587986,"content_type":"application/zip"}],"keyword":["tool","tracking","confocal microscopy"],"day":"21","month":"07","has_accepted_license":"1","article_processing_charge":"No","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"citation":{"chicago":"Hauschild, Robert. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:69.","short":"R. Hauschild, (2017).","mla":"Hauschild, Robert. Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:69.","apa":"Hauschild, R. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:69","ieee":"R. Hauschild, “Live tracking of moving samples in confocal microscopy for vertically grown roots.” Institute of Science and Technology Austria, 2017.","ista":"Hauschild R. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots, Institute of Science and Technology Austria, 10.15479/AT:ISTA:69.","ama":"Hauschild R. Live tracking of moving samples in confocal microscopy for vertically grown roots. 2017. doi:10.15479/AT:ISTA:69"},"oa":1,"doi":"10.15479/AT:ISTA:69","date_published":"2017-07-21T00:00:00Z"},{"publist_id":"7399","department":[{"_id":"UlWa"}],"editor":[{"first_name":"Martin","last_name":"Loebl","full_name":"Loebl, Martin"},{"full_name":"Nešetřil, Jaroslav","first_name":"Jaroslav","last_name":"Nešetřil"},{"full_name":"Thomas, Robin","last_name":"Thomas","first_name":"Robin"}],"publisher":"Springer","publication_status":"published","year":"2017","date_created":"2018-12-11T11:46:24Z","date_updated":"2024-02-28T12:59:37Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1512"}]},"author":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"full_name":"Paták, Pavel","last_name":"Paták","first_name":"Pavel"},{"orcid":"0000-0002-3975-1683","last_name":"Patakova","first_name":"Zuzana","full_name":"Patakova, Zuzana"},{"orcid":"0000-0002-1191-6714","last_name":"Tancer","first_name":"Martin","full_name":"Tancer, Martin"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"publication_identifier":{"isbn":["978-331944479-6"]},"month":"10","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1310.4613v3","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-44479-6_17","type":"book_chapter","abstract":[{"lang":"eng","text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b, d) such that the following holds. If F is a finite family of subsets of Rd such that βi(∩G)≤b for any G⊊F and every 0 ≤ i ≤ [d/2]-1 then F has Helly number at most h(b, d). Here βi denotes the reduced Z2-Betti numbers (with singular homology). These topological conditions are sharp: not controlling any of these [d/2] first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map C*(K)→C*(Rd)."}],"status":"public","title":"Bounding helly numbers via betti numbers","_id":"424","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","series_title":"A Journey Through Discrete Mathematics","scopus_import":1,"day":"06","page":"407 - 447","citation":{"ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding helly numbers via betti numbers. In: Loebl M, Nešetřil J, Thomas R, eds. A Journey through Discrete Mathematics: A Tribute to Jiri Matousek. A Journey Through Discrete Mathematics. Springer; 2017:407-447. doi:10.1007/978-3-319-44479-6_17","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2017). Bounding helly numbers via betti numbers. In M. Loebl, J. Nešetřil, & R. Thomas (Eds.), A Journey through Discrete Mathematics: A Tribute to Jiri Matousek (pp. 407–447). Springer. https://doi.org/10.1007/978-3-319-44479-6_17","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding helly numbers via betti numbers,” in A Journey through Discrete Mathematics: A Tribute to Jiri Matousek, M. Loebl, J. Nešetřil, and R. Thomas, Eds. Springer, 2017, pp. 407–447.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2017.Bounding helly numbers via betti numbers. In: A Journey through Discrete Mathematics: A Tribute to Jiri Matousek. , 407–447.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, M. Loebl, J. Nešetřil, R. Thomas (Eds.), A Journey through Discrete Mathematics: A Tribute to Jiri Matousek, Springer, 2017, pp. 407–447.","mla":"Goaoc, Xavier, et al. “Bounding Helly Numbers via Betti Numbers.” A Journey through Discrete Mathematics: A Tribute to Jiri Matousek, edited by Martin Loebl et al., Springer, 2017, pp. 407–47, doi:10.1007/978-3-319-44479-6_17.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers.” In A Journey through Discrete Mathematics: A Tribute to Jiri Matousek, edited by Martin Loebl, Jaroslav Nešetřil, and Robin Thomas, 407–47. A Journey Through Discrete Mathematics. Springer, 2017. https://doi.org/10.1007/978-3-319-44479-6_17."},"publication":"A Journey through Discrete Mathematics: A Tribute to Jiri Matousek","date_published":"2017-10-06T00:00:00Z"},{"date_updated":"2024-02-28T13:02:12Z","date_created":"2018-12-11T11:46:37Z","volume":27,"author":[{"full_name":"Altmeyer, Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","first_name":"Sebastian","last_name":"Altmeyer"},{"first_name":"Younghae","last_name":"Do","full_name":"Do, Younghae"},{"full_name":"Ryu, Soorok","last_name":"Ryu","first_name":"Soorok"}],"publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"BjHo"}],"year":"2017","file_date_updated":"2020-07-14T12:46:32Z","publist_id":"7358","article_number":"113112","language":[{"iso":"eng"}],"doi":"10.1063/1.5002771","quality_controlled":"1","oa":1,"month":"11","publication_identifier":{"issn":["10541500"]},"file":[{"file_name":"2017_Chaos_Altmeyer.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":7714020,"file_id":"6970","relation":"main_file","date_created":"2019-10-24T15:14:30Z","date_updated":"2020-07-14T12:46:32Z","checksum":"0731f9d416760c1062db258ca51f8bdc"}],"oa_version":"Published Version","title":"Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow","status":"public","ddc":["530"],"intvolume":" 27","_id":"463","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We investigate transient behaviors induced by magnetic fields on the dynamics of the flow of a ferrofluid in the gap between two concentric, independently rotating cylinders. Without applying any magnetic fields, we uncover emergence of flow states constituted by a combination of a localized spiral state (SPIl) in the top and bottom of the annulus and different multi-cell flow states (SPI2v, SPI3v) with toroidally closed vortices in the interior of the bulk (SPIl+2v = SPIl + SPI2v and SPIl+3v = SPIl + SPI3v). However, when a magnetic field is presented, we observe the transient behaviors between multi-cell states passing through two critical thresholds in a strength of an axial (transverse) magnetic field. Before the first critical threshold of a magnetic field strength, multi-stable states with different number of cells could be observed. After the first critical threshold, we find the transient behavior between the three- and two-cell flow states. For more strength of magnetic field or after the second critical threshold, we discover that multi-cell states are disappeared and a localized spiral state remains to be stimulated. The studied transient behavior could be understood by the investigation of various quantities including a modal kinetic energy, a mode amplitude of the radial velocity, wavenumber, angular momentum, and torque. In addition, the emergence of new flow states and the transient behavior between their states in ferrofluidic flows indicate that richer and potentially controllable dynamics through magnetic fields could be possible in ferrofluic flow.","lang":"eng"}],"issue":"11","type":"journal_article","date_published":"2017-11-01T00:00:00Z","article_type":"original","publication":"Chaos","citation":{"ieee":"S. Altmeyer, Y. Do, and S. Ryu, “Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow,” Chaos, vol. 27, no. 11. AIP Publishing, 2017.","apa":"Altmeyer, S., Do, Y., & Ryu, S. (2017). Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow. Chaos. AIP Publishing. https://doi.org/10.1063/1.5002771","ista":"Altmeyer S, Do Y, Ryu S. 2017. Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow. Chaos. 27(11), 113112.","ama":"Altmeyer S, Do Y, Ryu S. Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow. Chaos. 2017;27(11). doi:10.1063/1.5002771","chicago":"Altmeyer, Sebastian, Younghae Do, and Soorok Ryu. “Transient Behavior between Multi-Cell Flow States in Ferrofluidic Taylor-Couette Flow.” Chaos. AIP Publishing, 2017. https://doi.org/10.1063/1.5002771.","short":"S. Altmeyer, Y. Do, S. Ryu, Chaos 27 (2017).","mla":"Altmeyer, Sebastian, et al. “Transient Behavior between Multi-Cell Flow States in Ferrofluidic Taylor-Couette Flow.” Chaos, vol. 27, no. 11, 113112, AIP Publishing, 2017, doi:10.1063/1.5002771."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"language":[{"iso":"eng"}],"doi":"10.1063/1.4983703","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000405089400047"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.03684"}],"publication_identifier":{"issn":["00219606"]},"month":"06","volume":147,"date_created":"2018-12-11T11:49:36Z","date_updated":"2024-02-28T13:02:26Z","author":[{"full_name":"Shepperson, Benjamin","last_name":"Shepperson","first_name":"Benjamin"},{"last_name":"Chatterley","first_name":"Adam","full_name":"Chatterley, Adam"},{"first_name":"Anders","last_name":"Søndergaard","full_name":"Søndergaard, Anders"},{"full_name":"Christiansen, Lars","first_name":"Lars","last_name":"Christiansen"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"last_name":"Stapelfeldt","first_name":"Henrik","full_name":"Stapelfeldt, Henrik"}],"publisher":"AIP Publishing","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2017","publist_id":"6403","article_number":"013946","date_published":"2017-06-01T00:00:00Z","citation":{"ama":"Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt H. Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. 2017;147(1). doi:10.1063/1.4983703","ieee":"B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko, and H. Stapelfeldt, “Strongly aligned molecules inside helium droplets in the near-adiabatic regime,” The Journal of Chemical Physics, vol. 147, no. 1. AIP Publishing, 2017.","apa":"Shepperson, B., Chatterley, A., Søndergaard, A., Christiansen, L., Lemeshko, M., & Stapelfeldt, H. (2017). Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4983703","ista":"Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt H. 2017. Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. 147(1), 013946.","short":"B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko, H. Stapelfeldt, The Journal of Chemical Physics 147 (2017).","mla":"Shepperson, Benjamin, et al. “Strongly Aligned Molecules inside Helium Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics, vol. 147, no. 1, 013946, AIP Publishing, 2017, doi:10.1063/1.4983703.","chicago":"Shepperson, Benjamin, Adam Chatterley, Anders Søndergaard, Lars Christiansen, Mikhail Lemeshko, and Henrik Stapelfeldt. “Strongly Aligned Molecules inside Helium Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4983703."},"publication":"The Journal of Chemical Physics","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 147","status":"public","title":"Strongly aligned molecules inside helium droplets in the near-adiabatic regime","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"996","issue":"1","abstract":[{"text":"Iodine (I 2 ) molecules embedded in He nanodroplets are aligned by a 160 ps long laser pulse. The highest degree of alignment, occurring at the peak of the pulse and quantified by ⟨cos 2 θ 2D ⟩ , is measured as a function of the laser intensity. The results are well described by ⟨cos 2 θ 2D ⟩ calculated for a gas of isolated molecules each with an effective rotational constant of 0.6 times the gas-phase value, and at a temperature of 0.4 K. Theoretical analysis using the angulon quasiparticle to describe rotating molecules in superfluid helium rationalizes why the alignment mechanism is similar to that of isolated molecules with an effective rotational constant. A major advantage of molecules in He droplets is that their 0.4 K temperature leads to stronger alignment than what can generally be achieved for gas phase molecules -- here demonstrated by a direct comparison of the droplet results to measurements on a ∼ 1 K supersonic beam of isolated molecules. This point is further illustrated for more complex system by measurements on 1,4-diiodobenzene and 1,4-dibromobenzene. For all three molecular species studied the highest values of ⟨cos 2 θ 2D ⟩ achieved in He droplets exceed 0.96. ","lang":"eng"}],"type":"journal_article"},{"date_created":"2018-12-11T11:49:10Z","date_updated":"2024-02-28T13:07:56Z","volume":58,"author":[{"first_name":"Andreas","last_name":"Deuchert","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas"}],"publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"RoSe"}],"year":"2017","ec_funded":1,"publist_id":"6531","article_number":"081901","language":[{"iso":"eng"}],"doi":"10.1063/1.4996580","isi":1,"quality_controlled":"1","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"main_file_link":[{"url":"https://arxiv.org/abs/1703.04616","open_access":"1"}],"oa":1,"external_id":{"isi":["000409197200015"]},"month":"08","publication_identifier":{"issn":["00222488"]},"oa_version":"Submitted Version","status":"public","title":"A lower bound for the BCS functional with boundary conditions at infinity","intvolume":" 58","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"912","abstract":[{"text":"We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n","lang":"eng"}],"issue":"8","type":"journal_article","date_published":"2017-08-01T00:00:00Z","publication":" Journal of Mathematical Physics","citation":{"ieee":"A. Deuchert, “A lower bound for the BCS functional with boundary conditions at infinity,” Journal of Mathematical Physics, vol. 58, no. 8. AIP Publishing, 2017.","apa":"Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4996580","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. 58(8), 081901.","ama":"Deuchert A. A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. 2017;58(8). doi:10.1063/1.4996580","chicago":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” Journal of Mathematical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4996580.","short":"A. Deuchert, Journal of Mathematical Physics 58 (2017).","mla":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” Journal of Mathematical Physics, vol. 58, no. 8, 081901, AIP Publishing, 2017, doi:10.1063/1.4996580."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"},{"full_name":"Vishe, Pankaj","first_name":"Pankaj","last_name":"Vishe"}],"volume":11,"date_updated":"2024-03-05T11:43:38Z","date_created":"2018-12-11T11:45:30Z","year":"2017","acknowledgement":"While working on this paper the first author was supported by ERC grant 306457.","publisher":" Mathematical Sciences Publishers","publication_status":"published","publist_id":"7637","extern":"1","doi":"10.2140/ant.2017.11.1657","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1611.00553"]},"main_file_link":[{"url":"https://arxiv.org/abs/1611.00553","open_access":"1"}],"quality_controlled":"1","publication_identifier":{"eissn":["1944-7833"]},"month":"09","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"265","intvolume":" 11","status":"public","title":"Rational curves on smooth hypersurfaces of low degree","issue":"7","abstract":[{"text":"We establish the dimension and irreducibility of the moduli space of rational curves (of fixed degree) on arbitrary smooth hypersurfaces of sufficiently low degree. A spreading out argument reduces the problem to hypersurfaces defined over finite fields of large cardinality, which can then be tackled using a function field version of the Hardy-Littlewood circle method, in which particular care is taken to ensure uniformity in the size of the underlying finite field.","lang":"eng"}],"type":"journal_article","date_published":"2017-09-07T00:00:00Z","citation":{"ama":"Browning TD, Vishe P. Rational curves on smooth hypersurfaces of low degree. Geometric Methods in Algebra and Number Theory. 2017;11(7):1657-1675. doi:10.2140/ant.2017.11.1657","apa":"Browning, T. D., & Vishe, P. (2017). Rational curves on smooth hypersurfaces of low degree. Geometric Methods in Algebra and Number Theory. Mathematical Sciences Publishers. https://doi.org/10.2140/ant.2017.11.1657","ieee":"T. D. Browning and P. Vishe, “Rational curves on smooth hypersurfaces of low degree,” Geometric Methods in Algebra and Number Theory, vol. 11, no. 7. Mathematical Sciences Publishers, pp. 1657–1675, 2017.","ista":"Browning TD, Vishe P. 2017. Rational curves on smooth hypersurfaces of low degree. Geometric Methods in Algebra and Number Theory. 11(7), 1657–1675.","short":"T.D. Browning, P. Vishe, Geometric Methods in Algebra and Number Theory 11 (2017) 1657–1675.","mla":"Browning, Timothy D., and Pankaj Vishe. “Rational Curves on Smooth Hypersurfaces of Low Degree.” Geometric Methods in Algebra and Number Theory, vol. 11, no. 7, Mathematical Sciences Publishers, 2017, pp. 1657–75, doi:10.2140/ant.2017.11.1657.","chicago":"Browning, Timothy D, and Pankaj Vishe. “Rational Curves on Smooth Hypersurfaces of Low Degree.” Geometric Methods in Algebra and Number Theory. Mathematical Sciences Publishers, 2017. https://doi.org/10.2140/ant.2017.11.1657."},"publication":"Geometric Methods in Algebra and Number Theory","page":"1657 - 1675","article_type":"original","article_processing_charge":"No","day":"07"},{"publist_id":"7636","extern":"1","year":"2017","acknowledgement":"While working on this paper the first author was supported by ERC grant 306457.","publication_status":"published","publisher":"European Mathematical Society Publishing House","author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"},{"full_name":"Heath Brown, Roger","first_name":"Roger","last_name":"Heath Brown"}],"date_updated":"2024-03-05T11:47:15Z","date_created":"2018-12-11T11:45:31Z","volume":19,"month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.5937"}],"external_id":{"arxiv":["1403.5937"]},"quality_controlled":"1","doi":"10.4171/JEMS/668","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We generalise Birch's seminal work on forms in many variables to handle a system of forms in which the degrees need not all be the same. This allows us to prove the Hasse principle, weak approximation, and the Manin-Peyre conjecture for a smooth and geometrically integral variety X Pm, provided only that its dimension is large enough in terms of its degree."}],"issue":"2","_id":"266","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Forms in many variables and differing degrees","status":"public","intvolume":" 19","oa_version":"Preprint","day":"26","article_processing_charge":"No","publication":"Journal of the European Mathematical Society","citation":{"ieee":"T. D. Browning and R. Heath Brown, “Forms in many variables and differing degrees,” Journal of the European Mathematical Society, vol. 19, no. 2. European Mathematical Society Publishing House, pp. 357–394, 2017.","apa":"Browning, T. D., & Heath Brown, R. (2017). Forms in many variables and differing degrees. Journal of the European Mathematical Society. European Mathematical Society Publishing House. https://doi.org/10.4171/JEMS/668","ista":"Browning TD, Heath Brown R. 2017. Forms in many variables and differing degrees. Journal of the European Mathematical Society. 19(2), 357–394.","ama":"Browning TD, Heath Brown R. Forms in many variables and differing degrees. Journal of the European Mathematical Society. 2017;19(2):357-394. doi:10.4171/JEMS/668","chicago":"Browning, Timothy D, and Roger Heath Brown. “Forms in Many Variables and Differing Degrees.” Journal of the European Mathematical Society. European Mathematical Society Publishing House, 2017. https://doi.org/10.4171/JEMS/668.","short":"T.D. Browning, R. Heath Brown, Journal of the European Mathematical Society 19 (2017) 357–394.","mla":"Browning, Timothy D., and Roger Heath Brown. “Forms in Many Variables and Differing Degrees.” Journal of the European Mathematical Society, vol. 19, no. 2, European Mathematical Society Publishing House, 2017, pp. 357–94, doi:10.4171/JEMS/668."},"article_type":"original","page":"357 - 394","date_published":"2017-01-26T00:00:00Z"},{"publication":"Chemistry of Materials","citation":{"mla":"Berestok, Taisiia, et al. “Tuning Branching in Ceria Nanocrystals.” Chemistry of Materials, vol. 29, no. 10, American Chemical Society, 2017, pp. 4418–24, doi:10.1021/acs.chemmater.7b00896.","short":"T. Berestok, P. Guardia, J. Blanco, R. Nafria, P. Torruella, L. López Conesa, S. Estradé, M. Ibáñez, J. De Roo, Z. Luo, D. Cadavid, J. Martins, M. Kovalenko, F. Peiró, A. Cabot, Chemistry of Materials 29 (2017) 4418–4424.","chicago":"Berestok, Taisiia, Pablo Guardia, Javier Blanco, Raquel Nafria, Pau Torruella, Luis López Conesa, Sònia Estradé, et al. “Tuning Branching in Ceria Nanocrystals.” Chemistry of Materials. American Chemical Society, 2017. https://doi.org/10.1021/acs.chemmater.7b00896.","ama":"Berestok T, Guardia P, Blanco J, et al. Tuning branching in ceria nanocrystals. Chemistry of Materials. 2017;29(10):4418-4424. doi:10.1021/acs.chemmater.7b00896","ista":"Berestok T, Guardia P, Blanco J, Nafria R, Torruella P, López Conesa L, Estradé S, Ibáñez M, De Roo J, Luo Z, Cadavid D, Martins J, Kovalenko M, Peiró F, Cabot A. 2017. Tuning branching in ceria nanocrystals. Chemistry of Materials. 29(10), 4418–4424.","ieee":"T. Berestok et al., “Tuning branching in ceria nanocrystals,” Chemistry of Materials, vol. 29, no. 10. American Chemical Society, pp. 4418–4424, 2017.","apa":"Berestok, T., Guardia, P., Blanco, J., Nafria, R., Torruella, P., López Conesa, L., … Cabot, A. (2017). Tuning branching in ceria nanocrystals. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.7b00896"},"article_type":"original","page":"4418 - 4424","date_published":"2017-04-24T00:00:00Z","day":"24","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"375","title":"Tuning branching in ceria nanocrystals","status":"public","intvolume":" 29","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Branched nanocrystals (NCs) enable high atomic surface exposure within a crystalline network that provides avenues for charge transport. This combination of properties makes branched NCs particularly suitable for a range of applications where both interaction with the media and charge transport are involved. Herein we report on the colloidal synthesis of branched ceria NCs by means of a ligand-mediated overgrowth mechanism. In particular, the differential coverage of oleic acid as an X-type ligand at ceria facets with different atomic density, atomic coordination deficiency, and oxygen vacancy density resulted in a preferential growth in the [111] direction and thus in the formation of ceria octapods. Alcohols, through an esterification alcoholysis reaction, promoted faster growth rates that translated into nanostructures with higher geometrical complexity, increasing the branch aspect ratio and triggering the formation of side branches. On the other hand, the presence of water resulted in a significant reduction of the growth rate, decreasing the reaction yield and eliminating side branching, which we associate to a blocking of the surface reaction sites or a displacement of the alcoholysis reaction. Overall, adjusting the amounts of each chemical, well-defined branched ceria NCs with tuned number, thickness, and length of branches and with overall size ranging from 5 to 45 nm could be produced. We further demonstrate that such branched ceria NCs are able to provide higher surface areas and related oxygen storage capacities (OSC) than quasi-spherical NCs.\r\n\r\n"}],"issue":"10","quality_controlled":"1","doi":"10.1021/acs.chemmater.7b00896","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["0897-4756"],"eissn":["1520-5002"]},"year":"2017","acknowledgement":"This work was supported by the European Regional Development Funds and the Spanish MINECO project BOOSTER. T.B. is grateful for the FI-AGAUR Research Fellowship Program, Generalitat de Catalunya (2015 FI_B 00744). P.G. acknowledges the People Programme (Marie Curie Actions) of the FP7/2007-2013 European Union Program (TECNIOspring Grant Agreement No. 600388) and the Agency for Business Competitiveness of the Government of Catalonia, ACCIÓ. M.I. thanks AGAUR for Beatriu de Pinós postdoctoral grant (2013 BP-A00344). Z.L. thanks the China Scholarship Council for scholarship support.","publication_status":"published","publisher":"American Chemical Society","author":[{"last_name":"Berestok","first_name":"Taisiia","full_name":"Berestok, Taisiia"},{"last_name":"Guardia","first_name":"Pablo","full_name":"Guardia, Pablo"},{"last_name":"Blanco","first_name":"Javier","full_name":"Blanco, Javier"},{"last_name":"Nafria","first_name":"Raquel","full_name":"Nafria, Raquel"},{"full_name":"Torruella, Pau","first_name":"Pau","last_name":"Torruella"},{"last_name":"López Conesa","first_name":"Luis","full_name":"López Conesa, Luis"},{"first_name":"Sònia","last_name":"Estradé","full_name":"Estradé, Sònia"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibanez Sabate","full_name":"Ibanez Sabate, Maria"},{"first_name":"Jonathan","last_name":"De Roo","full_name":"De Roo, Jonathan"},{"last_name":"Luo","first_name":"Zhishan","full_name":"Luo, Zhishan"},{"last_name":"Cadavid","first_name":"Doris","full_name":"Cadavid, Doris"},{"full_name":"Martins, José","last_name":"Martins","first_name":"José"},{"full_name":"Kovalenko, Maksym","first_name":"Maksym","last_name":"Kovalenko"},{"full_name":"Peiró, Francesca","last_name":"Peiró","first_name":"Francesca"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"date_updated":"2024-03-05T12:19:17Z","date_created":"2018-12-11T11:46:07Z","volume":29,"publist_id":"7455","extern":"1"},{"date_published":"2017-04-10T00:00:00Z","article_type":"review","page":"5865 - 6109","publication":"Chemical Reviews","citation":{"ama":"Coughlan C, Ibáñez M, Dobrozhan O, Singh A, Cabot A, Ryan K. Compound copper chalcogenide nanocrystals. Chemical Reviews. 2017;117(9):5865-6109. doi:10.1021/acs.chemrev.6b00376","ieee":"C. Coughlan, M. Ibáñez, O. Dobrozhan, A. Singh, A. Cabot, and K. Ryan, “Compound copper chalcogenide nanocrystals,” Chemical Reviews, vol. 117, no. 9. American Chemical Society, pp. 5865–6109, 2017.","apa":"Coughlan, C., Ibáñez, M., Dobrozhan, O., Singh, A., Cabot, A., & Ryan, K. (2017). Compound copper chalcogenide nanocrystals. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.6b00376","ista":"Coughlan C, Ibáñez M, Dobrozhan O, Singh A, Cabot A, Ryan K. 2017. Compound copper chalcogenide nanocrystals. Chemical Reviews. 117(9), 5865–6109.","short":"C. Coughlan, M. Ibáñez, O. Dobrozhan, A. Singh, A. Cabot, K. Ryan, Chemical Reviews 117 (2017) 5865–6109.","mla":"Coughlan, Claudia, et al. “Compound Copper Chalcogenide Nanocrystals.” Chemical Reviews, vol. 117, no. 9, American Chemical Society, 2017, pp. 5865–6109, doi:10.1021/acs.chemrev.6b00376.","chicago":"Coughlan, Claudia, Maria Ibáñez, Oleksandr Dobrozhan, Ajay Singh, Andreu Cabot, and Kevin Ryan. “Compound Copper Chalcogenide Nanocrystals.” Chemical Reviews. American Chemical Society, 2017. https://doi.org/10.1021/acs.chemrev.6b00376."},"day":"10","article_processing_charge":"No","oa_version":"None","title":"Compound copper chalcogenide nanocrystals","status":"public","intvolume":" 117","_id":"373","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"This review captures the synthesis, assembly, properties, and applications of copper chalcogenide NCs, which have achieved significant research interest in the last decade due to their compositional and structural versatility. The outstanding functional properties of these materials stems from the relationship between their band structure and defect concentration, including charge carrier concentration and electronic conductivity character, which consequently affects their optoelectronic, optical, and plasmonic properties. This, combined with several metastable crystal phases and stoichiometries and the low energy of formation of defects, makes the reproducible synthesis of these materials, with tunable parameters, remarkable. Further to this, the review captures the progress of the hierarchical assembly of these NCs, which bridges the link between their discrete and collective properties. Their ubiquitous application set has cross-cut energy conversion (photovoltaics, photocatalysis, thermoelectrics), energy storage (lithium-ion batteries, hydrogen generation), emissive materials (plasmonics, LEDs, biolabelling), sensors (electrochemical, biochemical), biomedical devices (magnetic resonance imaging, X-ray computer tomography), and medical therapies (photochemothermal therapies, immunotherapy, radiotherapy, and drug delivery). The confluence of advances in the synthesis, assembly, and application of these NCs in the past decade has the potential to significantly impact society, both economically and environmentally. "}],"issue":"9","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1021/acs.chemrev.6b00376","quality_controlled":"1","external_id":{"pmid":["28394585"]},"month":"04","publication_identifier":{"eissn":["1520-6890"],"issn":["0009-2665"]},"date_created":"2018-12-11T11:46:06Z","date_updated":"2024-03-05T12:17:59Z","volume":117,"author":[{"full_name":"Coughlan, Claudia","first_name":"Claudia","last_name":"Coughlan"},{"full_name":"Ibanez Sabate, Maria","last_name":"Ibanez Sabate","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dobrozhan, Oleksandr","last_name":"Dobrozhan","first_name":"Oleksandr"},{"first_name":"Ajay","last_name":"Singh","full_name":"Singh, Ajay"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"},{"first_name":"Kevin","last_name":"Ryan","full_name":"Ryan, Kevin"}],"publication_status":"published","publisher":"American Chemical Society","year":"2017","acknowledgement":"C.C. and K.M.R. gratefully acknowledge support from Science Foundation Ireland (SFI) under the Principal Investigator Program under Contract No. 11PI-1148. This work was conducted under the framework of the Irish Government’s Programme for Research in Third Level Institutions Cycle 5, National Development Plan 2007−2013 with the assistance of the European Regional Development Fund. A.S. gratefully acknowledges Director’s Postdoctoral Fellowship support from the Los Alamos National Laboratory. M.I., O.D., and A.C. gratefully acknowledge support from the European Regional Development Funds and the Spanish MINECO Project BOOSTER (ENE2013-46624-C4-3-R). M.I. and O.D. thank AGAUR for their Beatriu de Pinós postdoctoral grant (2013 BP-A00344) and Ph.D. grant (2015 FI-B00810, 2016 FI-B100067), respectively.","pmid":1,"extern":"1","publist_id":"7456"},{"day":"01","article_processing_charge":"No","date_published":"2017-06-01T00:00:00Z","article_type":"original","page":"1044 - 1080","publication":"Proceedings of the London Mathematical Society","citation":{"mla":"Browning, Timothy D., and Alexander Gorodnik. “Power-Free Values of Polynomials on Symmetric Varieties.” Proceedings of the London Mathematical Society, vol. 114, no. 6, Wiley, 2017, pp. 1044–80, doi:10.1112/plms.12030.","short":"T.D. Browning, A. Gorodnik, Proceedings of the London Mathematical Society 114 (2017) 1044–1080.","chicago":"Browning, Timothy D, and Alexander Gorodnik. “Power-Free Values of Polynomials on Symmetric Varieties.” Proceedings of the London Mathematical Society. Wiley, 2017. https://doi.org/10.1112/plms.12030.","ama":"Browning TD, Gorodnik A. Power-free values of polynomials on symmetric varieties. Proceedings of the London Mathematical Society. 2017;114(6):1044-1080. doi:10.1112/plms.12030","ista":"Browning TD, Gorodnik A. 2017. Power-free values of polynomials on symmetric varieties. Proceedings of the London Mathematical Society. 114(6), 1044–1080.","ieee":"T. D. Browning and A. Gorodnik, “Power-free values of polynomials on symmetric varieties,” Proceedings of the London Mathematical Society, vol. 114, no. 6. Wiley, pp. 1044–1080, 2017.","apa":"Browning, T. D., & Gorodnik, A. (2017). Power-free values of polynomials on symmetric varieties. Proceedings of the London Mathematical Society. Wiley. https://doi.org/10.1112/plms.12030"},"abstract":[{"text":"Given a symmetric variety Y defined over Q and a non-zero polynomial with integer coefficients, we use techniques from homogeneous dynamics to establish conditions under which the polynomial can be made r-free for a Zariski dense set of integral points on Y . We also establish an asymptotic counting formula for this set. In the special case that Y is a quadric hypersurface, we give explicit bounds on the size of r by combining the argument with a uniform upper bound for the density of integral points on general affine quadrics defined over Q.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Preprint","title":"Power-free values of polynomials on symmetric varieties","status":"public","intvolume":" 114","_id":"270","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","publication_identifier":{"issn":["0024-6115"]},"language":[{"iso":"eng"}],"doi":"10.1112/plms.12030","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1606.06342","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1606.06342"]},"extern":"1","publist_id":"7632","date_updated":"2024-03-05T11:58:25Z","date_created":"2018-12-11T11:45:32Z","volume":114,"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D"},{"full_name":"Gorodnik, Alexander","last_name":"Gorodnik","first_name":"Alexander"}],"publication_status":"published","publisher":"Wiley","year":"2017","acknowledgement":"While working on this paper the authors were supported by ERC grants 306457 and 239606, respectively."},{"extern":"1","publist_id":"7634","publication_status":"published","publisher":"Oxford University Press","acknowledgement":"Whilst working on this paper the authors were supported by ERC grant 306457.","year":"2017","date_updated":"2024-03-05T11:52:36Z","date_created":"2018-12-11T11:45:31Z","volume":2017,"author":[{"last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"},{"full_name":"Prendiville, Sean","first_name":"Sean","last_name":"Prendiville"}],"month":"04","publication_identifier":{"issn":["1073-7928"]},"quality_controlled":"1","external_id":{"arxiv":["1510.00136"]},"main_file_link":[{"url":"https://arxiv.org/abs/1510.00136","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/imrn/rnw096","type":"journal_article","abstract":[{"lang":"eng","text":"We show that any subset of the squares of positive relative upper density contains nontrivial solutions to a translation-invariant linear equation in five or more variables, with explicit quantitative bounds. As a consequence, we establish the partition regularity of any diagonal quadric in five or more variables whose coefficients sum to zero. Unlike previous approaches, which are limited to equations in seven or more variables, we employ transference technology of Green to import bounds from the linear setting."}],"issue":"7","title":"A transference approach to a Roth-type theorem in the squares","status":"public","intvolume":" 2017","_id":"268","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","day":"01","article_processing_charge":"No","article_type":"original","page":"2219 - 2248","publication":"International Mathematics Research Notices","citation":{"chicago":"Browning, Timothy D, and Sean Prendiville. “A Transference Approach to a Roth-Type Theorem in the Squares.” International Mathematics Research Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnw096.","mla":"Browning, Timothy D., and Sean Prendiville. “A Transference Approach to a Roth-Type Theorem in the Squares.” International Mathematics Research Notices, vol. 2017, no. 7, Oxford University Press, 2017, pp. 2219–48, doi:10.1093/imrn/rnw096.","short":"T.D. Browning, S. Prendiville, International Mathematics Research Notices 2017 (2017) 2219–2248.","ista":"Browning TD, Prendiville S. 2017. A transference approach to a Roth-type theorem in the squares. International Mathematics Research Notices. 2017(7), 2219–2248.","apa":"Browning, T. D., & Prendiville, S. (2017). A transference approach to a Roth-type theorem in the squares. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnw096","ieee":"T. D. Browning and S. Prendiville, “A transference approach to a Roth-type theorem in the squares,” International Mathematics Research Notices, vol. 2017, no. 7. Oxford University Press, pp. 2219–2248, 2017.","ama":"Browning TD, Prendiville S. A transference approach to a Roth-type theorem in the squares. International Mathematics Research Notices. 2017;2017(7):2219-2248. doi:10.1093/imrn/rnw096"},"date_published":"2017-04-01T00:00:00Z"},{"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://research-information.bristol.ac.uk/en/publications/norm-forms-for-arbitrary-number-fields-as-products-of-linear-polynomials(f79a584b-ec58-47c8-aa97-8c5505e3f751).html"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.24033/asens.2348","month":"12","publication_status":"published","publisher":"Societe Mathematique de France","acknowledgement":"While working on this paper the first author was supported by ERC grant 306457 and the second author was supported by EPSRC grant EP/E053262/1 and by ERC grant 208091. Some of this work was carried out during the programme “Arithmetic and geometry” in 2013 at the Hausdorff Institute in Bonn.","year":"2017","date_created":"2018-12-11T11:45:32Z","date_updated":"2024-03-05T12:13:35Z","volume":50,"author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning"},{"first_name":"Lilian","last_name":"Matthiesen","full_name":"Matthiesen, Lilian"}],"extern":"1","publist_id":"7630","article_type":"original","page":"1383 - 1446","publication":"Annales Scientifiques de l'Ecole Normale Superieure","citation":{"short":"T.D. Browning, L. Matthiesen, Annales Scientifiques de l’Ecole Normale Superieure 50 (2017) 1383–1446.","mla":"Browning, Timothy D., and Lilian Matthiesen. “Norm Forms for Arbitrary Number Fields as Products of Linear Polynomials.” Annales Scientifiques de l’Ecole Normale Superieure, vol. 50, no. 6, Societe Mathematique de France, 2017, pp. 1383–446, doi:10.24033/asens.2348.","chicago":"Browning, Timothy D, and Lilian Matthiesen. “Norm Forms for Arbitrary Number Fields as Products of Linear Polynomials.” Annales Scientifiques de l’Ecole Normale Superieure. Societe Mathematique de France, 2017. https://doi.org/10.24033/asens.2348.","ama":"Browning TD, Matthiesen L. Norm forms for arbitrary number fields as products of linear polynomials. Annales Scientifiques de l’Ecole Normale Superieure. 2017;50(6):1383-1446. doi:10.24033/asens.2348","ieee":"T. D. Browning and L. Matthiesen, “Norm forms for arbitrary number fields as products of linear polynomials,” Annales Scientifiques de l’Ecole Normale Superieure, vol. 50, no. 6. Societe Mathematique de France, pp. 1383–1446, 2017.","apa":"Browning, T. D., & Matthiesen, L. (2017). Norm forms for arbitrary number fields as products of linear polynomials. Annales Scientifiques de l’Ecole Normale Superieure. Societe Mathematique de France. https://doi.org/10.24033/asens.2348","ista":"Browning TD, Matthiesen L. 2017. Norm forms for arbitrary number fields as products of linear polynomials. Annales Scientifiques de l’Ecole Normale Superieure. 50(6), 1383–1446."},"date_published":"2017-12-01T00:00:00Z","day":"01","article_processing_charge":"No","status":"public","title":"Norm forms for arbitrary number fields as products of linear polynomials","intvolume":" 50","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"272","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Given a number field K/Q and a polynomial P ε Q [t], all of whose roots are Q, let X be the variety defined by the equation NK (x) = P (t). Combining additive combinatiorics with descent we show that the Brauer-Manin obstruction is the only obstruction to the Hesse principle and weak approximation on any smooth and projective model of X.","lang":"eng"}],"issue":"6"},{"issue":"731","abstract":[{"lang":"eng","text":"We show that a non-singular integral form of degree d is soluble over the integers if and only if it is soluble over ℝ and over ℚp for all primes p, provided that the form has at least (d - 1/2 √d)2d variables. This improves on a longstanding result of Birch."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 2017","status":"public","title":"Improvements in Birch's theorem on forms in many variables","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"256","article_processing_charge":"No","day":"01","date_published":"2017-10-01T00:00:00Z","page":"122","article_type":"original","citation":{"chicago":"Browning, Timothy D, and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, 2017. https://doi.org/10.1515/crelle-2014-0122.","mla":"Browning, Timothy D., and Sean Prendiville. “Improvements in Birch’s Theorem on Forms in Many Variables.” Journal Fur Die Reine Und Angewandte Mathematik, vol. 2017, no. 731, Walter de Gruyter, 2017, p. 122, doi:10.1515/crelle-2014-0122.","short":"T.D. Browning, S. Prendiville, Journal Fur Die Reine Und Angewandte Mathematik 2017 (2017) 122.","ista":"Browning TD, Prendiville S. 2017. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017(731), 122.","apa":"Browning, T. D., & Prendiville, S. (2017). Improvements in Birch’s theorem on forms in many variables. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle-2014-0122","ieee":"T. D. Browning and S. Prendiville, “Improvements in Birch’s theorem on forms in many variables,” Journal fur die Reine und Angewandte Mathematik, vol. 2017, no. 731. Walter de Gruyter, p. 122, 2017.","ama":"Browning TD, Prendiville S. Improvements in Birch’s theorem on forms in many variables. Journal fur die Reine und Angewandte Mathematik. 2017;2017(731):122. doi:10.1515/crelle-2014-0122"},"publication":"Journal fur die Reine und Angewandte Mathematik","extern":"1","publist_id":"7646","volume":2017,"date_created":"2018-12-11T11:45:28Z","date_updated":"2024-03-05T12:09:21Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"271"}]},"author":[{"full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prendiville, Sean","last_name":"Prendiville","first_name":"Sean"}],"publisher":"Walter de Gruyter","publication_status":"published","year":"2017","acknowledgement":"While working on this paper the authors were supported by the Leverhulme Trust and ERC grant 306457.","publication_identifier":{"issn":["0075-4102"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1515/crelle-2014-0122","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1402.4489","open_access":"1"}],"external_id":{"arxiv":["1402.4489"]},"oa":1},{"extern":"1","publist_id":"7635","publisher":"Cambridge University Press","publication_status":"published","acknowledgement":"While working on this paper the author was supported by ERC grant 306457.","year":"2017","volume":63,"date_created":"2018-12-11T11:45:31Z","date_updated":"2024-03-05T11:49:27Z","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D"}],"publication_identifier":{"issn":["0025-5793"]},"month":"11","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1701.00525"}],"external_id":{"arxiv":["1701.00525"]},"language":[{"iso":"eng"}],"doi":"10.1112/S0025579317000195","type":"journal_article","issue":"3","abstract":[{"text":"Building on recent work of Bhargava, Elkies and Schnidman and of Kriz and Li, we produce infinitely many smooth cubic surfaces defined over the field of rational numbers that contain rational points.","lang":"eng"}],"intvolume":" 63","title":"Many cubic surfaces contain rational points","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"267","oa_version":"Preprint","article_processing_charge":"No","day":"29","page":"818 - 839","article_type":"original","citation":{"ista":"Browning TD. 2017. Many cubic surfaces contain rational points. Mathematika. 63(3), 818–839.","apa":"Browning, T. D. (2017). Many cubic surfaces contain rational points. Mathematika. Cambridge University Press. https://doi.org/10.1112/S0025579317000195","ieee":"T. D. Browning, “Many cubic surfaces contain rational points,” Mathematika, vol. 63, no. 3. Cambridge University Press, pp. 818–839, 2017.","ama":"Browning TD. Many cubic surfaces contain rational points. Mathematika. 2017;63(3):818-839. doi:10.1112/S0025579317000195","chicago":"Browning, Timothy D. “Many Cubic Surfaces Contain Rational Points.” Mathematika. Cambridge University Press, 2017. https://doi.org/10.1112/S0025579317000195.","mla":"Browning, Timothy D. “Many Cubic Surfaces Contain Rational Points.” Mathematika, vol. 63, no. 3, Cambridge University Press, 2017, pp. 818–39, doi:10.1112/S0025579317000195.","short":"T.D. Browning, Mathematika 63 (2017) 818–839."},"publication":"Mathematika","date_published":"2017-11-29T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1007/s00209-016-1746-2","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.5755"}],"external_id":{"arxiv":["1311.5755"]},"oa":1,"month":"04","volume":285,"date_created":"2018-12-11T11:45:32Z","date_updated":"2024-03-05T11:56:29Z","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"},{"first_name":"Daniel","last_name":"Loughran","full_name":"Loughran, Daniel"}],"publisher":"Springer","publication_status":"published","year":"2017","extern":"1","publist_id":"7633","date_published":"2017-04-01T00:00:00Z","page":"1249 - 1267","article_type":"original","citation":{"ama":"Browning TD, Loughran D. Varieties with too many rational points. Mathematische Zeitschrift. 2017;285(3-4):1249-1267. doi:10.1007/s00209-016-1746-2","ista":"Browning TD, Loughran D. 2017. Varieties with too many rational points. Mathematische Zeitschrift. 285(3–4), 1249–1267.","ieee":"T. D. Browning and D. Loughran, “Varieties with too many rational points,” Mathematische Zeitschrift, vol. 285, no. 3–4. Springer, pp. 1249–1267, 2017.","apa":"Browning, T. D., & Loughran, D. (2017). Varieties with too many rational points. Mathematische Zeitschrift. Springer. https://doi.org/10.1007/s00209-016-1746-2","mla":"Browning, Timothy D., and Daniel Loughran. “Varieties with Too Many Rational Points.” Mathematische Zeitschrift, vol. 285, no. 3–4, Springer, 2017, pp. 1249–67, doi:10.1007/s00209-016-1746-2.","short":"T.D. Browning, D. Loughran, Mathematische Zeitschrift 285 (2017) 1249–1267.","chicago":"Browning, Timothy D, and Daniel Loughran. “Varieties with Too Many Rational Points.” Mathematische Zeitschrift. Springer, 2017. https://doi.org/10.1007/s00209-016-1746-2."},"publication":"Mathematische Zeitschrift","article_processing_charge":"No","day":"01","oa_version":"Preprint","intvolume":" 285","status":"public","title":"Varieties with too many rational points","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"269","issue":"3-4","abstract":[{"lang":"eng","text":"We investigate Fano varieties defined over a number field that contain subvarieties whose number of rational points of bounded height is comparable to the total number on the variety."}],"type":"journal_article"},{"publisher":"Royal Society of Chemistry","publication_status":"published","pmid":1,"acknowledgement":"This work was supported by the European Regional Development Funds, the Spanish Ministerio de Econom?a y Competitividad through the projects BOOSTER (ENE2013-46624-C4-3-R) and SEHTOP (ENE2016-77798-C4-3-R). S. O. thanks AGAUR her PhD grant. Y. L. and Y. Z. thank the China Scholarship Council for scholarship support. M. I. acknowledges financial support by ETH Carrier Seed Grant (SEED-18 16-2) and M. V. K. acknowledges partial financial support by the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID, GA No. 306733).","year":"2017","volume":46,"date_created":"2018-12-11T11:46:06Z","date_updated":"2024-03-05T12:21:43Z","author":[{"full_name":"Ortega, Silvia","last_name":"Ortega","first_name":"Silvia"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibanez Sabate","full_name":"Ibanez Sabate, Maria"},{"orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu","full_name":"Liu, Yu"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Kovalenko, Maksym","first_name":"Maksym","last_name":"Kovalenko"},{"full_name":"Cadavid, Doris","last_name":"Cadavid","first_name":"Doris"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"extern":"1","publist_id":"7454","quality_controlled":"1","external_id":{"pmid":["28470243"]},"language":[{"iso":"eng"}],"doi":"10.1039/c6cs00567e","publication_identifier":{"issn":["0306-0012"],"eissn":["1460-4744"]},"month":"06","intvolume":" 46","status":"public","title":"Bottom up engineering of thermoelectric nanomaterials and devices from solution processed nanoparticle building blocks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"374","oa_version":"None","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"The conversion of thermal energy to electricity and vice versa by means of solid state thermoelectric devices is extremely appealing. However, its cost-effectiveness is seriously hampered by the relatively high production cost and low efficiency of current thermoelectric materials and devices. To overcome present challenges and enable a successful deployment of thermoelectric systems in their wide application range, materials with significantly improved performance need to be developed. Nanostructuration can help in several ways to reach the very particular group of properties required to achieve high thermoelectric performances. Nanodomains inserted within a crystalline matrix can provide large charge carrier concentrations without strongly influencing their mobility, thus allowing to reach very high electrical conductivities. Nanostructured materials contain numerous grain boundaries that efficiently scatter mid- and long-wavelength phonons thus reducing the thermal conductivity. Furthermore, nanocrystalline domains can enhance the Seebeck coefficient by modifying the density of states and/or providing type- and energy-dependent charge carrier scattering. All these advantages can only be reached when engineering a complex type of material, nanocomposites, with exquisite control over structural and chemical parameters at multiple length scales. Since current conventional nanomaterial production technologies lack such level of control, alternative strategies need to be developed and adjusted to the specifics of the field. A particularly suitable approach to produce nanocomposites with unique level of control over their structural and compositional parameters is their bottom-up engineering from solution-processed nanoparticles. In this work, we review the state-of-the-art of this technology applied to the thermoelectric field, including the synthesis of nanoparticles of suitable materials with precisely engineered composition and surface chemistry, their combination and consolidation into nanostructured materials, the strategies to electronically dope such materials and the attempts to fabricate thermoelectric devices using nanoparticle-based nanopowders and inks."}],"page":"3510 - 3528","article_type":"original","citation":{"chicago":"Ortega, Silvia, Maria Ibáñez, Yu Liu, Yu Zhang, Maksym Kovalenko, Doris Cadavid, and Andreu Cabot. “Bottom up Engineering of Thermoelectric Nanomaterials and Devices from Solution Processed Nanoparticle Building Blocks.” Chemical Society Reviews. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c6cs00567e.","mla":"Ortega, Silvia, et al. “Bottom up Engineering of Thermoelectric Nanomaterials and Devices from Solution Processed Nanoparticle Building Blocks.” Chemical Society Reviews, vol. 46, no. 12, Royal Society of Chemistry, 2017, pp. 3510–28, doi:10.1039/c6cs00567e.","short":"S. Ortega, M. Ibáñez, Y. Liu, Y. Zhang, M. Kovalenko, D. Cadavid, A. Cabot, Chemical Society Reviews 46 (2017) 3510–3528.","ista":"Ortega S, Ibáñez M, Liu Y, Zhang Y, Kovalenko M, Cadavid D, Cabot A. 2017. Bottom up engineering of thermoelectric nanomaterials and devices from solution processed nanoparticle building blocks. Chemical Society Reviews. 46(12), 3510–3528.","ieee":"S. Ortega et al., “Bottom up engineering of thermoelectric nanomaterials and devices from solution processed nanoparticle building blocks,” Chemical Society Reviews, vol. 46, no. 12. Royal Society of Chemistry, pp. 3510–3528, 2017.","apa":"Ortega, S., Ibáñez, M., Liu, Y., Zhang, Y., Kovalenko, M., Cadavid, D., & Cabot, A. (2017). Bottom up engineering of thermoelectric nanomaterials and devices from solution processed nanoparticle building blocks. Chemical Society Reviews. Royal Society of Chemistry. https://doi.org/10.1039/c6cs00567e","ama":"Ortega S, Ibáñez M, Liu Y, et al. Bottom up engineering of thermoelectric nanomaterials and devices from solution processed nanoparticle building blocks. Chemical Society Reviews. 2017;46(12):3510-3528. doi:10.1039/c6cs00567e"},"publication":"Chemical Society Reviews","date_published":"2017-06-21T00:00:00Z","article_processing_charge":"No","day":"21"},{"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"01","doi":"10.1073/pnas.1615310114","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1615310114","open_access":"1"}],"oa":1,"external_id":{"pmid":["28143926"]},"quality_controlled":"1","extern":"1","author":[{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","first_name":"Alicia Kathleen","full_name":"Michael, Alicia Kathleen"},{"first_name":"Jennifer L.","last_name":"Fribourgh","full_name":"Fribourgh, Jennifer L."},{"full_name":"Chelliah, Yogarany","last_name":"Chelliah","first_name":"Yogarany"},{"first_name":"Colby R.","last_name":"Sandate","full_name":"Sandate, Colby R."},{"last_name":"Hura","first_name":"Greg L.","full_name":"Hura, Greg L."},{"full_name":"Schneidman-Duhovny, Dina","last_name":"Schneidman-Duhovny","first_name":"Dina"},{"full_name":"Tripathi, Sarvind M.","last_name":"Tripathi","first_name":"Sarvind M."},{"first_name":"Joseph S.","last_name":"Takahashi","full_name":"Takahashi, Joseph S."},{"last_name":"Partch","first_name":"Carrie L.","full_name":"Partch, Carrie L."}],"volume":114,"date_created":"2024-03-21T07:56:50Z","date_updated":"2024-03-25T12:12:23Z","pmid":1,"year":"2017","publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","article_processing_charge":"No","day":"31","scopus_import":"1","keyword":["Multidisciplinary"],"date_published":"2017-01-31T00:00:00Z","citation":{"chicago":"Michael, Alicia K., Jennifer L. Fribourgh, Yogarany Chelliah, Colby R. Sandate, Greg L. Hura, Dina Schneidman-Duhovny, Sarvind M. Tripathi, Joseph S. Takahashi, and Carrie L. Partch. “Formation of a Repressive Complex in the Mammalian Circadian Clock Is Mediated by the Secondary Pocket of CRY1.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1615310114.","short":"A.K. Michael, J.L. Fribourgh, Y. Chelliah, C.R. Sandate, G.L. Hura, D. Schneidman-Duhovny, S.M. Tripathi, J.S. Takahashi, C.L. Partch, Proceedings of the National Academy of Sciences 114 (2017) 1560–1565.","mla":"Michael, Alicia K., et al. “Formation of a Repressive Complex in the Mammalian Circadian Clock Is Mediated by the Secondary Pocket of CRY1.” Proceedings of the National Academy of Sciences, vol. 114, no. 7, Proceedings of the National Academy of Sciences, 2017, pp. 1560–65, doi:10.1073/pnas.1615310114.","apa":"Michael, A. K., Fribourgh, J. L., Chelliah, Y., Sandate, C. R., Hura, G. L., Schneidman-Duhovny, D., … Partch, C. L. (2017). Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1615310114","ieee":"A. K. Michael et al., “Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1,” Proceedings of the National Academy of Sciences, vol. 114, no. 7. Proceedings of the National Academy of Sciences, pp. 1560–1565, 2017.","ista":"Michael AK, Fribourgh JL, Chelliah Y, Sandate CR, Hura GL, Schneidman-Duhovny D, Tripathi SM, Takahashi JS, Partch CL. 2017. Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proceedings of the National Academy of Sciences. 114(7), 1560–1565.","ama":"Michael AK, Fribourgh JL, Chelliah Y, et al. Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proceedings of the National Academy of Sciences. 2017;114(7):1560-1565. doi:10.1073/pnas.1615310114"},"publication":"Proceedings of the National Academy of Sciences","page":"1560-1565","article_type":"original","issue":"7","abstract":[{"lang":"eng","text":"The basic helix–loop–helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ∼24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here we show that CRY1 binds directly to the PAS domain core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solution X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1."}],"type":"journal_article","oa_version":"Published Version","_id":"15157","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 114","title":"Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1","status":"public"},{"keyword":["Physical and Theoretical Chemistry","General Medicine","Biochemistry"],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"128-140","article_type":"original","citation":{"ama":"Michael AK, Fribourgh JL, Van Gelder RN, Partch CL. Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond. Photochemistry and Photobiology. 2017;93(1):128-140. doi:10.1111/php.12677","ista":"Michael AK, Fribourgh JL, Van Gelder RN, Partch CL. 2017. Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond. Photochemistry and Photobiology. 93(1), 128–140.","ieee":"A. K. Michael, J. L. Fribourgh, R. N. Van Gelder, and C. L. Partch, “Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond,” Photochemistry and Photobiology, vol. 93, no. 1. Wiley, pp. 128–140, 2017.","apa":"Michael, A. K., Fribourgh, J. L., Van Gelder, R. N., & Partch, C. L. (2017). Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond. Photochemistry and Photobiology. Wiley. https://doi.org/10.1111/php.12677","mla":"Michael, Alicia K., et al. “Animal Cryptochromes: Divergent Roles in Light Perception, Circadian Timekeeping and Beyond.” Photochemistry and Photobiology, vol. 93, no. 1, Wiley, 2017, pp. 128–40, doi:10.1111/php.12677.","short":"A.K. Michael, J.L. Fribourgh, R.N. Van Gelder, C.L. Partch, Photochemistry and Photobiology 93 (2017) 128–140.","chicago":"Michael, Alicia K., Jennifer L. Fribourgh, Russell N. Van Gelder, and Carrie L. Partch. “Animal Cryptochromes: Divergent Roles in Light Perception, Circadian Timekeeping and Beyond.” Photochemistry and Photobiology. Wiley, 2017. https://doi.org/10.1111/php.12677."},"publication":"Photochemistry and Photobiology","date_published":"2017-02-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"Cryptochromes are evolutionarily related to the light‐dependent DNA repair enzyme photolyase, serving as major regulators of circadian rhythms in insects and vertebrate animals. There are two types of cryptochromes in the animal kingdom: Drosophila‐like CRYs that act as nonvisual photopigments linking circadian rhythms to the environmental light/dark cycle, and vertebrate‐like CRYs that do not appear to sense light directly, but control the generation of circadian rhythms by acting as transcriptional repressors. Some animals have both types of CRYs, while others possess only one. Cryptochromes have two domains, the photolyase homology region (PHR) and an extended, intrinsically disordered C‐terminus. While all animal CRYs share a high degree of sequence and structural homology in their PHR domains, the C‐termini are divergent in both length and sequence identity. Recently, cryptochrome function has been shown to extend beyond its pivotal role in circadian clocks, participating in regulation of the DNA damage response, cancer progression and glucocorticoid signaling, as well as being implicated as possible magnetoreceptors. In this review, we provide a historical perspective on the discovery of animal cryptochromes, examine similarities and differences of the two types of animal cryptochromes and explore some of the divergent roles for this class of proteins.","lang":"eng"}],"intvolume":" 93","title":"Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond","status":"public","_id":"15158","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","publication_identifier":{"eissn":["1751-1097"],"issn":["0031-8655"]},"month":"02","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1111/php.12677","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1111/php.12677","extern":"1","publisher":"Wiley","publication_status":"published","year":"2017","volume":93,"date_created":"2024-03-21T07:57:18Z","date_updated":"2024-03-25T12:09:21Z","author":[{"full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","first_name":"Alicia Kathleen"},{"last_name":"Fribourgh","first_name":"Jennifer L.","full_name":"Fribourgh, Jennifer L."},{"last_name":"Van Gelder","first_name":"Russell N.","full_name":"Van Gelder, Russell N."},{"full_name":"Partch, Carrie L.","last_name":"Partch","first_name":"Carrie L."}]},{"language":[{"iso":"eng"}],"doi":"10.7554/elife.26163","quality_controlled":"1","external_id":{"pmid":["28762945"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.7554/eLife.26163","open_access":"1"}],"month":"08","publication_identifier":{"issn":["2050-084X"]},"date_created":"2024-03-21T07:55:36Z","date_updated":"2024-03-25T12:22:54Z","volume":6,"author":[{"full_name":"Fong, Jiunn CN","first_name":"Jiunn CN","last_name":"Fong"},{"last_name":"Rogers","first_name":"Andrew","full_name":"Rogers, Andrew"},{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","first_name":"Alicia Kathleen","full_name":"Michael, Alicia Kathleen"},{"first_name":"Nicole C","last_name":"Parsley","full_name":"Parsley, Nicole C"},{"last_name":"Cornell","first_name":"William-Cole","full_name":"Cornell, William-Cole"},{"full_name":"Lin, Yu-Cheng","first_name":"Yu-Cheng","last_name":"Lin"},{"full_name":"Singh, Praveen K","first_name":"Praveen K","last_name":"Singh"},{"full_name":"Hartmann, Raimo","first_name":"Raimo","last_name":"Hartmann"},{"first_name":"Knut","last_name":"Drescher","full_name":"Drescher, Knut"},{"last_name":"Vinogradov","first_name":"Evgeny","full_name":"Vinogradov, Evgeny"},{"full_name":"Dietrich, Lars EP","last_name":"Dietrich","first_name":"Lars EP"},{"last_name":"Partch","first_name":"Carrie L","full_name":"Partch, Carrie L"},{"first_name":"Fitnat H","last_name":"Yildiz","full_name":"Yildiz, Fitnat H"}],"publication_status":"published","publisher":"eLife Sciences Publications","year":"2017","pmid":1,"extern":"1","article_number":"26163","date_published":"2017-08-01T00:00:00Z","article_type":"original","publication":"eLife","citation":{"chicago":"Fong, Jiunn CN, Andrew Rogers, Alicia K. Michael, Nicole C Parsley, William-Cole Cornell, Yu-Cheng Lin, Praveen K Singh, et al. “Structural Dynamics of RbmA Governs Plasticity of Vibrio Cholerae Biofilms.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.26163.","short":"J.C. Fong, A. Rogers, A.K. Michael, N.C. Parsley, W.-C. Cornell, Y.-C. Lin, P.K. Singh, R. Hartmann, K. Drescher, E. Vinogradov, L.E. Dietrich, C.L. Partch, F.H. Yildiz, ELife 6 (2017).","mla":"Fong, Jiunn CN, et al. “Structural Dynamics of RbmA Governs Plasticity of Vibrio Cholerae Biofilms.” ELife, vol. 6, 26163, eLife Sciences Publications, 2017, doi:10.7554/elife.26163.","apa":"Fong, J. C., Rogers, A., Michael, A. K., Parsley, N. C., Cornell, W.-C., Lin, Y.-C., … Yildiz, F. H. (2017). Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.26163","ieee":"J. C. Fong et al., “Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"Fong JC, Rogers A, Michael AK, Parsley NC, Cornell W-C, Lin Y-C, Singh PK, Hartmann R, Drescher K, Vinogradov E, Dietrich LE, Partch CL, Yildiz FH. 2017. Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. eLife. 6, 26163.","ama":"Fong JC, Rogers A, Michael AK, et al. Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. eLife. 2017;6. doi:10.7554/elife.26163"},"day":"01","article_processing_charge":"Yes","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"scopus_import":"1","oa_version":"Published Version","status":"public","title":"Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms","intvolume":" 6","_id":"15154","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Biofilm formation is critical for the infection cycle of Vibrio cholerae. Vibrio exopolysaccharides (VPS) and the matrix proteins RbmA, Bap1 and RbmC are required for the development of biofilm architecture. We demonstrate that RbmA binds VPS directly and uses a binary structural switch within its first fibronectin type III (FnIII-1) domain to control RbmA structural dynamics and the formation of VPS-dependent higher-order structures. The structural switch in FnIII-1 regulates interactions in trans with the FnIII-2 domain, leading to open (monomeric) or closed (dimeric) interfaces. The ability of RbmA to switch between open and closed states is important for V. cholerae biofilm formation, as RbmA variants with switches that are locked in either of the two states lead to biofilms with altered architecture and structural integrity."}],"type":"journal_article"},{"extern":"1","year":"2017","publisher":"Elsevier","publication_status":"published","author":[{"last_name":"Gustafson","first_name":"Chelsea L.","full_name":"Gustafson, Chelsea L."},{"first_name":"Nicole C.","last_name":"Parsley","full_name":"Parsley, Nicole C."},{"full_name":"Asimgil, Hande","first_name":"Hande","last_name":"Asimgil"},{"full_name":"Lee, Hsiau-Wei","last_name":"Lee","first_name":"Hsiau-Wei"},{"full_name":"Ahlbach, Christopher","first_name":"Christopher","last_name":"Ahlbach"},{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen","last_name":"Michael","full_name":"Michael, Alicia Kathleen"},{"first_name":"Haiyan","last_name":"Xu","full_name":"Xu, Haiyan"},{"first_name":"Owen L.","last_name":"Williams","full_name":"Williams, Owen L."},{"first_name":"Tara L.","last_name":"Davis","full_name":"Davis, Tara L."},{"full_name":"Liu, Andrew C.","first_name":"Andrew C.","last_name":"Liu"},{"full_name":"Partch, Carrie L.","last_name":"Partch","first_name":"Carrie L."}],"volume":66,"date_created":"2024-03-21T07:56:01Z","date_updated":"2024-03-25T12:19:20Z","publication_identifier":{"issn":["1097-2765"]},"month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2017.04.011"}],"oa":1,"quality_controlled":"1","doi":"10.1016/j.molcel.2017.04.011","language":[{"iso":"eng"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"The C-terminal transactivation domain (TAD) of BMAL1 (brain and muscle ARNT-like 1) is a regulatory hub for transcriptional coactivators and repressors that compete for binding and, consequently, contributes to period determination of the mammalian circadian clock. Here, we report the discovery of two distinct conformational states that slowly exchange within the dynamic TAD to control timing. This binary switch results from cis/trans isomerization about a highly conserved Trp-Pro imide bond in a region of the TAD that is required for normal circadian timekeeping. Both cis and trans isomers interact with transcriptional regulators, suggesting that isomerization could serve a role in assembling regulatory complexes in vivo. Toward this end, we show that locking the switch into the trans isomer leads to shortened circadian periods. Furthermore, isomerization is regulated by the cyclophilin family of peptidyl-prolyl isomerases, highlighting the potential for regulation of BMAL1 protein dynamics in period determination."}],"_id":"15155","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 66","title":"A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms","status":"public","oa_version":"Published Version","scopus_import":"1","keyword":["Cell Biology","Molecular Biology"],"article_processing_charge":"No","day":"18","citation":{"ista":"Gustafson CL, Parsley NC, Asimgil H, Lee H-W, Ahlbach C, Michael AK, Xu H, Williams OL, Davis TL, Liu AC, Partch CL. 2017. A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. Molecular Cell. 66(4), 447–457.e7.","ieee":"C. L. Gustafson et al., “A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms,” Molecular Cell, vol. 66, no. 4. Elsevier, p. 447–457.e7, 2017.","apa":"Gustafson, C. L., Parsley, N. C., Asimgil, H., Lee, H.-W., Ahlbach, C., Michael, A. K., … Partch, C. L. (2017). A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2017.04.011","ama":"Gustafson CL, Parsley NC, Asimgil H, et al. A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. Molecular Cell. 2017;66(4):447-457.e7. doi:10.1016/j.molcel.2017.04.011","chicago":"Gustafson, Chelsea L., Nicole C. Parsley, Hande Asimgil, Hsiau-Wei Lee, Christopher Ahlbach, Alicia K. Michael, Haiyan Xu, et al. “A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.” Molecular Cell. Elsevier, 2017. https://doi.org/10.1016/j.molcel.2017.04.011.","mla":"Gustafson, Chelsea L., et al. “A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.” Molecular Cell, vol. 66, no. 4, Elsevier, 2017, p. 447–457.e7, doi:10.1016/j.molcel.2017.04.011.","short":"C.L. Gustafson, N.C. Parsley, H. Asimgil, H.-W. Lee, C. Ahlbach, A.K. Michael, H. Xu, O.L. Williams, T.L. Davis, A.C. Liu, C.L. Partch, Molecular Cell 66 (2017) 447–457.e7."},"publication":"Molecular Cell","page":"447-457.e7","article_type":"original","date_published":"2017-05-18T00:00:00Z"},{"year":"2017","publisher":"American Association for the Advancement of Science","publication_status":"published","author":[{"full_name":"Tseng, Roger","first_name":"Roger","last_name":"Tseng"},{"last_name":"Goularte","first_name":"Nicolette F.","full_name":"Goularte, Nicolette F."},{"first_name":"Archana","last_name":"Chavan","full_name":"Chavan, Archana"},{"first_name":"Jansen","last_name":"Luu","full_name":"Luu, Jansen"},{"first_name":"Susan E.","last_name":"Cohen","full_name":"Cohen, Susan E."},{"full_name":"Chang, Yong-Gang","first_name":"Yong-Gang","last_name":"Chang"},{"first_name":"Joel","last_name":"Heisler","full_name":"Heisler, Joel"},{"full_name":"Li, Sheng","first_name":"Sheng","last_name":"Li"},{"first_name":"Alicia Kathleen","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen"},{"full_name":"Tripathi, Sarvind","first_name":"Sarvind","last_name":"Tripathi"},{"full_name":"Golden, Susan S.","last_name":"Golden","first_name":"Susan S."},{"last_name":"LiWang","first_name":"Andy","full_name":"LiWang, Andy"},{"full_name":"Partch, Carrie L.","first_name":"Carrie L.","last_name":"Partch"}],"volume":355,"date_updated":"2024-03-25T12:16:44Z","date_created":"2024-03-21T07:56:24Z","extern":"1","quality_controlled":"1","doi":"10.1126/science.aag2516","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"03","_id":"15156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 355","status":"public","title":"Structural basis of the day-night transition in a bacterial circadian clock","oa_version":"None","type":"journal_article","issue":"6330","abstract":[{"lang":"eng","text":"Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. In cyanobacteria, timing is generated by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA and CikA, which transduce this rhythm to control gene expression. Here, we describe crystal and nuclear magnetic resonance structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how the metamorphic properties of KaiB, a protein that adopts two distinct folds, and the post–adenosine triphosphate hydrolysis state of KaiC create a hub around which nighttime signaling events revolve, including inactivation of KaiA and reciprocal regulation of the mutually antagonistic signaling proteins, SasA and CikA."}],"citation":{"short":"R. Tseng, N.F. Goularte, A. Chavan, J. Luu, S.E. Cohen, Y.-G. Chang, J. Heisler, S. Li, A.K. Michael, S. Tripathi, S.S. Golden, A. LiWang, C.L. Partch, Science 355 (2017) 1174–1180.","mla":"Tseng, Roger, et al. “Structural Basis of the Day-Night Transition in a Bacterial Circadian Clock.” Science, vol. 355, no. 6330, American Association for the Advancement of Science, 2017, pp. 1174–80, doi:10.1126/science.aag2516.","chicago":"Tseng, Roger, Nicolette F. Goularte, Archana Chavan, Jansen Luu, Susan E. Cohen, Yong-Gang Chang, Joel Heisler, et al. “Structural Basis of the Day-Night Transition in a Bacterial Circadian Clock.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aag2516.","ama":"Tseng R, Goularte NF, Chavan A, et al. Structural basis of the day-night transition in a bacterial circadian clock. Science. 2017;355(6330):1174-1180. doi:10.1126/science.aag2516","apa":"Tseng, R., Goularte, N. F., Chavan, A., Luu, J., Cohen, S. E., Chang, Y.-G., … Partch, C. L. (2017). Structural basis of the day-night transition in a bacterial circadian clock. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag2516","ieee":"R. Tseng et al., “Structural basis of the day-night transition in a bacterial circadian clock,” Science, vol. 355, no. 6330. American Association for the Advancement of Science, pp. 1174–1180, 2017.","ista":"Tseng R, Goularte NF, Chavan A, Luu J, Cohen SE, Chang Y-G, Heisler J, Li S, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL. 2017. Structural basis of the day-night transition in a bacterial circadian clock. Science. 355(6330), 1174–1180."},"publication":"Science","page":"1174-1180","article_type":"original","date_published":"2017-03-17T00:00:00Z","scopus_import":"1","keyword":["Multidisciplinary"],"article_processing_charge":"No","day":"17"},{"abstract":[{"text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.","lang":"eng"}],"issue":"3","type":"journal_article","pubrep_id":"800","file":[{"content_type":"application/pdf","file_size":3429381,"creator":"system","access_level":"open_access","file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","date_created":"2018-12-12T10:09:47Z","date_updated":"2018-12-12T10:09:47Z","relation":"main_file","file_id":"4772"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1029","title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","ddc":["570"],"status":"public","intvolume":" 12","day":"16","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2017-03-16T00:00:00Z","publication":"PLoS One","citation":{"ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” PLoS One, vol. 12, no. 3. Public Library of Science, 2017.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066","ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066.","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0174066.","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066."},"file_date_updated":"2018-12-12T10:09:47Z","publist_id":"6361","article_number":"e0174066","author":[{"orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin","first_name":"Martin","full_name":"Lukacisin, Martin"},{"full_name":"Landon, Matthieu","first_name":"Matthieu","last_name":"Landon"},{"last_name":"Jajoo","first_name":"Rishi","full_name":"Jajoo, Rishi"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5556"},{"relation":"dissertation_contains","status":"public","id":"6392"}]},"date_created":"2018-12-11T11:49:46Z","date_updated":"2024-03-28T23:30:04Z","volume":12,"year":"2017","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"ToBo"}],"month":"03","publication_identifier":{"issn":["19326203"]},"doi":"10.1371/journal.pone.0174066","language":[{"iso":"eng"}],"external_id":{"isi":["000396318300121"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.immuni.2017.04.006","date_published":"2017-04-18T00:00:00Z","quality_controlled":"1","page":"519 - 520","publication":"Immunity","citation":{"ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.","ieee":"F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” Immunity, vol. 46, no. 4. Cell Press, pp. 519–520, 2017.","apa":"Assen, F. P., & Sixt, M. K. (2017). The dynamic cytokine niche. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2017.04.006","ama":"Assen FP, Sixt MK. The dynamic cytokine niche. Immunity. 2017;46(4):519-520. doi:10.1016/j.immuni.2017.04.006","chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” Immunity. Cell Press, 2017. https://doi.org/10.1016/j.immuni.2017.04.006.","mla":"Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” Immunity, vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:10.1016/j.immuni.2017.04.006.","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520."},"day":"18","month":"04","publication_identifier":{"issn":["10747613"]},"scopus_import":1,"date_updated":"2024-03-28T23:30:09Z","date_created":"2018-12-11T11:47:47Z","volume":46,"oa_version":"None","author":[{"id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119","first_name":"Frank P","last_name":"Assen","full_name":"Assen, Frank P"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"related_material":{"record":[{"id":"6947","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","status":"public","title":"The dynamic cytokine niche","intvolume":" 46","publisher":"Cell Press","department":[{"_id":"MiSi"}],"year":"2017","_id":"664","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it.","lang":"eng"}],"issue":"4","publist_id":"7065","type":"journal_article"},{"doi":"10.1371/journal.pone.0179377","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","publication_identifier":{"issn":["19326203"]},"month":"06","related_material":{"record":[{"id":"51","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Ukai, Hikari","first_name":"Hikari","last_name":"Ukai"},{"last_name":"Kawahara","first_name":"Aiko","full_name":"Kawahara, Aiko"},{"full_name":"Hirayama, Keiko","first_name":"Keiko","last_name":"Hirayama"},{"first_name":"Matthew J","last_name":"Case","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Case, Matthew J"},{"full_name":"Aino, Shotaro","last_name":"Aino","first_name":"Shotaro"},{"first_name":"Masahiro","last_name":"Miyabe","full_name":"Miyabe, Masahiro"},{"last_name":"Wakita","first_name":"Ken","full_name":"Wakita, Ken"},{"full_name":"Oogi, Ryohei","first_name":"Ryohei","last_name":"Oogi"},{"first_name":"Michiyo","last_name":"Kasayuki","full_name":"Kasayuki, Michiyo"},{"full_name":"Kawashima, Shihomi","first_name":"Shihomi","last_name":"Kawashima"},{"full_name":"Sugimoto, Shunichi","last_name":"Sugimoto","first_name":"Shunichi"},{"last_name":"Chikamatsu","first_name":"Kanako","full_name":"Chikamatsu, Kanako"},{"first_name":"Noritaka","last_name":"Nitta","full_name":"Nitta, Noritaka"},{"full_name":"Koga, Tsuneyuki","first_name":"Tsuneyuki","last_name":"Koga"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"last_name":"Takai","first_name":"Toshiyuki","full_name":"Takai, Toshiyuki"},{"first_name":"Isao","last_name":"Ito","full_name":"Ito, Isao"}],"volume":12,"date_created":"2018-12-11T11:47:54Z","date_updated":"2024-03-28T23:30:12Z","year":"2017","publisher":"Public Library of Science","department":[{"_id":"RySh"}],"publication_status":"published","publist_id":"7034","file_date_updated":"2020-07-14T12:47:40Z","article_number":"e0179377","date_published":"2017-06-01T00:00:00Z","citation":{"ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 2017;12(6). doi:10.1371/journal.pone.0179377","ieee":"H. Ukai et al., “PirB regulates asymmetries in hippocampal circuitry,” PLoS One, vol. 12, no. 6. Public Library of Science, 2017.","apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0179377","ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377.","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:10.1371/journal.pone.0179377.","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0179377."},"publication":"PLoS One","article_type":"original","has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"897","file":[{"file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","access_level":"open_access","content_type":"application/pdf","file_size":5798454,"creator":"system","relation":"main_file","file_id":"4934","date_created":"2018-12-12T10:12:16Z","date_updated":"2020-07-14T12:47:40Z","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8"}],"oa_version":"Published Version","_id":"682","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 12","ddc":["571"],"status":"public","title":"PirB regulates asymmetries in hippocampal circuitry","issue":"6","abstract":[{"lang":"eng","text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry."}],"type":"journal_article"},{"ec_funded":1,"publist_id":"6362","file_date_updated":"2019-01-18T09:39:55Z","publisher":"Wiley-Blackwell","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"publication_status":"published","acknowledgement":"This work was supported by a grant from the European Unions Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","year":"2017","volume":56,"date_updated":"2024-03-28T23:30:13Z","date_created":"2018-12-11T11:49:46Z","related_material":{"record":[{"id":"418","status":"public","relation":"dissertation_contains"},{"id":"7680","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Kainrath","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie"},{"first_name":"Manuela","last_name":"Stadler","full_name":"Stadler, Manuela"},{"full_name":"Gschaider-Reichhart, Eva","first_name":"Eva","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738"},{"first_name":"Martin","last_name":"Distel","full_name":"Distel, Martin"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"publication_identifier":{"issn":["14337851"]},"month":"03","project":[{"grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7"},{"name":"Molecular Drug Targets [do not use to be deleted]","call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000398154000038"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/anie.201611998","type":"journal_article","issue":"16","abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes."}],"intvolume":" 56","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","ddc":["540"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1028","file":[{"file_size":2614942,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_communications_Kainrath.pdf","success":1,"date_updated":"2019-01-18T09:39:55Z","date_created":"2019-01-18T09:39:55Z","relation":"main_file","file_id":"5845"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"20","page":"4608-4611","citation":{"ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell, pp. 4608–4611, 2017.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998","mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition, vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998."},"publication":"Angewandte Chemie - International Edition","date_published":"2017-03-20T00:00:00Z"},{"scopus_import":1,"has_accepted_license":"1","day":"17","page":"1 - 29","citation":{"ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29."},"publication":"Auxins and Cytokinins in Plant Biology","date_published":"2017-03-17T00:00:00Z","alternative_title":["Methods in Molecular Biology"],"type":"journal_article","abstract":[{"text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges.","lang":"eng"}],"intvolume":" 1569","title":"Methodological advances in auxin and cytokinin biology","ddc":["575"],"status":"public","_id":"1024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","file_size":840646,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5068","date_updated":"2019-10-15T07:47:05Z","date_created":"2018-12-12T10:14:18Z"}],"oa_version":"Submitted Version","pubrep_id":"1019","publication_identifier":{"issn":["10643745"]},"month":"03","project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-6831-2_1","publist_id":"6369","file_date_updated":"2019-10-15T07:47:05Z","department":[{"_id":"EvBe"}],"publisher":"Springer","publication_status":"published","year":"2017","volume":1569,"date_updated":"2024-03-28T23:30:17Z","date_created":"2018-12-11T11:49:45Z","related_material":{"record":[{"id":"539","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Hurny, Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3638-1426","first_name":"Andrej","last_name":"Hurny"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}]},{"oa_version":"Submitted Version","intvolume":" 127","status":"public","title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","_id":"679","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","abstract":[{"lang":"eng","text":"Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections."}],"type":"journal_article","date_published":"2017-06-01T00:00:00Z","page":"2051 - 2065","citation":{"chicago":"Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill, Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation. American Society for Clinical Investigation, 2017. https://doi.org/10.1172/JCI80631.","short":"F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L. Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation 127 (2017) 2051–2065.","mla":"Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation, vol. 127, no. 6, American Society for Clinical Investigation, 2017, pp. 2051–65, doi:10.1172/JCI80631.","apa":"Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N., … Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI80631","ieee":"F. Ebner et al., “The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection,” The Journal of Clinical Investigation, vol. 127, no. 6. American Society for Clinical Investigation, pp. 2051–2065, 2017.","ista":"Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 127(6), 2051–2065.","ama":"Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 2017;127(6):2051-2065. doi:10.1172/JCI80631"},"publication":"The Journal of Clinical Investigation","day":"01","scopus_import":1,"volume":127,"date_created":"2018-12-11T11:47:53Z","date_updated":"2024-03-28T23:30:23Z","related_material":{"record":[{"id":"12401","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Florian","last_name":"Ebner","full_name":"Ebner, Florian"},{"last_name":"Sedlyarov","first_name":"Vitaly","full_name":"Sedlyarov, Vitaly"},{"full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan"},{"full_name":"Ivin, Masa","first_name":"Masa","last_name":"Ivin"},{"first_name":"Franz","last_name":"Kratochvill","full_name":"Kratochvill, Franz"},{"first_name":"Nina","last_name":"Gratz","full_name":"Gratz, Nina"},{"full_name":"Kenner, Lukas","first_name":"Lukas","last_name":"Kenner"},{"full_name":"Villunger, Andreas","last_name":"Villunger","first_name":"Andreas"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Pavel","last_name":"Kovarik","full_name":"Kovarik, Pavel"}],"publisher":"American Society for Clinical Investigation","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"year":"2017","acknowledgement":"This work was supported by grants from the Austrian Science Fund (FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN) for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement PITN-GA-2012-316682; and by a joint research cluster initiative of the University of Vienna and the Medical University of Vienna.","publist_id":"7038","language":[{"iso":"eng"}],"doi":"10.1172/JCI80631","project":[{"call_identifier":"FWF","name":"The biochemical basis of PAR polarization","grant_number":"T00817-B21","_id":"25985A36-B435-11E9-9278-68D0E5697425"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"}],"quality_controlled":"1","external_id":{"pmid":["28504646"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["00219738"]},"month":"06"},{"oa_version":"Published Version","file":[{"checksum":"bc25125fb664706cdf180e061429f91d","date_created":"2019-09-24T06:56:22Z","date_updated":"2020-07-14T12:47:39Z","relation":"main_file","file_id":"6905","file_size":8194516,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_Development_Krens.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"676","status":"public","ddc":["570"],"title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","intvolume":" 144","abstract":[{"lang":"eng","text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation."}],"issue":"10","type":"journal_article","date_published":"2017-05-15T00:00:00Z","publication":"Development","citation":{"chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144964.","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:10.1242/dev.144964.","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806.","ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., & Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.144964","ieee":"G. Krens et al., “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” Development, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 2017;144(10):1798-1806. doi:10.1242/dev.144964"},"article_type":"original","page":"1798 - 1806","day":"15","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"author":[{"full_name":"Krens, Gabriel","first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996"},{"last_name":"Veldhuis","first_name":"Jim","full_name":"Veldhuis, Jim"},{"last_name":"Barone","first_name":"Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa"},{"full_name":"Capek, Daniel","first_name":"Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940"},{"last_name":"Maître","first_name":"Jean-Léon","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","full_name":"Maître, Jean-Léon"},{"full_name":"Brodland, Wayne","first_name":"Wayne","last_name":"Brodland"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"id":"50","relation":"dissertation_contains","status":"public"}]},"date_updated":"2024-03-28T23:30:26Z","date_created":"2018-12-11T11:47:52Z","volume":144,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"Bio"},{"_id":"CaHe"}],"publisher":"Company of Biologists","file_date_updated":"2020-07-14T12:47:39Z","publist_id":"7047","doi":"10.1242/dev.144964","language":[{"iso":"eng"}],"external_id":{"pmid":["28512197"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"05","publication_identifier":{"issn":["09501991"]}},{"pubrep_id":"890","oa_version":"Published Version","file":[{"file_size":2092088,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","access_level":"open_access","date_created":"2018-12-12T10:12:54Z","date_updated":"2020-07-14T12:47:48Z","checksum":"6b908b5db9f61f6820ebd7f8fa815571","relation":"main_file","file_id":"4975"},{"relation":"main_file","file_id":"4976","date_updated":"2020-07-14T12:47:48Z","date_created":"2018-12-12T10:12:55Z","checksum":"ca21530389b720243552678125fdba35","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3428681,"creator":"system"}],"_id":"704","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","ddc":["576"],"status":"public","abstract":[{"lang":"eng","text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data."}],"type":"journal_article","date_published":"2017-07-25T00:00:00Z","citation":{"chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25100.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife, vol. 6, e25100, eLife Sciences Publications, 2017, doi:10.7554/eLife.25100.","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Steinrück, M., & Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25100","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 2017;6. doi:10.7554/eLife.25100"},"publication":"eLife","has_accepted_license":"1","day":"25","scopus_import":1,"related_material":{"record":[{"id":"5564","status":"public","relation":"popular_science"},{"id":"26","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Steinrück","first_name":"Magdalena","orcid":"0000-0003-1229-9719","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","full_name":"Steinrück, Magdalena"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"volume":6,"date_updated":"2024-03-28T23:30:28Z","date_created":"2018-12-11T11:48:01Z","year":"2017","publisher":"eLife Sciences Publications","department":[{"_id":"CaGu"}],"publication_status":"published","publist_id":"6990","file_date_updated":"2020-07-14T12:47:48Z","article_number":"e25100","doi":"10.7554/eLife.25100","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","publication_identifier":{"issn":["2050084X"]},"month":"07"},{"volume":13,"date_created":"2018-12-11T11:47:58Z","date_updated":"2024-03-28T23:30:28Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9849"},{"id":"9850","relation":"research_data","status":"public"},{"id":"9851","relation":"research_data","status":"public"},{"id":"9852","relation":"research_data","status":"public"},{"id":"6263","relation":"dissertation_contains","status":"public"}]},"author":[{"orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta"},{"full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X"},{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"}],"publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","year":"2017","ec_funded":1,"publist_id":"7004","file_date_updated":"2020-07-14T12:47:46Z","article_number":"e1005609","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1005609","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["1553734X"]},"month":"07","file":[{"relation":"main_file","file_id":"5117","checksum":"9143c290fa6458ed2563bff4b295554a","date_created":"2018-12-12T10:15:01Z","date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","file_size":3775716,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","pubrep_id":"894","intvolume":" 13","ddc":["576"],"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"696","issue":"7","abstract":[{"lang":"eng","text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy."}],"type":"journal_article","date_published":"2017-07-18T00:00:00Z","article_type":"original","citation":{"chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609"},"publication":"PLoS Computational Biology","has_accepted_license":"1","day":"18","scopus_import":1},{"date_published":"2017-08-01T00:00:00Z","citation":{"ieee":"M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding of antibiotic resistance evolution,” Current Opinion in Biotechnology, vol. 46. Elsevier, pp. 90–97, 2017.","apa":"Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.013","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.","ama":"Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97. doi:10.1016/j.copbio.2017.02.013","chicago":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013.","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97.","mla":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology, vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013."},"publication":"Current Opinion in Biotechnology","page":"90 - 97","article_type":"original","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","scopus_import":"1","pubrep_id":"801","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":858338,"creator":"dernst","access_level":"open_access","file_name":"2017_CurrentOpinion_Lukaciinova.pdf","success":1,"date_updated":"2019-01-18T09:57:57Z","date_created":"2019-01-18T09:57:57Z","relation":"main_file","file_id":"5846"}],"_id":"1027","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 46","ddc":["570"],"status":"public","title":"Toward a quantitative understanding of antibiotic resistance evolution","abstract":[{"lang":"eng","text":"The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance."}],"type":"journal_article","doi":"10.1016/j.copbio.2017.02.013","language":[{"iso":"eng"}],"external_id":{"isi":["000408077400015"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507"},{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"month":"08","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6263"}]},"author":[{"full_name":"Lukacisinova, Marta","first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"},{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"volume":46,"date_updated":"2024-03-28T23:30:29Z","date_created":"2018-12-11T11:49:45Z","year":"2017","publisher":"Elsevier","department":[{"_id":"ToBo"}],"publication_status":"published","ec_funded":1,"publist_id":"6364","file_date_updated":"2019-01-18T09:57:57Z"},{"page":"41 - 63","citation":{"mla":"Chatterjee, Krishnendu, et al. Non-Polynomial Worst Case Analysis of Recursive Programs. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 41–63, doi:10.1007/978-3-319-63390-9_3.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 41–63.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst Case Analysis of Recursive Programs.” edited by Rupak Majumdar and Viktor Kunčak, 10427:41–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_3.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst case analysis of recursive programs. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:41-63. doi:10.1007/978-3-319-63390-9_3","ista":"Chatterjee K, Fu H, Goharshady AK. 2017. Non-polynomial worst case analysis of recursive programs. CAV: Computer Aided Verification, LNCS, vol. 10427, 41–63.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst case analysis of recursive programs,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 41–63.","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2017). Non-polynomial worst case analysis of recursive programs. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_3"},"date_published":"2017-01-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"01","intvolume":" 10427","title":"Non-polynomial worst case analysis of recursive programs","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"639","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving worst-case bounds of non-deterministic recursive programs. Ranking functions are sound and complete for proving termination and worst-case bounds of non-recursive programs. First, we apply ranking functions to recursion, resulting in measure functions, and show that they provide a sound and complete approach to prove worst-case bounds of non-deterministic recursive programs. Our second contribution is the synthesis of measure functions in non-polynomial forms. We show that non-polynomial measure functions with logarithm and exponentiation can be synthesized through abstraction of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem using linear programming. While previous methods obtain worst-case polynomial bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr) where r is not an integer. We present experimental results to demonstrate that our approach can efficiently obtain worst-case bounds of classical recursive algorithms such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm."}],"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.00317","open_access":"1"}],"external_id":{"arxiv":["1705.00317"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-63390-9_3","conference":{"name":"CAV: Computer Aided Verification","end_date":"2017-07-28","location":"Heidelberg, Germany","start_date":"2017-07-24"},"publication_identifier":{"isbn":["978-331963389-3"]},"month":"01","editor":[{"last_name":"Majumdar","first_name":"Rupak","full_name":"Majumdar, Rupak"},{"first_name":"Viktor","last_name":"Kunčak","full_name":"Kunčak, Viktor"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","year":"2017","volume":10427,"date_updated":"2024-03-28T23:30:33Z","date_created":"2018-12-11T11:47:39Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"7014"},{"id":"8934","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir","full_name":"Goharshady, Amir"}],"ec_funded":1,"publist_id":"7149"},{"publication_identifier":{"issn":["03029743"]},"month":"01","external_id":{"isi":["000723567800004"]},"oa":1,"project":[{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"isi":1,"quality_controlled":"1","doi":"10.1007/978-3-319-68167-2_4","conference":{"end_date":"2017-10-06","start_date":"2017-10-03","location":"Pune, India","name":"ATVA: Automated Technology for Verification and Analysis"},"language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"6468","file_date_updated":"2020-07-14T12:48:16Z","year":"2017","editor":[{"full_name":"D'Souza, Deepak","first_name":"Deepak","last_name":"D'Souza"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Amir","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"volume":10482,"date_created":"2018-12-11T11:49:22Z","date_updated":"2024-03-28T23:30:35Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66.","apa":"Chatterjee, K., Goharshady, A. K., & Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. https://doi.org/10.1007/978-3-319-68167-2_4","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66.","ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:10.1007/978-3-319-68167-2_4","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66. Springer, 2017. https://doi.org/10.1007/978-3-319-68167-2_4.","mla":"Chatterjee, Krishnendu, et al. JTDec: A Tool for Tree Decompositions in Soot. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:10.1007/978-3-319-68167-2_4.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66."},"page":"59 - 66","date_published":"2017-01-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs."}],"_id":"949","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 10482","title":"JTDec: A tool for tree decompositions in soot","ddc":["005"],"status":"public","pubrep_id":"845","file":[{"date_created":"2018-12-12T10:10:45Z","date_updated":"2020-07-14T12:48:16Z","checksum":"a0d9f5f94dc594c4e71e78525c9942f1","file_id":"4835","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":948514,"file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","access_level":"open_access"}],"oa_version":"Submitted Version"},{"publist_id":"7074","ec_funded":1,"pmid":1,"year":"2017","publisher":"Nature Publishing Group","department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"50"},{"id":"8350","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Smutny, Michael","last_name":"Smutny","first_name":"Michael","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ákos, Zsuzsa","last_name":"Ákos","first_name":"Zsuzsa"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"},{"full_name":"Ruprecht, Verena","first_name":"Verena","last_name":"Ruprecht"},{"first_name":"Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel"},{"last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin"},{"id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","last_name":"Papusheva","full_name":"Papusheva, Ekaterina"},{"full_name":"Tada, Masazumi","first_name":"Masazumi","last_name":"Tada"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"},{"full_name":"Vicsek, Tamás","first_name":"Tamás","last_name":"Vicsek"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"volume":19,"date_updated":"2024-03-28T23:30:39Z","date_created":"2018-12-11T11:47:46Z","publication_identifier":{"issn":["14657392"]},"month":"03","external_id":{"pmid":["28346437"]},"main_file_link":[{"open_access":"1","url":"https://europepmc.org/articles/pmc5635970"}],"oa":1,"project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"grant_number":"I 930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1038/ncb3492","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"type":"journal_article","abstract":[{"lang":"eng","text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo."}],"_id":"661","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 19","status":"public","title":"Friction forces position the neural anlage","oa_version":"Submitted Version","scopus_import":1,"day":"27","citation":{"ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. Nature Cell Biology. 2017;19:306-317. doi:10.1038/ncb3492","apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3492","ieee":"M. Smutny et al., “Friction forces position the neural anlage,” Nature Cell Biology, vol. 19. Nature Publishing Group, pp. 306–317, 2017.","ista":"Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M, Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction forces position the neural anlage. Nature Cell Biology. 19, 306–317.","short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317.","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:10.1038/ncb3492.","chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3492."},"publication":"Nature Cell Biology","page":"306 - 317","date_published":"2017-03-27T00:00:00Z"},{"page":"198 - 211","citation":{"chicago":"Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014.","short":"V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.","mla":"Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell, vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:10.1016/j.devcel.2017.09.014.","ieee":"V. Barone et al., “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” Developmental Cell, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.","apa":"Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg, C.-P. J. (2017). An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.09.014","ista":"Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.","ama":"Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 2017;43(2):198-211. doi:10.1016/j.devcel.2017.09.014"},"publication":"Developmental Cell","date_published":"2017-10-23T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"23","intvolume":" 43","title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"735","oa_version":"None","type":"journal_article","issue":"2","abstract":[{"text":"Cell-cell contact formation constitutes an essential step in evolution, leading to the differentiation of specialized cell types. However, remarkably little is known about whether and how the interplay between contact formation and fate specification affects development. Here, we identify a positive feedback loop between cell-cell contact duration, morphogen signaling, and mesendoderm cell-fate specification during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for ppl cell-fate specification. We further show that Nodal signaling promotes ppl cell-cell contact duration, generating a positive feedback loop between ppl cell-cell contact duration and cell-fate specification. Finally, by combining mathematical modeling and experimentation, we show that this feedback determines whether anterior axial mesendoderm cells become ppl or, instead, turn into endoderm. Thus, the interdependent activities of cell-cell signaling and contact formation control fate diversification within the developing embryo.","lang":"eng"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Cell segregation in gastrulation: the role of cell fate specification","call_identifier":"FWF","_id":"252DD2A6-B435-11E9-9278-68D0E5697425","grant_number":"I2058"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000413443700011"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2017.09.014","publication_identifier":{"issn":["15345807"]},"month":"10","department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Cell Press","publication_status":"published","year":"2017","volume":43,"date_created":"2018-12-11T11:48:13Z","date_updated":"2024-03-28T23:30:39Z","related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"id":"8350","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","first_name":"Vanessa","last_name":"Barone"},{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","last_name":"Lang"},{"orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel","full_name":"Krens, Gabriel"},{"full_name":"Pradhan, Saurabh","first_name":"Saurabh","last_name":"Pradhan"},{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"full_name":"Sako, Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075","first_name":"Keisuke","last_name":"Sako"},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"ec_funded":1,"publist_id":"6934"},{"pubrep_id":"830","oa_version":"Published Version","file":[{"checksum":"dc1f5a475b918d09a0f9f587400b1626","date_created":"2018-12-12T10:09:40Z","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","file_id":"4764","file_size":2153858,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf"}],"_id":"960","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 11","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","ddc":["570"],"status":"public","abstract":[{"text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context.","lang":"eng"}],"type":"journal_article","date_published":"2017-06-28T00:00:00Z","citation":{"ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., & Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncel.2017.00176","ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” Frontiers in Cellular Neuroscience, vol. 11. Frontiers Research Foundation, 2017.","ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 2017;11. doi:10.3389/fncel.2017.00176","chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fncel.2017.00176.","mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience, vol. 11, 176, Frontiers Research Foundation, 2017, doi:10.3389/fncel.2017.00176.","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017)."},"publication":"Frontiers in Cellular Neuroscience","article_processing_charge":"Yes","has_accepted_license":"1","day":"28","scopus_import":"1","related_material":{"record":[{"id":"9962","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","last_name":"Hansen"},{"full_name":"Düllberg, Christian F","first_name":"Christian F","last_name":"Düllberg","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748"},{"full_name":"Mieck, Christine","last_name":"Mieck","first_name":"Christine","orcid":"0000-0003-1919-7416","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"volume":11,"date_created":"2018-12-11T11:49:25Z","date_updated":"2024-03-28T23:30:41Z","year":"2017","publisher":"Frontiers Research Foundation","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"publication_status":"published","ec_funded":1,"publist_id":"6445","file_date_updated":"2020-07-14T12:48:16Z","article_number":"176","doi":"10.3389/fncel.2017.00176","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000404486700001"]},"project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"T00817-B21","_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The biochemical basis of PAR polarization"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["16625102"]},"month":"06"}]