[{"language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","month":"10","file":[{"access_level":"closed","file_size":9190845,"file_id":"5941","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","creator":"dernst","relation":"source_file","embargo_to":"open_access","file_name":"Thesis_Steinrueck_final.docx","date_created":"2019-02-08T10:51:22Z","date_updated":"2020-07-14T12:45:43Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_name":"Thesis_Steinrueck_final.pdf","date_updated":"2021-02-11T11:17:14Z","date_created":"2019-02-08T10:51:22Z","content_type":"application/pdf","file_size":7521973,"access_level":"open_access","creator":"dernst","checksum":"3def8b7854c8b42d643597ce0215efac","file_id":"5942","embargo":"2019-11-02","relation":"main_file"}],"author":[{"last_name":"Steinrück","first_name":"Magdalena","orcid":"0000-0003-1229-9719","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","full_name":"Steinrück, Magdalena"}],"oa_version":"Published Version","pubrep_id":"1059","status":"public","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:44:14Z","_id":"26","type":"dissertation","publisher":"Institute of Science and Technology Austria","date_published":"2018-10-30T00:00:00Z","file_date_updated":"2021-02-11T11:17:14Z","title":"The influence of sequence context on the evolution of bacterial gene expression","publication_status":"published","abstract":[{"text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer.","lang":"eng"}],"ddc":["576","579"],"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"CaGu"}],"date_updated":"2023-09-07T12:48:43Z","citation":{"ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>.","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","apa":"Steinrück, M. (2018). <i>The influence of sequence context on the evolution of bacterial gene expression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","mla":"Steinrück, Magdalena. <i>The Influence of Sequence Context on the Evolution of Bacterial Gene Expression</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>."},"publist_id":"8029","supervisor":[{"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","id":"704","relation":"part_of_dissertation"}]},"day":"30","doi":"10.15479/AT:ISTA:th1059","year":"2018","page":"109","oa":1},{"ec_funded":1,"conference":{"end_date":"2018-06-22","start_date":"2018-06-18","name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Salt Lake City, UT, USA"},"date_created":"2018-12-11T11:45:33Z","_id":"273","type":"conference","status":"public","publication_identifier":{"isbn":["9781538664209"]},"main_file_link":[{"url":"https://arxiv.org/abs/1604.08269","open_access":"1"}],"month":"06","language":[{"iso":"eng"}],"article_processing_charge":"No","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"quality_controlled":"1","oa_version":"Preprint","author":[{"full_name":"Mohapatra, Pritish","first_name":"Pritish","last_name":"Mohapatra"},{"last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"},{"full_name":"Jawahar, C V","last_name":"Jawahar","first_name":"C V"},{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"last_name":"Kumar","first_name":"M Pawan","full_name":"Kumar, M Pawan"}],"scopus_import":"1","arxiv":1,"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","oa":1,"year":"2018","page":"3693-3701","doi":"10.1109/cvpr.2018.00389","day":"28","abstract":[{"text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time.","lang":"eng"}],"publication_status":"published","isi":1,"publisher":"IEEE","date_published":"2018-06-28T00:00:00Z","title":"Efficient optimization for rank-based loss functions","date_updated":"2023-09-11T13:24:43Z","department":[{"_id":"VlKo"}],"citation":{"short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 3693–701, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>.","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 3693–3701. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>.","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:3693-3701. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., &#38; Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000457843603087"],"arxiv":["1604.08269"]}},{"ec_funded":1,"date_created":"2018-12-11T11:45:33Z","type":"journal_article","_id":"275","status":"public","month":"04","has_accepted_license":"1","file":[{"relation":"main_file","creator":"dernst","file_id":"5704","checksum":"9c7eba51a35c62da8c13f98120b64df4","file_size":2252043,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-17T12:50:07Z","file_name":"2018_JournalCellBiology_Brown.pdf"}],"issue":"6","language":[{"iso":"eng"}],"volume":217,"article_processing_charge":"No","quality_controlled":"1","project":[{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"oa_version":"Published Version","author":[{"first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Louise","last_name":"Johnson","full_name":"Johnson, Louise"},{"first_name":"Dario","last_name":"Leone","full_name":"Leone, Dario"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"last_name":"Vaahtomeri","first_name":"Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","full_name":"Vaahtomeri, Kari"},{"last_name":"Senfter","first_name":"Daniel","full_name":"Senfter, Daniel"},{"first_name":"Nora","last_name":"Bukosza","full_name":"Bukosza, Nora"},{"full_name":"Schachner, Helga","last_name":"Schachner","first_name":"Helga"},{"first_name":"Gabriele","last_name":"Asfour","full_name":"Asfour, Gabriele"},{"full_name":"Langer, Brigitte","last_name":"Langer","first_name":"Brigitte"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"last_name":"Parapatics","first_name":"Katja","full_name":"Parapatics, Katja"},{"first_name":"Young","last_name":"Hong","full_name":"Hong, Young"},{"first_name":"Keiryn","last_name":"Bennett","full_name":"Bennett, Keiryn"},{"last_name":"Kain","first_name":"Renate","full_name":"Kain, Renate"},{"first_name":"Michael","last_name":"Detmar","full_name":"Detmar, Michael"},{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Jackson, David","first_name":"David","last_name":"Jackson"},{"last_name":"Kerjaschki","first_name":"Dontscho","full_name":"Kerjaschki, Dontscho"}],"scopus_import":"1","publist_id":"7627","intvolume":"       217","publication":"Journal of Cell Biology","oa":1,"acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","year":"2018","day":"12","doi":"10.1083/jcb.201612051","page":"2205 - 2221","publication_status":"published","abstract":[{"lang":"eng","text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified &gt; 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments."}],"isi":1,"ddc":["570"],"pmid":1,"publisher":"Rockefeller University Press","date_published":"2018-04-12T00:00:00Z","file_date_updated":"2020-07-14T12:45:45Z","title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","department":[{"_id":"MiSi"},{"_id":"Bio"}],"date_updated":"2023-09-13T08:51:29Z","citation":{"chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. 2018;217(6):2205-2221. doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>","ieee":"M. Brown <i>et al.</i>, “Lymphatic exosomes promote dendritic cell migration along guidance cues,” <i>Journal of Cell Biology</i>, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>."},"external_id":{"pmid":["29650776"],"isi":["000438077800026"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"citation":{"mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>.","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","ieee":"C. Frick <i>et al.</i>, “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” <i>PLoS One</i>, vol. 13, no. 6. Public Library of Science, 2018.","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. 2018;13(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330.","chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>.","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>"},"department":[{"_id":"MiSi"}],"date_updated":"2023-09-13T09:00:15Z","external_id":{"isi":["000434384900031"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"isi":1,"publication_status":"published","abstract":[{"text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo.","lang":"eng"}],"title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","file_date_updated":"2020-07-14T12:45:45Z","date_published":"2018-06-07T00:00:00Z","publisher":"Public Library of Science","oa":1,"year":"2018","doi":"10.1371/journal.pone.0198330","day":"07","acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","scopus_import":"1","publication":"PLoS One","publist_id":"7626","intvolume":"        13","oa_version":"Published Version","quality_controlled":"1","author":[{"first_name":"Corina","last_name":"Frick","full_name":"Frick, Corina"},{"full_name":"Dettinger, Philip","first_name":"Philip","last_name":"Dettinger"},{"last_name":"Renkawitz","first_name":"Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg"},{"first_name":"Annaïse","last_name":"Jauch","full_name":"Jauch, Annaïse"},{"first_name":"Christoph","last_name":"Berger","full_name":"Berger, Christoph"},{"full_name":"Recher, Mike","first_name":"Mike","last_name":"Recher"},{"first_name":"Timm","last_name":"Schroeder","full_name":"Schroeder, Timm"},{"full_name":"Mehling, Matthias","last_name":"Mehling","first_name":"Matthias"}],"article_number":"e0198330","file":[{"date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-17T14:10:32Z","content_type":"application/pdf","file_name":"2018_Plos_Frick.pdf","relation":"main_file","file_size":7682167,"access_level":"open_access","creator":"dernst","checksum":"95fc5dc3938b3ad3b7697d10c83cc143","file_id":"5709"}],"issue":"6","has_accepted_license":"1","month":"06","volume":13,"article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","_id":"276","type":"journal_article","date_created":"2018-12-11T11:45:34Z","status":"public"},{"day":"12","year":"2018","page":"407 - 420","doi":"10.1007/s11103-018-0747-4","oa":1,"publist_id":"7625","intvolume":"        97","publication":"Plant Molecular Biology","scopus_import":"1","external_id":{"isi":["000438981700009"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"EvBe"}],"date_updated":"2023-09-08T13:21:05Z","citation":{"apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., &#38; Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>","ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420.","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>.","ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. 2018;97(5):407-420. doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>","ieee":"L. Dokládal <i>et al.</i>, “An armadillo-domain protein participates in a telomerase interaction network,” <i>Plant Molecular Biology</i>, vol. 97, no. 5. Springer, pp. 407–420, 2018.","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>.","short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420."},"file_date_updated":"2020-07-14T12:45:45Z","publisher":"Springer","date_published":"2018-06-12T00:00:00Z","title":"An armadillo-domain protein participates in a telomerase interaction network","publication_status":"published","abstract":[{"lang":"eng","text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions."}],"isi":1,"ddc":["580"],"status":"public","date_created":"2018-12-11T11:45:34Z","article_type":"original","_id":"277","type":"journal_article","author":[{"last_name":"Dokládal","first_name":"Ladislav","full_name":"Dokládal, Ladislav"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Honys","full_name":"Honys, David"},{"first_name":"Nikoleta","last_name":"Dupláková","full_name":"Dupláková, Nikoleta"},{"last_name":"Lee","first_name":"Lan","full_name":"Lee, Lan"},{"full_name":"Gelvin, Stanton","last_name":"Gelvin","first_name":"Stanton"},{"full_name":"Sýkorová, Eva","first_name":"Eva","last_name":"Sýkorová"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":97,"article_processing_charge":"No","month":"06","has_accepted_license":"1","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:45Z","date_created":"2020-05-14T12:23:08Z","file_name":"2018_PlantMolecBio_Dokladal.pdf","relation":"main_file","creator":"dernst","checksum":"451ae47616e6af2533099f596b2a47fb","file_id":"7834","file_size":1150679,"access_level":"open_access"}],"issue":"5"},{"author":[{"orcid":"0000-0001-8126-0426","last_name":"Villányi","first_name":"Márton","full_name":"Villányi, Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"E-Lib"}],"date_updated":"2024-02-21T13:44:07Z","oa_version":"Published Version","citation":{"mla":"Villányi, Márton. <i>Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken</i>. Universität Wien, 2018.","short":"M. Villányi, Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken, Universität Wien, 2018.","ieee":"M. Villányi, “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken,” Universität Wien, 2018.","apa":"Villányi, M. (2018). <i>Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken</i>. Universität Wien.","chicago":"Villányi, Márton. “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken.” Universität Wien, 2018.","ista":"Villányi M. 2018. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. Universität Wien.","ama":"Villányi M. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. 2018."},"language":[{"iso":"ger"}],"date_published":"2018-04-06T00:00:00Z","publisher":"Universität Wien","title":"Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken","publication_status":"published","month":"04","abstract":[{"lang":"eng","text":"Consortial subscription contracts regulate the digital access to publications between publishers and scientific libraries. However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? Publications reports of the publishers and database queries from Scopus form the data basis. The analysis of the data points out that differing approaches of contracts result in highly divergent results: Particular deals can prioritize a saving in costs or else the increase of the open access rate. It is to be assumed that within the following years further numerous open access deals will be negotiated. The finding of this study shall provide guidance."}],"status":"public","year":"2018","main_file_link":[{"url":"http://othes.univie.ac.at/51113/","open_access":"1"}],"day":"06","page":"94","date_created":"2018-12-11T11:45:34Z","oa":1,"type":"dissertation","_id":"278","publist_id":"7624","supervisor":[{"full_name":"Kromp, Brigitte","last_name":"Kromp","first_name":"Brigitte"}],"related_material":{"record":[{"status":"public","id":"5577","relation":"dissertation_contains"},{"id":"5574","relation":"dissertation_contains","status":"public"},{"id":"5578","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"5579","status":"public"},{"status":"public","relation":"dissertation_contains","id":"5576"},{"id":"5575","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"5582","status":"public"},{"status":"public","id":"5581","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"5580","status":"public"}]}},{"title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","date_published":"2018-05-31T00:00:00Z","file_date_updated":"2020-07-14T12:45:47Z","publisher":"BioMed Central","ddc":["570"],"isi":1,"abstract":[{"lang":"eng","text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments."}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000433986200001"]},"citation":{"ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>, vol. 19, 67, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>."},"date_updated":"2023-09-13T09:01:32Z","department":[{"_id":"FyKo"}],"publication":"Genome Biology","intvolume":"        19","publist_id":"7620","related_material":{"record":[{"status":"public","relation":"research_data","id":"9811"},{"id":"9812","relation":"research_data","status":"public"}]},"scopus_import":"1","year":"2018","doi":"10.1186/s13059-018-1434-0","day":"31","oa":1,"article_processing_charge":"No","volume":19,"language":[{"iso":"eng"}],"file":[{"file_size":1414722,"access_level":"open_access","creator":"dernst","checksum":"f3e4922486bd9bf1483271bdbed394a7","file_id":"5708","relation":"main_file","file_name":"2018_GenomeBiology_Zapata.pdf","date_updated":"2020-07-14T12:45:47Z","date_created":"2018-12-17T14:05:01Z","content_type":"application/pdf"}],"article_number":"67","month":"05","has_accepted_license":"1","author":[{"last_name":"Zapata","first_name":"Luis","full_name":"Zapata, Luis"},{"last_name":"Pich","first_name":"Oriol","full_name":"Pich, Oriol"},{"full_name":"Serrano, Luis","first_name":"Luis","last_name":"Serrano"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"oa_version":"Published Version","project":[{"name":"Systematic investigation of epistasis in molecular evolution","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","call_identifier":"FP7"}],"quality_controlled":"1","ec_funded":1,"status":"public","_id":"279","type":"journal_article","date_created":"2018-12-11T11:45:35Z"},{"oa_version":"None","quality_controlled":"1","author":[{"last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"}],"issue":"9","month":"09","article_processing_charge":"No","volume":141,"language":[{"iso":"eng"}],"type":"journal_article","_id":"28","date_created":"2018-12-11T11:44:14Z","status":"public","citation":{"short":"X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>, vol. 141, no. 9, Oxford University Press, 2018, pp. 2542–44, doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>.","apa":"Contreras, X., &#38; Hippenmeyer, S. (2018). Incorrect trafficking route leads to autism. <i>Brain a Journal of Neurology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>","ista":"Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism. Brain a journal of neurology. 141(9), 2542–2544.","ama":"Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. <i>Brain a journal of neurology</i>. 2018;141(9):2542-2544. doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>.","ieee":"X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,” <i>Brain a journal of neurology</i>, vol. 141, no. 9. Oxford University Press, pp. 2542–2544, 2018."},"date_updated":"2024-03-25T23:30:23Z","department":[{"_id":"SiHi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000446548100012"]},"isi":1,"abstract":[{"text":"This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate cortical development and core behaviours related to autism disorders in mice’ by Szczurkowska et al. ","lang":"eng"}],"publication_status":"published","title":"Incorrect trafficking route leads to autism","publisher":"Oxford University Press","date_published":"2018-09-01T00:00:00Z","page":"2542 - 2544","year":"2018","day":"01","doi":"10.1093/brain/awy218","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7902"}]},"scopus_import":"1","publication":"Brain a journal of neurology","intvolume":"       141"},{"citation":{"ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. 2018;4(6):365-375. doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>.","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>","ieee":"Z. Gao <i>et al.</i>, “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>."},"date_updated":"2023-09-13T08:24:17Z","department":[{"_id":"JiFr"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000435571000017"]},"isi":1,"abstract":[{"lang":"eng","text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span."}],"publication_status":"published","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","publisher":"Nature Publishing Group","date_published":"2018-05-28T00:00:00Z","day":"28","year":"2018","page":"365 - 375","doi":"10.1038/s41477-018-0160-7","acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","scopus_import":"1","publication":"Nature Plants","intvolume":"         4","publist_id":"7619","oa_version":"None","quality_controlled":"1","author":[{"full_name":"Gao, Zhen","last_name":"Gao","first_name":"Zhen"},{"first_name":"Anna","last_name":"Daneva","full_name":"Daneva, Anna"},{"first_name":"Yuliya","last_name":"Salanenka","full_name":"Salanenka, Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Van Durme","first_name":"Matthias","full_name":"Van Durme, Matthias"},{"last_name":"Huysmans","first_name":"Marlies","full_name":"Huysmans, Marlies"},{"full_name":"Lin, Zongcheng","last_name":"Lin","first_name":"Zongcheng"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Karimi","first_name":"Mansour","full_name":"Karimi, Mansour"},{"last_name":"Van De Velde","first_name":"Jan","full_name":"Van De Velde, Jan"},{"full_name":"Vandepoele, Klaas","first_name":"Klaas","last_name":"Vandepoele"},{"first_name":"Davy","last_name":"Van De Walle","full_name":"Van De Walle, Davy"},{"full_name":"Dewettinck, Koen","first_name":"Koen","last_name":"Dewettinck"},{"first_name":"Bart","last_name":"Lambrecht","full_name":"Lambrecht, Bart"},{"first_name":"Moritz","last_name":"Nowack","full_name":"Nowack, Moritz"}],"issue":"6","month":"05","article_processing_charge":"No","volume":4,"language":[{"iso":"eng"}],"type":"journal_article","_id":"280","date_created":"2018-12-11T11:45:35Z","status":"public"},{"date_created":"2018-12-11T11:45:35Z","article_type":"original","type":"journal_article","_id":"281","status":"public","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/09/21/192039","open_access":"1"}],"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"quality_controlled":"1","oa_version":"Preprint","author":[{"last_name":"Granados","first_name":"Alejandro","full_name":"Granados, Alejandro"},{"full_name":"Pietsch, Julian","first_name":"Julian","last_name":"Pietsch"},{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A","last_name":"Cepeda Humerez"},{"last_name":"Farquhar","first_name":"Isebail","full_name":"Farquhar, Isebail"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper"},{"first_name":"Peter","last_name":"Swain","full_name":"Swain, Peter"}],"month":"06","issue":"23","language":[{"iso":"eng"}],"volume":115,"article_processing_charge":"No","oa":1,"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","doi":"10.1073/pnas.1716659115","day":"05","page":"6088 - 6093","year":"2018","scopus_import":"1","related_material":{"record":[{"id":"6473","relation":"part_of_dissertation","status":"public"}]},"publist_id":"7618","intvolume":"       115","publication":"PNAS","department":[{"_id":"GaTk"}],"date_updated":"2023-09-11T12:58:24Z","citation":{"ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” <i>PNAS</i>, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., &#38; Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>","chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. 2018;115(23):6088-6093. doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>.","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093."},"external_id":{"pmid":["29784812"],"isi":["000434114900071"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","abstract":[{"lang":"eng","text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making."}],"isi":1,"pmid":1,"date_published":"2018-06-05T00:00:00Z","publisher":"National Academy of Sciences","title":"Distributed and dynamic intracellular organization of extracellular information"},{"date_updated":"2023-09-13T08:22:32Z","department":[{"_id":"NiBa"}],"citation":{"ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. 2018;209(4):1279-1303. doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” <i>Genetics</i>, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000440014100020"]},"abstract":[{"text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci.","lang":"eng"}],"publication_status":"published","isi":1,"publisher":"Genetics Society of America","date_published":"2018-08-01T00:00:00Z","title":"Introgression of a block of genome under infinitesimal selection","oa":1,"doi":"10.1534/genetics.118.301018","page":"1279 - 1303","year":"2018","day":"01","scopus_import":"1","intvolume":"       209","publist_id":"7617","publication":"Genetics","quality_controlled":"1","oa_version":"Submitted Version","author":[{"last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"month":"08","issue":"4","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":209,"date_created":"2018-12-11T11:45:36Z","_id":"282","type":"journal_article","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"status":"public"},{"citation":{"ieee":"R. M. Ceinos <i>et al.</i>, “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018.","apa":"Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>","chicago":"Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>.","ista":"Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.","ama":"Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>","short":"R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).","mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>."},"date_updated":"2023-09-13T08:59:27Z","department":[{"_id":"EvBe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000434640800008"]},"isi":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors."}],"publication_status":"published","title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","file_date_updated":"2020-07-14T12:45:49Z","publisher":"Nature Publishing Group","date_published":"2018-06-08T00:00:00Z","oa":1,"day":"08","year":"2018","doi":"10.1038/s41598-018-27080-2","scopus_import":"1","publication":"Scientific Reports","intvolume":"         8","publist_id":"7616","oa_version":"Published Version","quality_controlled":"1","author":[{"full_name":"Ceinos, Rosa Maria","first_name":"Rosa Maria","last_name":"Ceinos"},{"first_name":"Elena","last_name":"Frigato","full_name":"Frigato, Elena"},{"last_name":"Pagano","first_name":"Cristina","full_name":"Pagano, Cristina"},{"full_name":"Frohlich, Nadine","last_name":"Frohlich","first_name":"Nadine"},{"full_name":"Negrini, Pietro","last_name":"Negrini","first_name":"Pietro"},{"first_name":"Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"last_name":"Vallone","first_name":"Daniela","full_name":"Vallone, Daniela"},{"full_name":"Fuselli, Silvia","last_name":"Fuselli","first_name":"Silvia"},{"full_name":"Bertolucci, Cristiano","last_name":"Bertolucci","first_name":"Cristiano"},{"first_name":"Nicholas S","last_name":"Foulkes","full_name":"Foulkes, Nicholas S"}],"issue":"1","article_number":"8754","file":[{"relation":"main_file","creator":"dernst","file_id":"5707","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","file_size":1855324,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:49Z","date_created":"2018-12-17T13:04:46Z","file_name":"2018_ScientificReports_Ceinos.pdf"}],"month":"06","has_accepted_license":"1","article_processing_charge":"No","volume":8,"language":[{"iso":"eng"}],"type":"journal_article","_id":"283","date_created":"2018-12-11T11:45:36Z","status":"public"},{"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Preprint","author":[{"full_name":"Virosztek, Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511","first_name":"Daniel","last_name":"Virosztek"}],"month":"06","issue":"1-2","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":84,"date_created":"2018-12-11T11:45:36Z","type":"journal_article","_id":"284","article_type":"original","main_file_link":[{"url":"https://arxiv.org/abs/1802.03305","open_access":"1"}],"status":"public","publication_identifier":{"issn":["0001-6969"],"eissn":["2064-8316"]},"ec_funded":1,"date_updated":"2023-10-16T10:29:22Z","department":[{"_id":"LaEr"}],"citation":{"ieee":"D. Virosztek, “Maps on probability measures preserving certain distances - a survey and some new results,” <i>Acta Scientiarum Mathematicarum</i>, vol. 84, no. 1–2. Springer Nature, pp. 65–80, 2018.","apa":"Virosztek, D. (2018). Maps on probability measures preserving certain distances - a survey and some new results. <i>Acta Scientiarum Mathematicarum</i>. Springer Nature. <a href=\"https://doi.org/10.14232/actasm-018-753-y\">https://doi.org/10.14232/actasm-018-753-y</a>","ista":"Virosztek D. 2018. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.","chicago":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” <i>Acta Scientiarum Mathematicarum</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.14232/actasm-018-753-y\">https://doi.org/10.14232/actasm-018-753-y</a>.","ama":"Virosztek D. Maps on probability measures preserving certain distances - a survey and some new results. <i>Acta Scientiarum Mathematicarum</i>. 2018;84(1-2):65-80. doi:<a href=\"https://doi.org/10.14232/actasm-018-753-y\">10.14232/actasm-018-753-y</a>","mla":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” <i>Acta Scientiarum Mathematicarum</i>, vol. 84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:<a href=\"https://doi.org/10.14232/actasm-018-753-y\">10.14232/actasm-018-753-y</a>.","short":"D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1802.03305"]},"abstract":[{"lang":"eng","text":"Borel probability measures living on metric spaces are fundamental\r\nmathematical objects. There are several meaningful distance functions that make the collection of the probability measures living on a certain space a metric space. We are interested in the description of the structure of the isometries of such metric spaces. We overview some of the recent results of the topic and we also provide some new ones concerning the Wasserstein distance. More specifically, we consider the space of all Borel probability measures on the unit sphere of a Euclidean space endowed with the Wasserstein metric W_p for arbitrary p &gt;= 1, and we show that the action of a Wasserstein isometry on the set of Dirac measures is induced by an isometry of the underlying unit sphere."}],"publication_status":"published","publisher":"Springer Nature","date_published":"2018-06-04T00:00:00Z","title":"Maps on probability measures preserving certain distances - a survey and some new results","oa":1,"acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office, NKFIH (grant no. K124152).","year":"2018","day":"04","doi":"10.14232/actasm-018-753-y","page":"65 - 80","scopus_import":"1","intvolume":"        84","arxiv":1,"publist_id":"7615","publication":"Acta Scientiarum Mathematicarum"},{"author":[{"orcid":"0000-0002-5445-5057","first_name":"Kristóf","last_name":"Huszár","full_name":"Huszár, Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Spreer, Jonathan","first_name":"Jonathan","last_name":"Spreer"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":99,"month":"06","has_accepted_license":"1","article_number":"46","file":[{"date_created":"2018-12-17T15:32:38Z","date_updated":"2020-07-14T12:45:51Z","content_type":"application/pdf","file_name":"2018_LIPIcs_Huszar.pdf","relation":"main_file","access_level":"open_access","file_size":642522,"file_id":"5713","checksum":"530d084116778135d5bffaa317479cac","creator":"dernst"}],"publication_identifier":{"issn":["18688969"]},"status":"public","date_created":"2018-12-11T11:45:37Z","type":"conference","_id":"285","conference":{"start_date":"2018-06-11","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"external_id":{"arxiv":["1712.00434"]},"date_updated":"2023-09-06T11:13:41Z","department":[{"_id":"UlWa"}],"citation":{"short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Huszár, Kristóf, et al. <i>On the Treewidth of Triangulated 3-Manifolds</i>. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">10.4230/LIPIcs.SoCG.2018.46</a>.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">10.4230/LIPIcs.SoCG.2018.46</a>","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">https://doi.org/10.4230/LIPIcs.SoCG.2018.46</a>.","apa":"Huszár, K., Spreer, J., &#38; Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">https://doi.org/10.4230/LIPIcs.SoCG.2018.46</a>"},"date_published":"2018-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:51Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"On the treewidth of triangulated 3-manifolds","abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how &quot;simple&quot; or &quot;thin&quot; a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1))."}],"publication_status":"published","ddc":["516","000"],"acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","doi":"10.4230/LIPIcs.SoCG.2018.46","year":"2018","day":"01","oa":1,"intvolume":"        99","publist_id":"7614","arxiv":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"7093"}]},"scopus_import":1},{"abstract":[{"lang":"eng","text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. "}],"publication_status":"published","isi":1,"publisher":"Wiley","date_published":"2018-09-01T00:00:00Z","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","date_updated":"2025-05-28T11:42:43Z","department":[{"_id":"NiBa"}],"citation":{"chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” <i>Molecular Ecology Resources</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/1755-0998.12782\">https://doi.org/10.1111/1755-0998.12782</a>.","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999.","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. <i>Molecular Ecology Resources</i>. 2018;18(5):988-999. doi:<a href=\"https://doi.org/10.1111/1755-0998.12782\">10.1111/1755-0998.12782</a>","apa":"Ellis, T., Field, D., &#38; Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.12782\">https://doi.org/10.1111/1755-0998.12782</a>","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” <i>Molecular Ecology Resources</i>, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” <i>Molecular Ecology Resources</i>, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:<a href=\"https://doi.org/10.1111/1755-0998.12782\">10.1111/1755-0998.12782</a>.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000441753000007"]},"related_material":{"record":[{"id":"5583","relation":"popular_science","status":"public"}]},"scopus_import":"1","intvolume":"        18","publication":"Molecular Ecology Resources","acknowledgement":"ERC, Grant/Award Number: 250152","day":"01","doi":"10.1111/1755-0998.12782","year":"2018","page":"988 - 999","month":"09","issue":"5","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":18,"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7"}],"oa_version":"None","author":[{"first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"ec_funded":1,"date_created":"2018-12-11T11:45:37Z","_id":"286","type":"journal_article","status":"public"},{"scopus_import":"1","intvolume":"        23","publication":"Frontiers in Bioscience - Landmark","oa":1,"acknowledgement":"The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.","day":"01","year":"2018","doi":"10.2741/4651","page":"1391 - 1406","abstract":[{"text":"In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy.","lang":"eng"}],"publication_status":"published","isi":1,"date_published":"2018-03-01T00:00:00Z","publisher":"Frontiers in Bioscience","pmid":1,"title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment","date_updated":"2023-09-11T13:38:14Z","department":[{"_id":"JoFi"}],"citation":{"ieee":"V. Salari <i>et al.</i>, “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” <i>Frontiers in Bioscience - Landmark</i>, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.","ista":"Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406.","chicago":"Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” <i>Frontiers in Bioscience - Landmark</i>. Frontiers in Bioscience, 2018. <a href=\"https://doi.org/10.2741/4651\">https://doi.org/10.2741/4651</a>.","ama":"Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. <i>Frontiers in Bioscience - Landmark</i>. 2018;23(8):1391-1406. doi:<a href=\"https://doi.org/10.2741/4651\">10.2741/4651</a>","apa":"Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., &#38; Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. <i>Frontiers in Bioscience - Landmark</i>. Frontiers in Bioscience. <a href=\"https://doi.org/10.2741/4651\">https://doi.org/10.2741/4651</a>","mla":"Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” <i>Frontiers in Bioscience - Landmark</i>, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:<a href=\"https://doi.org/10.2741/4651\">10.2741/4651</a>.","short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["29293441"],"isi":["000439042800001"]},"ec_funded":1,"date_created":"2018-12-11T11:45:37Z","type":"journal_article","_id":"287","main_file_link":[{"url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm","open_access":"1"}],"status":"public","month":"03","issue":"8","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":23,"quality_controlled":"1","project":[{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Submitted Version","author":[{"first_name":"Vahid","last_name":"Salari","full_name":"Salari, Vahid"},{"full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","first_name":"Shabir"},{"last_name":"Cifra","first_name":"Michal","full_name":"Cifra, Michal"},{"full_name":"Simon, Christoph","first_name":"Christoph","last_name":"Simon"},{"full_name":"Scholkmann, Felix","last_name":"Scholkmann","first_name":"Felix"},{"last_name":"Alirezaei","first_name":"Zahra","full_name":"Alirezaei, Zahra"},{"full_name":"Tuszynski, Jack","first_name":"Jack","last_name":"Tuszynski"}]},{"oa_version":"Submitted Version","quality_controlled":"1","author":[{"first_name":"Anna","last_name":"Lilja","full_name":"Lilja, Anna"},{"full_name":"Rodilla, Veronica","last_name":"Rodilla","first_name":"Veronica"},{"last_name":"Huyghe","first_name":"Mathilde","full_name":"Huyghe, Mathilde"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Landragin, Camille","first_name":"Camille","last_name":"Landragin"},{"full_name":"Renaud, Olivier","last_name":"Renaud","first_name":"Olivier"},{"last_name":"Leroy","first_name":"Olivier","full_name":"Leroy, Olivier"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"},{"last_name":"Fré","first_name":"Silvia","full_name":"Fré, Silvia"}],"issue":"6","month":"05","volume":20,"article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","_id":"288","type":"journal_article","date_created":"2018-12-11T11:45:38Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964"}],"status":"public","citation":{"apa":"Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41556-018-0108-1\">https://doi.org/10.1038/s41556-018-0108-1</a>","ama":"Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. <i>Nature Cell Biology</i>. 2018;20(6):677-687. doi:<a href=\"https://doi.org/10.1038/s41556-018-0108-1\">10.1038/s41556-018-0108-1</a>","ista":"Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687.","chicago":"Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41556-018-0108-1\">https://doi.org/10.1038/s41556-018-0108-1</a>.","ieee":"A. Lilja <i>et al.</i>, “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” <i>Nature Cell Biology</i>, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018.","short":"A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687.","mla":"Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” <i>Nature Cell Biology</i>, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:<a href=\"https://doi.org/10.1038/s41556-018-0108-1\">10.1038/s41556-018-0108-1</a>."},"department":[{"_id":"EdHa"}],"date_updated":"2023-09-11T12:44:08Z","external_id":{"isi":["000433237300003"],"pmid":["29784917"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"publication_status":"published","abstract":[{"text":"Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer.","lang":"eng"}],"title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","pmid":1,"publisher":"Nature Publishing Group","date_published":"2018-05-21T00:00:00Z","oa":1,"doi":"10.1038/s41556-018-0108-1","page":"677 - 687","year":"2018","day":"21","scopus_import":"1","publication":"Nature Cell Biology","publist_id":"7594","intvolume":"        20"},{"oa_version":"Preprint","quality_controlled":"1","author":[{"full_name":"Zibrov, Alexander","last_name":"Zibrov","first_name":"Alexander"},{"last_name":"Peng","first_name":"Rao","orcid":"0000-0003-1250-0021","id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","full_name":"Peng, Rao"},{"first_name":"Carlos","last_name":"Kometter","full_name":"Kometter, Carlos"},{"first_name":"Jia","last_name":"Li","full_name":"Li, Jia"},{"full_name":"Dean, Cory","first_name":"Cory","last_name":"Dean"},{"full_name":"Taniguchi, Takashi","first_name":"Takashi","last_name":"Taniguchi"},{"full_name":"Watanabe, Kenji","last_name":"Watanabe","first_name":"Kenji"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"},{"full_name":"Young, Andrea","first_name":"Andrea","last_name":"Young"}],"issue":"16","article_number":"167601","month":"10","article_processing_charge":"No","volume":121,"language":[{"iso":"eng"}],"_id":"289","type":"journal_article","article_type":"original","date_created":"2018-12-11T11:45:38Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.01038"}],"status":"public","citation":{"ista":"Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601.","chicago":"Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevLett.121.167601\">https://doi.org/10.1103/PhysRevLett.121.167601</a>.","ama":"Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. <i>Physical Review Letters</i>. 2018;121(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.121.167601\">10.1103/PhysRevLett.121.167601</a>","apa":"Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young, A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.121.167601\">https://doi.org/10.1103/PhysRevLett.121.167601</a>","ieee":"A. Zibrov <i>et al.</i>, “Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene,” <i>Physical Review Letters</i>, vol. 121, no. 16. American Physical Society, 2018.","mla":"Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” <i>Physical Review Letters</i>, vol. 121, no. 16, 167601, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.121.167601\">10.1103/PhysRevLett.121.167601</a>.","short":"A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (2018)."},"date_updated":"2023-09-11T13:39:50Z","department":[{"_id":"MaSe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000447307500007"],"arxiv":["1805.01038"]},"isi":1,"abstract":[{"lang":"eng","text":"We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry."}],"publication_status":"published","title":"Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene","publisher":"American Physical Society","date_published":"2018-10-19T00:00:00Z","oa":1,"doi":"10.1103/PhysRevLett.121.167601","year":"2018","day":"19","acknowledgement":"The experimental work at UCSB was funded by the National Science Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japan Society for the Promotion of Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Fellowship from the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator funded through the Major Research Instrumentation program of the U.S. National Science Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities, which are supported by the MRSEC Program of the U.S. National Science Foundation under Grant No. DMR- 1720256.","scopus_import":"1","publication":"Physical Review Letters","intvolume":"       121","arxiv":1},{"abstract":[{"text":"Social insects have evolved enormous capacities to collectively build nests and defend their colonies against both predators and pathogens. The latter is achieved by a combination of individual immune responses and sophisticated collective behavioral and organizational disease defenses, that is, social immunity. We investigated how the presence or absence of these social defense lines affects individual-level immunity in ant queens after bacterial infection. To this end, we injected queens of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control solution, reared them either with workers or alone and analyzed their gene expression patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us to test for the effect of bacterial infection, social context, as well as the interaction between the two over the course of infection and raising of an immune response. We found that social isolation per se affected queen gene expression for metabolism genes, but not for immune genes. When infected, queens reared with and without workers up-regulated similar numbers of innate immune genes revealing activation of Toll and Imd signaling pathways and melanization. Interestingly, however, they mostly regulated different genes along the pathways and showed a different pattern of overall gene up-regulation or down-regulation. Hence, we can conclude that the absence of workers does not compromise the onset of an individual immune response by the queens, but that the social environment impacts the route of the individual innate immune responses.","lang":"eng"}],"publication_status":"published","ddc":["576","591"],"isi":1,"file_date_updated":"2020-07-14T12:45:52Z","publisher":"Wiley","date_published":"2018-11-01T00:00:00Z","title":"Social environment affects the transcriptomic response to bacteria in ant queens","date_updated":"2023-09-19T09:29:12Z","department":[{"_id":"SyCr"}],"citation":{"mla":"Viljakainen, Lumi, et al. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” <i>Ecology and Evolution</i>, vol. 8, no. 22, Wiley, 2018, pp. 11031–70, doi:<a href=\"https://doi.org/10.1002/ece3.4573\">10.1002/ece3.4573</a>.","short":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer, Ecology and Evolution 8 (2018) 11031–11070.","ieee":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, and S. Cremer, “Social environment affects the transcriptomic response to bacteria in ant queens,” <i>Ecology and Evolution</i>, vol. 8, no. 22. Wiley, pp. 11031–11070, 2018.","apa":"Viljakainen, L., Jurvansuu, J., Holmberg, I., Pamminger, T., Erler, S., &#38; Cremer, S. (2018). Social environment affects the transcriptomic response to bacteria in ant queens. <i>Ecology and Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/ece3.4573\">https://doi.org/10.1002/ece3.4573</a>","chicago":"Viljakainen, Lumi, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio Erler, and Sylvia Cremer. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” <i>Ecology and Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/ece3.4573\">https://doi.org/10.1002/ece3.4573</a>.","ista":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. 2018. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 8(22), 11031–11070.","ama":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. Social environment affects the transcriptomic response to bacteria in ant queens. <i>Ecology and Evolution</i>. 2018;8(22):11031-11070. doi:<a href=\"https://doi.org/10.1002/ece3.4573\">10.1002/ece3.4573</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000451611000032"]},"scopus_import":"1","intvolume":"         8","publist_id":"8026","publication":"Ecology and Evolution","oa":1,"day":"01","year":"2018","doi":"10.1002/ece3.4573","page":"11031-11070","month":"11","has_accepted_license":"1","issue":"22","file":[{"access_level":"open_access","file_size":1272096,"checksum":"0d1355c78627ca7210aadd9a17a01915","file_id":"5682","creator":"dernst","relation":"main_file","file_name":"Viljakainen_et_al-2018-Ecology_and_Evolution.pdf","date_created":"2018-12-17T08:27:04Z","date_updated":"2020-07-14T12:45:52Z","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":8,"quality_controlled":"1","oa_version":"Published Version","author":[{"last_name":"Viljakainen","first_name":"Lumi","full_name":"Viljakainen, Lumi"},{"full_name":"Jurvansuu, Jaana","first_name":"Jaana","last_name":"Jurvansuu"},{"full_name":"Holmberg, Ida","first_name":"Ida","last_name":"Holmberg"},{"full_name":"Pamminger, Tobias","last_name":"Pamminger","first_name":"Tobias"},{"full_name":"Erler, Silvio","last_name":"Erler","first_name":"Silvio"},{"first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"date_created":"2018-12-11T11:44:15Z","_id":"29","type":"journal_article","publication_identifier":{"issn":["20457758"]},"status":"public"},{"language":[{"iso":"eng"}],"volume":3,"article_processing_charge":"No","month":"05","article_number":"054401","issue":"5","author":[{"first_name":"Nazmi B","last_name":"Budanur","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"quality_controlled":"1","oa_version":"Preprint","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01918"}],"date_created":"2018-12-11T11:45:39Z","type":"journal_article","_id":"291","date_published":"2018-05-30T00:00:00Z","publisher":"American Physical Society","title":"Complexity of the laminar-turbulent boundary in pipe flow","publication_status":"published","abstract":[{"lang":"eng","text":"Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions."}],"isi":1,"external_id":{"isi":["000433426200001"],"arxiv":["1802.01918"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BjHo"}],"date_updated":"2023-09-11T12:45:44Z","citation":{"ieee":"N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in pipe flow,” <i>Physical Review Fluids</i>, vol. 3, no. 5. American Physical Society, 2018.","apa":"Budanur, N. B., &#38; Hof, B. (2018). Complexity of the laminar-turbulent boundary in pipe flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.054401\">https://doi.org/10.1103/PhysRevFluids.3.054401</a>","chicago":"Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.054401\">https://doi.org/10.1103/PhysRevFluids.3.054401</a>.","ista":"Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 3(5), 054401.","ama":"Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow. <i>Physical Review Fluids</i>. 2018;3(5). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.054401\">10.1103/PhysRevFluids.3.054401</a>","short":"N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018).","mla":"Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 5, 054401, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.054401\">10.1103/PhysRevFluids.3.054401</a>."},"publist_id":"7590","arxiv":1,"intvolume":"         3","publication":"Physical Review Fluids","scopus_import":"1","day":"30","year":"2018","doi":"10.1103/PhysRevFluids.3.054401","oa":1}]